WO2016168446A1 - Methods for typing of lung cancer - Google Patents

Methods for typing of lung cancer Download PDF

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Publication number
WO2016168446A1
WO2016168446A1 PCT/US2016/027503 US2016027503W WO2016168446A1 WO 2016168446 A1 WO2016168446 A1 WO 2016168446A1 US 2016027503 W US2016027503 W US 2016027503W WO 2016168446 A1 WO2016168446 A1 WO 2016168446A1
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WIPO (PCT)
Prior art keywords
biomarkers
classifier biomarkers
sample
classifier
hybridization
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PCT/US2016/027503
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French (fr)
Inventor
Hawazin FARUKI
Myla LAI-GOLDMAN
Greg MAYHEW
Charles Perou
David Neil Hayes
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University of North Carolina at Chapel Hill
Genecentric Diagnostics Inc
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University of North Carolina at Chapel Hill
Genecentric Diagnostics Inc
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Application filed by University of North Carolina at Chapel Hill, Genecentric Diagnostics Inc filed Critical University of North Carolina at Chapel Hill
Priority to EP16780736.1A priority Critical patent/EP3283654A4/en
Priority to US15/566,363 priority patent/US20190203296A1/en
Priority to CA2982775A priority patent/CA2982775A1/en
Priority to JP2017553970A priority patent/JP2018512160A/en
Priority to CN201680034117.9A priority patent/CN107849613A/en
Publication of WO2016168446A1 publication Critical patent/WO2016168446A1/en
Anticipated expiration legal-status Critical
Priority to US17/144,644 priority patent/US20210147948A1/en
Priority to US17/471,716 priority patent/US20220002820A1/en
Priority to US17/725,936 priority patent/US20220243283A1/en
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • Lung cancer is the leading cause of cancer death in the United States and over 220,000 new lung cancer cases are identified each year.
  • Lung cancer is a heterogeneous disease with subtypes generally determined by histology (small cell, non-small cell, carcinoid, adenocarcinoma, and squamous cell carcinoma). Differentiation among various morphologic subtypes of lung cancer is essential in guiding patient management and additional molecular testing is used to identify specific therapeutic target markers. Variability in morphology, limited tissue samples, and the need for assessment of a growing list of therapeutically targeted markers pose challenges to the current diagnostic standard. Studies of histologic diagnosis reproducibility have shown limited intra- pathologist agreement and inter-pathologist agreement.
  • the method comprises probing the levels of at least five classifier biomarkers of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 at the nucleic acid level, in a lung cancer sample obtained from the patient.
  • the probing step comprises mixing the sample with five or more oligonucleotides that are substantially complementary to portions of cDNA molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for hybridization of the five or more oligonucleotides to their complements or substantial complements; detecting whether hybridization occurs between the five or more
  • the adenocarcinoma lung cancer sample is classified as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype based on the results of the comparing step.
  • the comparing step comprises determining a correlation between the hybridization values of the at least five classifier biomarkers and the reference hybridization values.
  • the comparing step further comprises determining an average expression ratio of the at least five biomarkers and comparing the average expression ratio to an average expression ratio of the at least five biomarkers, obtained from the references values in the sample training set.
  • the probing step comprises isolating the nucleic acid or portion thereof prior to the mixing step.
  • the hybridization comprises hybridization of a cDNA to a cDNA, thereby forming a non-natural complex; or hybridization of a cDNA to an mRNA, thereby forming a non-natural complex.
  • the probing step comprises amplifying the nucleic acid in the sample.
  • the lung cancer sample comprises lung cells embedded in paraffin.
  • the lung cancer sample is a fresh frozen sample.
  • the lung cancer sample is selected from a formalin-fixed, paraffin-embedded (FFPE) lung tissue sample, fresh and a frozen tissue sample.
  • FFPE formalin-fixed, paraffin-embedded
  • a method for assessing whether a lung tissue sample from a human patient is a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative) adenocarcinoma lung cancer subtype.
  • the method comprises detecting expression levels of at least five of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 at the nucleic acid level by RNA-seq, a reverse transcriptase polymerase chain reaction (RT-PCR) or a hybridization assay with oligonucleotides specific to the classifier biomarkers; comparing the detected levels of expression of the at least five of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 to the expression levels of the at least five of the classifier biomarkers from at least one sample training set.
  • RT-PCR reverse transcriptase polymerase chain reaction
  • the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the lung tissue sample and the expression data from the at least one training set(s); and classifying the lung tissue sample as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype based on the results of the statistical algorithm.
  • the comparing step further comprises determining an average expression ratio of the at least five biomarkers and comparing the average expression ratio to an average expression ratio of the at least five biomarkers, obtained from the references values in the sample training set.
  • the lung tissue sample is selected from a formalin-fixed, paraffin-embedded (FFPE) lung tissue sample, fresh and a frozen tissue sample.
  • FFPE formalin-fixed, paraffin-embedded
  • a method for determining a disease outcome for a patient suffering from lung cancer comprising: determining a subtype of the lung cancer through gene expression analysis of a first sample obtained from the patient to produce a gene expression based subtype; determining the subtype of the lung cancer through a morphological analysis of a second sample obtained from the patient to produce a morphological based subtype; and comparing the gene expression based subtype to the morphological based subtype, wherein a presence or absence of concordance between the gene expression based subtype and the morphological based subtype is predictive of the disease outcome.
  • the gene expression analysis comprises determining expression levels of at least five classifier biomarkers in Table 1 A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 at a nucleic acid level in the first sample by performing RNA sequencing, reverse transcriptase polymerase chain reaction (RT-PCR) or hybridization based analyses.
  • RT-PCR reverse transcriptase polymerase chain reaction
  • the RT-PCR is quantitative real time reverse transcriptase polymerase chain reaction (qRT-PCR).
  • the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the first sample and the expression data from the at least one training set(s); and classifying the first sample as an adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype based on the results of the statistical algorithm.
  • the primers specific for the at least five classifier biomarkers are forward and reverse primers listed in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6.
  • the hybridization analysis comprises: (a) probing the levels of at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 in a lung cancer sample obtained from the patient at the nucleic acid level, wherein the probing step comprises; (i) mixing the sample with five or more oligonucleotides that are substantially complementary to portions of nucleic acid molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for hybridization of the five or more oligonucleotides to their complements or substantial complements; (ii) detecting whether hybridization occurs between the five or more oligonucleotides to their complements or substantial complements; (iii) obtaining hybridization values of the at least five classifier biomarkers based on the detecting step; (b) comparing the hybridization values of the at least five classifier biomarkers to reference hybridization value(s)
  • the comparing step comprises determining a correlation between the hybridization values of the at least five classifier biomarkers and the reference hybridization values. In one embodiment, the comparing step further comprises determining an average expression ratio of the at least five biomarkers and comparing the average expression ratio to an average expression ratio of the at least five biomarkers, obtained from the references values in the sample training set. In one embodiment, the probing step comprises isolating the nucleic acid or portion thereof prior to the mixing step. In one embodiment, the hybridization comprises hybridization of a cDNA probe to a cDNA biomarker, thereby forming a non- natural complex. In one embodiment, the hybridization comprises hybridization of a cDNA probe to an mRNA biomarker, thereby forming a non-natural complex. In one embodiment, the morphological analysis of the second sample is a histological analysis.
  • the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 6. In one embodiment, the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 1A, Table IB or Table 1C. In one embodiment, the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 2. In one embodiment, the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 3.
  • the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 1A. In one embodiment, the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table IB. In one embodiment, the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 1C.
  • FIGs 1A-1D illustrate exemplary gene expression heatmaps for adenocarcinoma (FIG 1A), squamous cell carcinoma (FIG IB), small cell carcinoma (FIG 1C), and carcinoid (FIG ID).
  • FIG 3 illustrates a comparison of path review and LSP prediction for 77 FFPE samples. Each rectangle represents a single sample ordered by sample number. Arrows indicate 6 samples that disagreed with the original diagnosis by both pathology review and gene expression (for sample details see Table 18).
  • FIGs 4-7 illustrates Kaplan Meier plots showing the predicted lung cancer subtype
  • FIG. 12 illustrates the proliferation score (11 gene PAM50 signature) is higher in AD-NE/SQ compared to AD- AD in all 3 datasets shown in FIGs. 4-6.
  • FIG, 13 illustrates gene mutation prevalence in histology-gene expression concordant (AD-AD) as compared to discordant (AD-NE/SQ) samples using Fisher's exact test.
  • FIG. 14 illustrates reduction in lung adenocarcinoma prognostic strength following exclusion of histologically defined adenocarcinoma samples that are NE or SQ by LSP gene expression (AD-NE/SQ).
  • TRU Terminal Respiratory Unit
  • PI Proximal Inflammatory
  • PP Proximal Proliferative
  • the present invention addresses the need in the field for determining a prognosis or disease outcome for adenocarcinoma patient populations based in part on the adenocarcinoma subtype (Terminal Respiratory Unit (TRU), Proximal Inflammatory (PI), Proximal Proliferative (PP)) of the patient.
  • TRU Terminal Respiratory Unit
  • PI Proximal Inflammatory
  • PP Proximal Proliferative
  • an "expression profile" comprises one or more values corresponding to a measurement of the relative abundance, level, presence, or absence of expression of a discriminative gene.
  • An expression profile can be derived from a subject prior to or subsequent to a diagnosis of lung cancer, can be derived from a biological sample collected from a subject at one or more time points prior to or following treatment or therapy, can be derived from a biological sample collected from a subject at one or more time points during which there is no treatment or therapy (e.g., to monitor progression of disease or to assess development of disease in a subject diagnosed with or at risk for lung cancer), or can be collected from a healthy subject.
  • the term subject can be used interchangeably with patient.
  • the patient can be a human patient.
  • determining an expression level or “determining an expression profile” or “detecting an expression level” or “detecting an expression profile” as used in reference to a biomarker or classifier means the application of a biomarker specific reagent such as a probe, primer or antibody and/or a method to a sample, for example a sample of the subject or patient and/or a control sample, for ascertaining or measuring quantitatively, semi-quantitatively or qualitatively the amount of a biomarker or biomarkers, for example the amount of biomarker polypeptide or mRNA (or cDNA derived therefrom).
  • a biomarker specific reagent such as a probe, primer or antibody and/or a method
  • a level of a biomarker can be determined by a number of methods including for example immunoassays including for example immunohistochemistry, ELISA, Western blot, immunoprecipation and the like, where a biomarker detection agent such as an antibody for example, a labeled antibody, specifically binds the biomarker and permits for example relative or absolute ascertaining of the amount of polypeptide biomarker, hybridization and PCR protocols where a probe or primer or primer set are used to ascertain the amount of nucleic acid biomarker, including for example probe based and amplification based methods including for example microarray analysis, RT-PCR such as quantitative RT-PCR (qRT- PCR), serial analysis of gene expression (SAGE), Northern Blot, digital molecular barcoding technology, for example Nanostring Counter Analysis, and TaqMan quantitative PCR assays.
  • immunoassays including for example immunohistochemistry, ELISA, Western blot, immunoprecipation and the like
  • a biomarker detection agent such as an
  • mRNA in situ hybridization in formalin-fixed, paraffin-embedded (FFPE) tissue samples or cells can be applied, such as mRNA in situ hybridization in formalin-fixed, paraffin-embedded (FFPE) tissue samples or cells.
  • FFPE paraffin-embedded
  • This technology is currently offered by the QuantiGene ViewRNA (Affymetrix), which uses probe sets for each mRNA that bind specifically to an amplification system to amplify the hybridization signals; these amplified signals can be visualized using a standard fluorescence microscope or imaging system.
  • This system for example can detect and measure transcript levels in heterogeneous samples; for example, if a sample has normal and tumor cells present in the same tissue section.
  • TaqMan probe-based gene expression analysis can also be used for measuring gene expression levels in tissue samples, and this technology has been shown to be useful for measuring mRNA levels in FFPE samples.
  • TaqMan probe-based assays utilize a probe that hybridizes specifically to the mRNA target. This probe contains a quencher dye and a reporter dye (fluorescent molecule) attached to each end, and fluorescence is emitted only when specific hybridization to the mRNA target occurs.
  • the exonuclease activity of the polymerase enzyme causes the quencher and the reporter dyes to be detached from the probe, and fluorescence emission can occur. This fluorescence emission is recorded and signals are measured by a detection system; these signal intensities are used to calculate the abundance of a given transcript (gene expression) in a sample.
  • biomarkers or “classifier biomarkers” of the invention include genes and proteins, and variants and fragments thereof. Such biomarkers include DNA comprising the entire or partial sequence of the nucleic acid sequence encoding the biomarker, or the complement of such a sequence.
  • the biomarker nucleic acids also include any expression product or portion thereof of the nucleic acid sequences of interest.
  • a biomarker protein is a protein encoded by or corresponding to a DNA biomarker of the invention.
  • a biomarker protein comprises the entire or partial amino acid sequence of any of the biomarker proteins or polypeptides.
  • a “biomarker” is any gene or protein whose level of expression in a tissue or cell is altered compared to that of a normal or healthy cell or tissue. The detection, and in some cases the level, of the biomarkers of the invention permits the differentiation of samples.
  • the methods provided herein further comprise characterizing a patient's lung cancer (adenocarcinoma) sample as proximal inflammatory (squamoid), proximal proliferative (magnoid) or terminal respiratory unit (bronchioid).
  • adenocarcinoma proximal inflammatory
  • magnoid proximal proliferative
  • bronchioid terminal respiratory unit
  • a biomarker capable of reliable classification can be one that is upregulated (e.g., expression is increased) or downregulated (e.g., expression is decreased) relative to a control.
  • the control can be any control as provided herein.
  • the biomarker panels, or subsets thereof, as disclosed in Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 and Table 6 are used in various embodiments to assess and classify a patient's lung cancer subtype.
  • the methods provided herein are used to classify a lung cancer sample as a particular lung cancer subtype (e.g. subtype of adenocarcinoma).
  • the method comprises detecting or determining an expression level of at least five of the classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 in a lung cancer sample obtained from a patient or subject.
  • the detecting step is at the nucleic acid level by performing RNA-seq, a reverse transcriptase polymerase chain reaction (RT-PCR) or a hybridization assay with oligonucleotides that are substantially complementary to portions of cDNA molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for RNA-seq, RT-PCR or hybridization and obtaining expression levels of the at least five classifier biomarkers based on the detecting step.
  • RNA-seq a reverse transcriptase polymerase chain reaction
  • RT-PCR reverse transcriptase polymerase chain reaction
  • the expression levels of the at least five of the classifier biomarkers are then compared to reference expression levels ofthe at least five of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 from at least one sample training set.
  • the at least one sample training set can comprise, (i) expression levels(s) of the at least five biomarkers from a sample that overexpresses the at least five biomarkers, or overexpresses a subset of the at least five biomarkers, (ii) expression levels from a reference squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative) sample, or (iii) expression levels from an adenocarcinoma free lung sample, and classifying the lung tissue sample as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype.
  • the method comprises probing the levels of at least five of the classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 at the nucleic acid level, in a lung cancer sample obtained from the patient.
  • the at least one sample training set comprises hybridization values from a reference adenocarcinoma, squamous cell carcinoma, a neuroendocrine sample, small cell carcinoma sample.
  • the lung cancer sample is classified, for example, as an adenocarcinoma, squamous cell carcinoma, a neuroendocrine or small cell carcinoma based on the results of the comparing step.
  • the lung tissue sample can be any sample isolated from a human subject or patient.
  • the analysis is performed on lung biopsies that are embedded in paraffin wax.
  • This aspect of the invention provides a means to improve current diagnostics by accurately identifying the major histological types, even from small biopsies.
  • the methods of the invention including the RT-PCR methods, are sensitive, precise and have multianalyte capability for use with paraffin embedded samples. See, for example, Cronin et al. (2004) Am. J Pathol. 164(l):35-42, herein incorporated by reference.
  • the sample used herein is obtained from an individual, and comprises fresh-frozen paraffin embedded (FFPE) tissue.
  • FFPE fresh-frozen paraffin embedded
  • other tissue and sample types are amenable for use herein (e.g., fresh tissue, or frozen tissue).
  • RNA can be isolated from FFPE tissues as described by Bibikova et al. (2004) American Journal of Pathology 165: 1799-1807, herein incorporated by reference.
  • the High Pure RNA Paraffin Kit (Roche) can be used. Paraffin is removed by xylene extraction followed by ethanol wash.
  • RNA can be isolated from sectioned tissue blocks using the MasterPure Purification kit (Epicenter, Madison, Wis.); a DNase I treatment step is included. RNA can be extracted from frozen samples using Trizol reagent according to the supplier's instructions (Invitrogen Life Technologies, Carlsbad, Calif).
  • Samples with measurable residual genomic DNA can be resubjected to DNasel treatment and assayed for DNA contamination. All purification, DNase treatment, and other steps can be performed according to the manufacturer's protocol. After total RNA isolation, samples can be stored at -80 °C until use.
  • RNA from cells in culture can be isolated using Qiagen RNeasy mini-columns.
  • Other commercially available RNA isolation kits include MasterPure. TM. Complete DNA and RNA Purification Kit (Epicentre, Madison, Wis.) and Paraffin Block RNA Isolation Kit (Ambion, Austin, Tex.).
  • Total RNA from tissue samples can be isolated, for example, using RNA Stat-60 (Tel-Test, Friendswood, Tex.).
  • RNA prepared from a tumor can be isolated, for example, by cesium chloride density gradient centrifugation.
  • large numbers of tissue samples can readily be processed using techniques well known to those of skill in the art, such as, for example, the single-step RNA isolation process of Chomczynski (U.S.
  • a sample comprises cells harvested from a lung tissue sample, for example, an adenocarcinoma sample.
  • Cells can be harvested from a biological sample using standard techniques known in the art. For example, in one embodiment, cells are harvested by centrifuging a cell sample and resuspending the pelleted cells. The cells can be resuspended in a buffered solution such as phosphate-buffered saline (PBS). After centrifuging the cell suspension to obtain a cell pellet, the cells can be lysed to extract nucleic acid, e.g, messenger RNA. All samples obtained from a subject, including those subjected to any sort of further processing, are considered to be obtained from the subject.
  • PBS phosphate-buffered saline
  • the sample in one embodiment, is further processed before the detection of the biomarker levels of the combination of biomarkers set forth herein.
  • mRNA in a cell or tissue sample can be separated from other components of the sample.
  • the sample can be concentrated and/or purified to isolate mRNA in its non-natural state, as the mRNA is not in its natural environment.
  • studies have indicated that the higher order structure of mRNA in vivo differs from the in vitro structure of the same sequence (see, e.g. , Rouskin et al. (2014). Nature 505, pp. 701-705, incorporated herein in its entirety for all purposes).
  • cDNA complementary DNA
  • cDNA-mRNA hybrids are synthetic and do not exist in vivo.
  • cDNA is necessarily different than mRNA, as it includes deoxyribonucleic acid and not ribonucleic acid.
  • the cDNA is then amplified, for example, by the polymerase chain reaction (PCR) or other amplification method known to those of ordinary skill in the art.
  • LCR ligase chain reaction
  • Genomics 4:560 (1989)
  • Landegren et al. Science, 241 : 1077 (1988)
  • transcription amplification Kwoh et al., Proc. Natl. Acad. Sci. USA, 86: 1173 (1989), incorporated by reference in its entirety for all purposes
  • self-sustained sequence replication Guatelli et al., Proc. Nat. Acad. Sci.
  • RNA based sequence amplification RNA based sequence amplification
  • NASBA nucleic acid based sequence amplification
  • the product of this amplification reaction i.e. , amplified cDNA is also necessarily a non-natural product.
  • cDNA is a non-natural molecule.
  • the amplification process serves to create hundreds of millions of cDNA copies for every individual cDNA molecule of starting material. The number of copies generated are far removed from the number of copies of mRNA that are present in vivo.
  • cDNA is amplified with primers that introduce an additional DNA sequence (e.g., adapter, reporter, capture sequence or moiety, barcode) onto the fragments (e.g., with the use of adapter-specific primers), or mRNA or cDNA biomarker sequences are hybridized directly to a cDNA probe comprising the additional sequence (e.g., adapter, reporter, capture sequence or moiety, barcode).
  • Amplification and/or hybridization of mRNA to a cDNA probe therefore serves to create non-natural double stranded molecules from the non-natural single stranded cDNA, or the mRNA, by introducing additional sequences and forming non-natural hybrids.
  • amplification procedures have error rates associated with them. Therefore, amplification introduces further modifications into the cDNA molecules.
  • a detectable label e.g. , a fluorophore
  • a detectable label is added to single strand cDNA molecules.
  • Amplification therefore also serves to create DNA complexes that do not occur in nature, at least because (i) cDNA does not exist in vivo, (i) adapter sequences are added to the ends of cDNA molecules to make DNA sequences that do not exist in vivo, (ii) the error rate associated with amplification further creates DNA sequences that do not exist in vivo, (iii) the disparate structure of the cDNA molecules as compared to what exists in nature and (iv) the chemical addition of a detectable label to the cDNA molecules. [0038] In some embodiments, the expression of a biomarker of interest is detected at the nucleic acid level via detection of non-natural cDNA molecules.
  • the method for lung cancer subtyping includes detecting expression levels of a classifier biomarker set.
  • the detecting includes all of the classifier biomarkers of Table 1 (also characterized as a lung cancer subtype gene panel), Table 2, Table 3, Table 4, Table 5 or Table 6 at the nucleic acid level or protein level.
  • a single or a subset of the classifier biomarkers of Table 1 are detected, for example, from about five to about twenty.
  • the biomarkers described herein include RNA comprising the entire or partial sequence of any of the nucleic acid sequences of interest, or their non-natural cDNA product, obtained synthetically in vitro in a reverse transcription reaction.
  • fragment is intended to refer to a portion of the polynucleotide that generally comprise at least 10, 15, 20, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 800, 900, 1,000, 1,200, or 1,500 contiguous nucleotides, or up to the number of nucleotides present in a full- length biomarker polynucleotide disclosed herein.
  • a fragment of a biomarker polynucleotide will generally encode at least 15, 25, 30, 50, 100, 150, 200, or 250 contiguous amino acids, or up to the total number of amino acids present in a full-length biomarker protein of the invention.
  • overexpression is determined by normalization to the level of reference RNA transcripts or their expression products, which can be all measured transcripts (or their products) in the sample or a particular reference set of RNA transcripts (or their non-natural cDNA products). Normalization is performed to correct for or normalize away both differences in the amount of RNA or cDNA assayed and variability in the quality of the RNA or cDNA used. Therefore, an assay typically measures and incorporates the expression of certain normalizing genes, including well known housekeeping genes, such as, for example, GAPDH and/or ⁇ - Actin. Alternatively, normalization can be based on the mean or median signal of all of the assayed biomarkers or a large subset thereof (global normalization approach).
  • from about 5 to about 10, from about 5 to about 15, from about 5 to about 20, from about 5 to about 25, from about 5 to about 30, from about 5 to about 35, from about 5 to about 40, from about 5 to about 45, from about 5 to about 50 of the biomarkers in any of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 and Table 6 are detected in a method to determine the lung cancer subtype.
  • each of the biomarkers from any one of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, or from Table 6 are detected in a method to determine the lung cancer subtype.
  • CAPG capping protein (aciin GGGACAGCrrC 13 GTTCC AG GATGTT 70 filament), gelso!in-like AACACT GGA l Ti C
  • ABCC5 ⁇ -binding cassette CAAGTTCAGGA 19 GGCATCAAGAGA 76 sub-family C(CFTR RP), GAACTCGAC GAGGC
  • ANTXR1 Anthrax toxin receptor 1 ACCCGAGGAAC 21 TCTAGGCCTTGAC 78
  • GJB5 gap junction protein ACCACAAGGAC 30 GGGACACAGGGA 87 beta ⁇ 5 (connexin 31.1) TTCGAC AGAAC
  • HPN Hepsin transmembrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1
  • ME3 malic enzyme 3 CGCGGATACGA 38 CCTTTCTTCAAGG 95
  • PI 3C2A phospboi no si is de -3 -kinase , GGATTTCAGCT 43 AGTCATCATGTAC 100 ci ss 2, alpha ACCAGTTA CTT CCAGCA
  • PSMD14 proteasome proteasome (prosome, AGTGATTGATG 45 CACTGGATCAAC 102 macropain) 26S subu ' t, TGTTTGCTATG TGCCTC
  • TCF2 transcription factor 2 ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic; LF-B3; variant GTCAGAA GTTGAAT
  • CLEC3B C -type lecti n domain CCAGAAGCCCA 2 GCTCCTCAAACAT 5 family 3, member B AG A A GATTGT A CTTTGTGTTCA
  • ACVR1 activin A receptor ACTGGTGTAAC AACCTCCAAGTG 64 type 1 AG GA AC AT GAAATTCT
  • INSM1 insuiinoma-associated 1 ATTGAACTTCCC 10 AAGGTAA GCCA 67
  • LRP10 iow density lipoprotein GGAACAGACTG ⁇ GGGAGCGTAGGG 68 receptor-related protein TCACCAT TTAAG
  • ANTXR1 Anthrax toxin receptor i ACCCGAGGAAC 2i TCTAGGCCTTGAC 78
  • DOK1 docking protein 1 62 CTTTCTGCCCTG 26 CAGTCCTCTGCAC 83 kDa (downstream of GAGATG CGTTA
  • GJB5 gap junction protein ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (connexiti 31.1) TTCGAC AGAAC
  • ME3 malic enzyme 3 CGCGGATACGA 38 CCTTTCTTCAAGG 95
  • NFIL3 nuclear factor ACTCTCCACAA 42 TCCTGCGTGTGTT 99 interleukin 3 regulated AGCTCG CTACT
  • PSK3C2A phosphoinositide-3 -kinase PSK3C2A phosphoinositide-3 -kinase, GGATTTCAGCT 43 AGTCATCATGTAC 100 class 2, alpha ACCAGTTACTT CCAGCA
  • PSMD14 proteasome proteasome (prosome, AGTGATTGATG 45 CACTGGATCAAC 102 macropaiti) 26S subunit, TGi i i ' GCTATG TGCCTC
  • TTF1 thyroid transcription ATGAGTCCAAA 50 CCATGCCCACTTT 107 factor 1 GCACACGA CTTGTA
  • RPL10 ribosomaJ protein L10 GGTGTGCCACT 55 GGCAGAAGCGAG 112
  • CAPG capping protein actin GGGACAGCTTC 13 GTTCCAGGATGTT 70 filament
  • ABCC5 ATP-bindmg cassette CAAGTTCAGGA 19 GGCATCAAGAGA 76 sub-family C(CFTR/ RP), GAACTCGAC GAGGC
  • ANTXR1 Anthrax toxin receptor 1 ACCCGAGGAAC TCTAGGCCTTGAC 78
  • DSC3 desmocollin 3 GCGCCATTTGCT 27 CATCCAGATCCCT 84
  • GIBS gap junction protein ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (conaexin 31.1) TTCGAC AGAAC
  • HPN Hepsirt transmembrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1 GGATTA TTTGA
  • GRN1 mahogunia ring finger GAACTCGGCCT 39 TCGAATTTCTCTC 96
  • PSK3C2A phosphoinositide-3 -kinase PSK3C2A phosphoinositide-3 -kinase, GGATTTCAGCT 43 AGTCATCATGTAC 100 class 2, alpha ACCAGTTACTT CCAGCA
  • TCF2 transcription factor 2 ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic; LF-B3; variant GTCAGAA GTTGAAT
  • CDH5 cadherin 5 type 2
  • AAGAGAGATTG I TTCTTGCGACTCACGCT 58
  • ACVR1 activin A receptor ACTGGTGTAAC AACCTCCAAGTG 64 type 1 AGGAACAT GAAATTCT
  • CAPG capping protein actio GGGACAGCTTC 1 GTTCCAGGATGTT 70 filament
  • ANTXR1 Anthrax toxin receptor i ACCCGAGGAAC TCTAGGCCTTGAC 78
  • GJB5 gap junction protein ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (connexiti 31.1) TTCGAC AGAAC
  • HPN He psin transme nibrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1 GGATTA TTTGA
  • ME3 malic enzyme 3 CGCGGATACGA 38 CCTTTCTTCAAGG 95
  • NFIL3 nuclear factor ACTCTCCACAA 42 TCCTGCGTGTGTT 99 interleukin 3 regulated AGCTCG CTACT
  • PSMD14 proteasome prosome A GTGATTG ATG 45 CACTGGATCAAC 102 maeropain.
  • TCF2 transcription factor 2 ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic, LF-B3; variant GTCAGAA GTTGAAT
  • RPL10 ribosomal protein L10 GGTGTGCCACT 55 GGCAGAAGCGAG 1 12
  • CDH5 cadlierin 5 type 2
  • AAGAGAGATTG 1 TTCTTGCGACTCACGCT 58
  • ACVR1 activin A receptor ACTGGTGTAAC AACCTCCAAGTG 64 type 1 AGGAACAT GAAATTCT
  • INSM1 insulinoma-associated 1 ATTGAACTTCCC 10 AAGGTAAAGCCA
  • CAPG capping protein (actio GGGACAGCTTC 13 GTTCCAGGATGTT 70 filament), gelsolin-iike AACACT GGACTTTC
  • DOK1 docking protein i 62 CTTTCTGCCCTG 26 CAGTCCTCTGCAC 83 kDa (downstream of GAGATG CGTTA
  • DSC3 desmocollin 3 GCGCCATTTGCT 27 CATCCAGATCCCT 84
  • GJB5 gap junction protein ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (connexin 31.1) TTCGAC AGAAC
  • HPN Hepsin transmembrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1
  • ME3 malic enzyme 3 CGCGGATACGA 38 CCTTTCTTCAAGG 95
  • PJK3C2A phosphoinositide-3 -kinase GGATTTCAGCT 43 AGTCATCATGTAC too class 2, alpha ACCAGTTACTT CCAGCA
  • TCF2 transcription factor 2 ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic; LF-B3; variant GTCAGAA GTTGAAT
  • RPL10 ribosomal protein L10 GGTGTGCCACT 55 GGCAGAAGCGAG 112
  • ACVR1 activin A receptor ACTGGTGTAAC AACCTCCAAGTG 64 type 1 AG GA AC AT GAAATTCT Table 4
  • CAPG capping protein actin GGGACAGCTTC 13 GTTCCAGGATGTT 70 filament
  • ANTXR 1 Anthrax toxin receptor i ACCCGAGGAAC 21 TCTAGGCCTTGAC 78
  • DSC3 desmocollin 3 GCGCCATTTGCT 27 CATCCAGATCCCT 84
  • FEN 1 flap structure-specific AGAGAAGATGG 28 CCAAGACACAGC 85 endonvjcJease 1 GCAGAAAG CAGTAAT
  • GJB5 gap junction protein ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (connexin 31.1) TTCGAC AGAAC
  • HPN Hepsin transmembrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1
  • ITGA6 integrin alpha 6 ACGCGGATCGA 36 ATCC ACTG ATCTT 93
  • NFIL3 nuclear factor ACTCTCCACAA 42 TCCTGCGTGTGTT 99 interieukin 3 regulated AGCTCG CTACT
  • PSMD14 proteasome proteasome (prosome, AGTGATTGATG 45 CACTGGATCAAC 102 maciopaiti) 26S subunit, TGi i i ' GCTATG TGCCTC
  • TCF2 transcription factor 2 ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic; LF-B3; variant GTCAGAA GTTGAAT
  • TTF1 thyroid transcription ATGAGTCCAAA 50 CCATGCCCACTTT 107 factor 1 GCACACGA CTTGTA
  • Isolated mRNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, PCR analyses and probe arrays, NanoString Assays.
  • One method for the detection of mRNA levels involves contacting the isolated mRNA or synthesized cDNA with a nucleic acid molecule (probe) that can hybridize to the mRNA encoded by the gene being detected.
  • the nucleic acid probe can be, for example, a cDNA, or a portion thereof, such as an oligonucleotide of at least 7, 15, 30, 50, 100, 250, or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to the non-natural cDNA or mRNA biomarker of the present invention.
  • cDNA complementary DNA
  • Conversion of the mRNA to cDNA can be performed with oligonucleotides or primers comprising sequence that is complementary to a portion of a specific mRNA. Conversion of the mRNA to cDNA can be performed with oligonucleotides or primers comprising random sequence. Conversion of the mRNA to cDNA can be performed with oligonucleotides or primers comprising sequence that is complementary to the poly(A) tail of an mRNA. cDNA does not exist in vivo and therefore is a non-natural molecule.
  • the cDNA is then amplified, for example, by the polymerase chain reaction (PCR) or other amplification method known to those of ordinary skill in the art.
  • PCR can be performed with the forward and/or reverse primers provided in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, or Table 6.
  • the product of this amplification reaction, i.e. , amplified cDNA is necessarily a non-natural product.
  • cDNA is a non-natural molecule.
  • the amplification process serves to create hundreds of millions of cDNA copies for every individual cDNA molecule of starting material. The number of copies generated is far removed from the number of copies of mRNA that are present in vivo.
  • cDNA is amplified with primers that introduce an additional DNA sequence (adapter sequence) onto the fragments (with the use of adapter-specific primers).
  • the adaptor sequence can be a tail, wherein the tail sequence is not complementary to the cDNA.
  • the forward and/or reverse primers provided in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, or Table 6 can comprise tail sequence. Amplification therefore serves to create non-natural double stranded molecules from the non- natural single stranded cDNA, by introducing barcode, adapter and/or reporter sequences onto the already non-natural cDNA.
  • a detectable label e.g., a fluorophore
  • Amplification therefore also serves to create DNA complexes that do not occur in nature, at least because (i) cDNA does not exist in vivo, (i) adapter sequences are added to the ends of cDNA molecules to make DNA sequences that do not exist in vivo, (ii) the error rate associated with amplification further creates DNA sequences that do not exist in vivo, (iii) the disparate structure of the cDNA molecules as compared to what exists in nature and (iv) the chemical addition of a detectable label to the cDNA molecules.
  • a detectable label e.g., a fluorophore
  • the synthesized cDNA (for example, amplified cDNA) is immobilized on a solid surface via hybridization with a probe, e.g., via a microarray.
  • cDNA products are detected via real-time polymerase chain reaction (PCR) via the introduction of fluorescent probes that hybridize with the cDNA products.
  • PCR real-time polymerase chain reaction
  • biomarker detection is assessed by quantitative fluorogenic RT-PCR (e.g., with TaqMan® probes).
  • PCR analysis well known methods are available in the art for the determination of primer sequences for use in the analysis.
  • Biomarkers provided herein in one embodiment are detected via a hybridization reaction that employs a capture probe and/or a reporter probe.
  • the hybridization probe is a probe derivatized to a solid surface such as a bead, glass or silicon substrate.
  • the capture probe is present in solution and mixed with the patient's sample, followed by attachment of the hybridization product to a surface, e.g., via a biotin- avidin interaction (e.g., where biotin is a part of the capture probe and avidin is on the surface).
  • the hybridization assay employs both a capture probe and a reporter probe.
  • the reporter probe can hybridize to either the capture probe or the biomarker nucleic acid.
  • Reporter probes e.g., are then counted and detected to determine the level of biomarker(s) in the sample.
  • the capture and/or reporter probe in one embodiment contain a detectable label, and/or a group that allows functionalization to a surface.
  • nCounter gene analysis system see, e.g., Geiss et al. (2008) Nat. Biotechnol. 26, pp. 317-325, incorporated by reference in its entirety for all purposes, is amenable for use with the methods provided herein.
  • Hybridization assays described in U.S. Patent Nos. 7,473,767 and 8,492,094, the disclosures of which are incorporated by reference in their entireties for all purposes, are amenable for use with the methods provided herein, i.e., to detect the biomarkers and biomarker combinations described herein.
  • Biomarker levels may be monitored using a membrane blot (such as used in hybridization analysis such as Northem, Southem, dot, and the like), or microwells, sample tubes, gels, beads, or fibers (or any solid support comprising bound nucleic acids). See, for example, U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, each incorporated by reference in their entireties.
  • microarrays are used to detect biomarker levels. Microarrays are particularly well suited for this purpose because of the reproducibility between different experiments. DNA microarrays provide one method for the simultaneous measurement of the expression levels of large numbers of genes. Each array consists of a reproducible partem of capture probes attached to a solid support. Labeled RNA or DNA is hybridized to complementary probes on the array and then detected by laser scanning Hybridization intensities for each probe on the array are determined and converted to a quantitative value representing relative gene expression levels. See, for example, U.S. Pat. Nos. 6,040,138, 5,800,992 and 6,020,135, 6,033,860, and 6,344,316, each incorporated by reference in their entireties. High-density oligonucleotide arrays are particularly useful for determining the gene expression profile for a large number of RNAs in a sample.
  • arrays can be nucleic acids (or peptides) on beads, gels, polymeric surfaces, fibers (such as fiber optics), glass, or any other appropriate substrate. See, for example, U.S. Pat. Nos. 5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992, each incorporated by reference in their entireties. Arrays can be packaged in such a manner as to allow for diagnostics or other manipulation of an all-inclusive device. See, for example, U.S. Pat. Nos. 5,856,174 and 5,922,591, each incorporated by reference in their entireties.
  • Serial analysis of gene expression in one embodiment is employed in the methods described herein.
  • SAGE is a method that allows the simultaneous and quantitative analysis of a large number of gene transcripts, without the need of providing an individual hybridization probe for each transcript.
  • a short sequence tag (about 10-14 bp) is generated that contains sufficient information to uniquely identify a transcript, provided that the tag is obtained from a unique position within each transcript.
  • many transcripts are linked together to form long serial molecules, that can be sequenced, revealing the identity of the multiple tags simultaneously.
  • the expression partem of any population of transcripts can be quantitatively evaluated by determining the abundance of individual tags, and identifying the gene corresponding to each tag. See, Velculescu et al. Science 270:484-87, 1995; Cell 88:243-51, 1997, incorporated by reference in its entirety.
  • An additional method of biomarker level analysis at the nucleic acid level is the use of a sequencing method, for example, RNAseq, next generation sequencing, and massively parallel signature sequencing (MPSS), as described by Brenner et al. (Nat. Biotech. 18:630- 34, 2000, incorporated by reference in its entirety).
  • This is a sequencing approach that combines non-gel-based signature sequencing with in vitro cloning of millions of templates on separate 5 ⁇ diameter microbeads.
  • a microbead library of DNA templates is constructed by in vitro cloning.
  • biomarker level analysis at the nucleic acid level is the use of an amplification method such as, for example, RT-PCR or quantitative RT-PCR (qRT-PCR).
  • amplification method such as, for example, RT-PCR or quantitative RT-PCR (qRT-PCR).
  • Methods for determining the level of biomarker mRNA in a sample may involve the process of nucleic acid amplification, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88: 189-193), self-sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci.
  • PCR qRT-PCR protocols
  • a target polynucleotide sequence is amplified by reaction with at least one oligonucleotide primer or pair of oligonucleotide primers.
  • the primer(s) hybridize to a complementary region of the target nucleic acid and a DNA polymerase extends the primer(s) to amplify the target sequence.
  • a nucleic acid fragment of one size dominates the reaction products (the target polynucleotide sequence which is the amplification product).
  • the amplification cycle is repeated to increase the concentration of the single target polynucleotide sequence.
  • the reaction can be performed in any thermocycler commonly used for PCR.
  • Quantitative RT-PCR (also referred as real-time RT-PCR) is preferred under some circumstances because it provides not only a quantitative measurement, but also reduced time and contamination.
  • quantitative PCR or “real time qRT- PCR” refers to the direct monitoring of the progress of a PCR amplification as it is occurring without the need for repeated sampling of the reaction products.
  • the reaction products may be monitored via a signaling mechanism (e.g., fluorescence) as they are generated and are tracked after the signal rises above a background level but before the reaction reaches a plateau.
  • a signaling mechanism e.g., fluorescence
  • a DNA binding dye e.g., SYBR green
  • a labeled probe can be used to detect the extension product generated by PCR amplification. Any probe format utilizing a labeled probe comprising the sequences of the invention may be used.
  • Immunohistochemistry methods are also suitable for detecting the levels of the biomarkers of the present invention.
  • Samples can be frozen for later preparation or immediately placed in a fixative solution.
  • Tissue samples can be fixed by treatment with a reagent, such as formalin, gluteraldehyde, methanol, or the like and embedded in paraffin.
  • a reagent such as formalin, gluteraldehyde, methanol, or the like and embedded in paraffin.
  • the levels of the biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 are normalized against the expression levels of all RNA transcripts or their non-natural cDNA expression products, or protein products in the sample, or of a reference set of RNA transcripts or a reference set of their non-natural cDNA expression products, or a reference set of their protein products in the sample.
  • the methods set forth herein provide a method for determining the lung cancer subtype of a patient.
  • the biomarker levels are compared to reference values or a reference sample, for example with the use of statistical methods or direct comparison of detected levels, to make a determination of the lung cancer molecular subtype. Based on the comparison, the patient's lung cancer sample is classified, e.g., as neuroendocrine, squamous cell carcinoma, adenocarcinoma. In another embodiment, based on the comparison, the patient's lung cancer sample is classified as squamous cell carcinoma, adenocarcinoma or small cell carcinoma. In yet another embodiment, based on the comparison, the patient's lung cancer sample is classified as squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative).
  • squamoid proximal inflammatory
  • bronchoid terminal respiratory unit
  • magnoid proximal proliferative
  • expression level values of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 are compared to reference expression level value(s) from at least one sample training set, wherein the at least one sample training set comprises expression level values from a reference sample(s).
  • the at least one sample training set comprises expression level values of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 from an adenocarcinoma sample, a squamous cell carcinoma sample, a neuroendocrine sample, a small cell lung carcinoma sample, a proximal inflammatory (squamoid), proximal proliferative (magnoid), a terminal respiratory unit (bronchioid) sample, or a combination thereof.
  • Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 from an adenocarcinoma sample, a squamous cell carcinoma sample, a neuroendocrine sample, a small cell lung carcinoma sample, a proximal inflammatory (squamoid), proximal proliferative (magnoid), a terminal respiratory unit (bronchioid) sample, or a combination thereof.
  • hybridization values of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 are compared to reference hybridization value(s) from at least one sample training set, wherein the at least one sample training set comprises hybridization values from a reference sample(s).
  • Methods for comparing detected levels of biomarkers to reference values and/or reference samples are provided herein. Based on this comparison, in one embodiment a correlation between the biomarker levels obtained from the subject's sample and the reference values is obtained. An assessment of the lung cancer subtype is then made.
  • biomarker levels obtained from the patient and reference biomarker levels for example, from at least one sample training set.
  • a supervised pattern recognition method is employed.
  • supervised partem recognition methods can include, but are not limited to, the nearest centroid methods (Dabney (2005) Bioinformatics 21(22):4148-4154 and Tibshirani et al. (2002) Proc. Natl. Acad. Sci.
  • the classifier for identifying tumor subtypes based on gene expression data is the centroid based method described in Mullins et al. (2007) Clin Chem. 53(7): 1273-9, each of which is herein incorporated by reference in its entirety.
  • a sample training set(s) can include expression data of all of the classifier biomarkers (e.g., all the classifier biomarkers of any of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, Table 6) from an adenocarcinoma sample.
  • a sample training set(s) can include expression data of all of the classifier biomarkers (e.g., all the classifier biomarkers of any of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, Table 6) from a squamous cell carcinoma sample, an adenocarcinoma sample and/or a neuroendocrine sample.
  • the sample training set(s) are normalized to remove sample-to-sample variation.
  • comparing can include applying a statistical algorithm, such as, for example, any suitable multivariate statistical analysis model, which can be parametric or non-parametric.
  • applying the statistical algorithm can include determining a correlation between the expression data obtained from the human lung tissue sample and the expression data from the adenocarcinoma and squamous cell carcinoma training set(s).
  • cross-validation is performed, such as (for example), leave-one-out cross-validation (LOOCV).
  • integrative correlation is performed.
  • LOOCV leave-one-out cross-validation
  • Spearman correlation is performed.
  • a centroid based method is employed for the statistical algorithm as described in Mullins et al. (2007) Clin Chem.
  • Results of the gene expression performed on a sample from a subject may be compared to a biological sample(s) or data derived from a biological sample(s) that is known or suspected to be normal ("reference sample” or "normal sample”, e.g., non- adenocarcinoma sample).
  • the reference sample may be assayed at the same time, or at a different time from the test sample.
  • the biomarker level information from a reference sample may be stored in a database or other means for access at a later date.
  • the biomarker level results of an assay on the test sample may be compared to the results of the same assay on a reference sample.
  • the results of the assay on the reference sample are from a database, or a reference value(s).
  • the results of the assay on the reference sample are a known or generally accepted value or range of values by those skilled in the art.
  • the comparison is qualitative.
  • the comparison is quantitative.
  • qualitative or quantitative comparisons may involve but are not limited to one or more of the following: comparing fluorescence values, spot intensities, absorbance values, chemiluminescent signals, histograms, critical threshold values, statistical significance values, expression levels of the genes described herein, mRNA copy numbers.
  • an odds ratio is calculated for each biomarker level panel measurement.
  • the OR is a measure of association between the measured biomarker values for the patient and an outcome, e.g. , lung cancer subtype.
  • an outcome e.g. , lung cancer subtype.
  • the specified confidence level for providing the likelihood of response may be chosen on the basis of the expected number of false positives or false negatives.
  • Methods for choosing parameters for achieving a specified confidence level or for identifying markers with diagnostic power include but are not limited to Receiver Operating Characteristic (ROC) curve analysis, binormal ROC, principal component analysis, odds ratio analysis, partial least squares analysis, singular value decomposition, least absolute shrinkage and selection operator analysis, least angle regression, and the threshold gradient directed regularization method.
  • ROC Receiver Operating Characteristic
  • the biomarker levels are in one embodiment subjected to the algorithm in order to classify the profile.
  • Supervised learning generally involves "training" a classifier to recognize the distinctions among classes (e.g., adenocarcinoma positive, adenocarcinoma negative, squamous positive, squamous negative, neuroendocrine positive, neuroendocrine negative, small cell positive, small cell negative, squamoid (proximal inflammatory) positive, bronchoid (terminal respiratory unit) positive or magnoid (proximal proliferative) positive, and then "testing" the accuracy of the classifier on an independent test set.
  • classes e.g., adenocarcinoma positive, adenocarcinoma negative, squamous positive, squamous negative, neuroendocrine positive, neuroendocrine negative, small cell positive, small cell negative, squamoid (proximal inflammatory) positive, bronchoid (terminal respiratory unit) positive or
  • the base-2 logarithm of each background corrected matched-cell intensity is then obtained.
  • the background corrected, log-transformed, matched intensity on each microarray is then normalized using the quantile normalization method in which for each input array and each probe value, the array percentile probe value is replaced with the average of all array percentile points, this method is more completely described by Bolstad et al. Bioinformatics 2003, incorporated by reference in its entirety.
  • the normalized data may then be fit to a linear model to obtain an intensity measure for each probe on each microarray. Tukey's median polish algorithm (Tukey, J. W., Exploratory Data Analysis. 1977, incorporated by reference in its entirety for all purposes) may then be used to determine the log-scale intensity level for the normalized probe set data.
  • Various other software programs may be implemented.
  • feature selection and model estimation may be performed by logistic regression with lasso penalty using glmnet (Friedman et al. (2010). Journal of statistical software 33(1): 1-22, incorporated by reference in its entirety).
  • Raw reads may be aligned using TopHat (Trapnell et al. (2009). Bioinformatics 25(9): 1105-11, incorporated by reference in its entirety).
  • top features N ranging from 10 to 200
  • SVM linear support vector machine
  • Confidence intervals are computed using the pROC package (Robin X, Turck N, Hainard A, et al. pROC: an open- source package for R and S+ to analyze and compare ROC curves. BMC bioinformatics 2011; 12: 77, incorporated by reference in its entirety).
  • data may be filtered to remove data that may be considered suspect.
  • data derived from microarray probes that have fewer than about 4, 5, 6, 7 or 8 guanosine+cytosine nucleotides may be considered to be unreliable due to their aberrant hybridization propensity or secondary structure issues.
  • data deriving from microarray probes that have more than about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 guanosine+cytosine nucleotides may in one embodiment be considered unreliable due to their aberrant hybridization propensity or secondary structure issues.
  • data from probe-sets may be excluded from analysis if they are not identified at a detectable level (above background).
  • probe-sets that exhibit no, or low variance may be excluded from further analysis.
  • Low-variance probe-sets are excluded from the analysis via a Chi-Square test.
  • a probe-set is considered to be low- variance if its transformed variance is to the left of the 99 percent confidence interval of the Chi-Squared distribution with (N-l) degrees of freedom.
  • Chi-Sq(N-l) where N is the number of input CEL files, (N-l) is the degrees of freedom for the Chi-Squared distribution, and the "probe-set variance for the gene" is the average of probe-set variances across the gene.
  • probe-sets for a given mRNA or group of mRNAs may be excluded from further analysis if they contain less than a minimum number of probes that pass through the previously described filter steps for GC content, reliability, variance and the like.
  • probe-sets for a given gene or transcript cluster may be excluded from further analysis if they contain less than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or less than about 20 probes.
  • Methods of biomarker level data analysis in one embodiment further include the use of a feature selection algorithm as provided herein.
  • feature selection is provided by use of the LIMMA software package (Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397-420, incorporated by reference in its entirety for all purposes).
  • Methods of biomarker level data analysis further include the use of a classifier algorithm as provided herein.
  • a classifier algorithm as provided herein.
  • a diagonal linear discriminant analysis k-nearest neighbor algorithm, support vector machine (SVM) algorithm, linear support vector machine, random forest algorithm, or a probabilistic model-based method or a combination thereof is provided for classification of microarray data.
  • SVM support vector machine
  • identified markers that distinguish samples are selected based on statistical significance of the difference in biomarker levels between classes of interest. In some cases, the statistical significance is adjusted by applying a Benjamin Hochberg or another correction for false discovery rate (FDR).
  • FDR false discovery rate
  • a statistical evaluation of the results of the biomarker level profiling may provide a quantitative value or values indicative of one or more of the following: the lung cancer subtype (adenocarcinoma, squamous cell carcinoma, neuroendocrine); molecular subtype of adenocarcinoma (squamoid, bronchoid or magnoid); the likelihood of the success of a particular therapeutic intervention, e.g., angiogenesis inhibitor therapy or chemotherapy.
  • the data is presented directly to the physician in its most useful form to guide patient care, or is used to define patient populations in clinical trials or a patient population for a given medication.
  • accuracy may be determined by tracking the subject over time to determine the accuracy of the original diagnosis.
  • accuracy may be established in a deterministic manner or using statistical methods. For example, receiver operator characteristic (ROC) analysis may be used to determine the optimal assay parameters to achieve a specific level of accuracy, specificity, positive predictive value, negative predictive value, and/or false discovery rate.
  • ROC receiver operator characteristic
  • the results of the biomarker level profiling assays are entered into a database for access by representatives or agents of a molecular profiling business, the individual, a medical provider, or insurance provider.
  • assay results include sample classification, identification, or diagnosis by a representative, agent or consultant of the business, such as a medical professional.
  • a computer or algorithmic analysis of the data is provided automatically.
  • the molecular profiling business may bill the individual, insurance provider, medical provider, researcher, or govemment entity for one or more of the following: molecular profiling assays performed, consulting services, data analysis, reporting of results, or database access.
  • the results of the biomarker level profiling assays are presented as a report on a computer screen or as a paper record.
  • the report may include, but is not limited to, such information as one or more of the following: the levels of biomarkers (e.g. , as reported by copy number or fluorescence intensity, etc.) as compared to the reference sample or reference value(s); the likelihood the subject will respond to a particular therapy, based on the biomarker level values and the lung cancer subtype and proposed therapies.
  • the results of the gene expression profiling may be classified into one or more of the following: adenocarcinoma positive, adenocarcinoma negative, squamous cell carcinoma positive, squamous cell carcinoma negative, neuroendocrine positive, neuroendocrine negative, small cell carcinoma positive, small cell carcinoma negative, squamoid (proximal inflammatory) positive, bronchoid (terminal respiratory unit) positive, magnoid (proximal proliferative) positive, squamoid (proximal inflammatory) negative, bronchoid (terminal respiratory unit) negative, magnoid (proximal proliferative) negative; likely to respond to angiogenesis inhibitor or chemotherapy; unlikely to respond to angiogenesis inhibitor or chemotherapy; or a combination thereof.
  • results are classified using a trained algorithm.
  • Trained algorithms of the present invention include algorithms that have been developed using a reference set of known gene expression values and/or normal samples, for example, samples from individuals diagnosed with a particular molecular subtype of adenocarcinoma.
  • a reference set of known gene expression values are obtained from individuals who have been diagnosed with a particular molecular subtype of adenocarcinoma, and are also known to respond (or not respond) to angiogenesis inhibitor therapy.
  • Algorithms suitable for categorization of samples include but are not limited to k- nearest neighbor algorithms, support vector machines, linear discriminant analysis, diagonal linear discriminant analysis, updown, naive Bayesian algorithms, neural network algorithms, hidden Markov model algorithms, genetic algorithms, or any combination thereof.
  • a binary classifier When a binary classifier is compared with actual true values (e.g., values from a biological sample), there are typically four possible outcomes. If the outcome from a prediction is p (where "p" is a positive classifier output, such as the presence of a deletion or duplication syndrome) and the actual value is also p, then it is called a true positive (TP); however if the actual value is n then it is said to be a false positive (FP). Conversely, a true negative has occurred when both the prediction outcome and the actual value are n (where "n" is a negative classifier output, such as no deletion or duplication syndrome), and false negative is when the prediction outcome is n while the actual value is p.
  • p is a positive classifier output, such as the presence of a deletion or duplication syndrome
  • the positive predictive value is the proportion of subjects with positive test results who are correctly diagnosed as likely or unlikely to respond, or diagnosed with the correct lung cancer subtype, or a combination thereof. It reflects the probability that a positive test reflects the underlying condition being tested for. Its value does however depend on the prevalence of the disease, which may vary. In one example the following characteristics are provided: FP (false positive); TN (true negative); TP (true positive); FN (false negative).
  • False positive rate ( ⁇ ) FP/(FP+TN)-specificity
  • False negative rate (D) FN/(TP+FN)-sensitivity
  • Likelihood-ratio positive sensitivity/(l-specificity)
  • Likelihood-ratio negative ( 1 -sensitivity )/specificity.
  • the negative predictive value (NPV) is the proportion of subjects with negative test results who are correctly diagnosed.
  • the results of the biomarker level analysis of the subject methods provide a statistical confidence level that a given diagnosis is correct.
  • such statistical confidence level is at least about, or more than about 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% 99.5%, or more.
  • the method further includes classifying the lung tissue sample as a particular lung cancer subtype based on the comparison of biomarker levels in the sample and reference biomarker levels, for example present in at least one training set.
  • the lung tissue sample is classified as a particular subtype if the results of the comparison meet one or more criterion such as, for example, a minimum percent agreement, a value of a statistic calculated based on the percentage agreement such as (for example) a kappa statistic, a minimum correlation (e.g., Pearson's correlation) and/or the like.
  • Hardware modules may include, for example, a general-purpose processor, a field programmable gate array (FPGA), and/or an application specific integrated circuit (ASIC).
  • Software modules (executed on hardware) can be expressed in a variety of software languages (e.g., computer code), including Unix utilities, C, C++, JavaTM, Ruby, SQL, SAS®, the R programming language/software environment, Visual BasicTM, and other object-oriented, procedural, or other programming language and development tools.
  • Examples of computer code include, but are not limited to, micro-code or micro-instructions, machine instructions, such as produced by a compiler, code used to produce a web service, and files containing higher-level instructions that are executed by a computer using an interpreter. Additional examples of computer code include, but are not limited to, control signals, encrypted code, and compressed code.
  • non-transitory computer-readable media include, but are not limited to: magnetic storage media such as hard disks, floppy disks, and magnetic tape; optical storage media such as Compact Disc/Digital Video Discs (CD/DVDs), Compact Disc- Read Only Memories (CD-ROMs), and holographic devices; magneto-optical storage media such as optical disks; carrier wave signal processing modules; and hardware devices that are specially configured to store and execute program code, such as Application-Specific Integrated Circuits (ASICs), Programmable Logic Devices (PLDs), Read-Only Memory (ROM) and Random-Access Memory (RAM) devices.
  • ASICs Application-Specific Integrated Circuits
  • PLDs Programmable Logic Devices
  • ROM Read-Only Memory
  • RAM Random-Access Memory
  • Other embodiments described herein relate to a computer program product, which can include, for example, the instructions and/or computer code discussed herein.
  • a single biomarker or from about 5 to about 10, from about 5 to about 15, from about 5 to about 20, from about 5 to about 25, from about 5 to about 30, from about 5 to about 35, from about 5 to about 40, from about 5 to about 45, from about 5 to about 50 biomarkers (e.g., as disclosed in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 and Table 6) is capable of classifying types and/or subtypes of lung cancer with a predictive success of at least about 70%, at least about 71%, at least about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%,
  • any combination of biomarkers disclosed herein can used to obtain a predictive success of at least about 70%, at least about 71%, at least about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, up to 100%, and all values in between.
  • a single biomarker or from about 5 to about 10, from about 5 to about 15, from about 5 to about 20, from about 5 to about 25, from about 5 to about 30, from about 5 to about 35, from about 5 to about 40, from about 5 to about 45, from about 5 to about 50 biomarkers (e.g., as disclosed in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 and Table 6) is capable of classifying lung cancer types and/or subtypes with a sensitivity or specificity of at least about 70%, at least about 71%, at least about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about
  • any combination of biomarkers disclosed herein can be used to obtain a sensitivity or specificity of at least about 70%, at least about 71%, at least about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, up to 100%, and all values in between.
  • kits for practicing the methods of the invention are further provided.
  • the kit can encompass any manufacture (e.g., a package or a container) including at least one reagent, e.g., an antibody, a nucleic acid probe or primer, and/or the like, for detecting the biomarker level of a classifier biomarker.
  • the kit can be promoted, distributed, or sold as a unit for performing the methods of the present invention.
  • the kits can contain a package insert describing the kit and methods for its use.
  • a method for determining a disease outcome or prognosis for a patient suffering from cancer.
  • the cancer is lung cancer.
  • the method can comprise determining a disease outcome or prognosis for the patient by comparing a molecular subtype of the patient's cancer with a morphological subtype of the patient's cancer, whereby the presence or absence of concordance between the molecular and morphological subtypes predicts the disease outcome or prognosis of the patient.
  • discordance between the molecular subtype and the morphological subtype indicates a poor prognosis or poor disease outcome.
  • the poor prognosis or disease outcome can be in comparison to a patient suffering from the same type of cancer (e.g., lung cancer) whose molecular and morphological subtype determinations are concordant.
  • the disease outcome or prognosis can be measured by examining the overall survival for a period of time or intervals (e.g., 0 to 36 months or 0 to 60 months).
  • survival is analyzed as a function of subtype (e.g., for lung cancer, adenocarcinoma (TRU, PI, and PP), neuroendocrine (small cell carcinoma and carcinoid), or squamous).
  • Relapse-free and overall survival can be assessed using standard Kaplan-Meier plots (see FIGs. 4-11) as well as Cox proportional hazards modeling.
  • the molecular subtype is determined by detecting expression levels of classifier biomarkers, thereby obtaining an expression profile.
  • the expression profile can be determined using any of the methods provided herein.
  • the patient is suffering from lung cancer and the molecular subtype of a lung tissue sample obtained from the patient is determined by detecting the levels of a single biomarker, or from about 5 to about 10, from about 5 to about 15, from about 5 to about 20, from about 5 to about 25, from about 5 to about 30, from about 5 to about 35, from about 5 to about 40, from about 5 to about 45, from about 5 to about 50 classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 using any of the methods provided herein for detecting the expression levels (e.g., RNA-seq, RT-PCR, or hybridization assay such as, for example, microarray hybridization assay).
  • RNA-seq e.g., RNA-seq, RT-PCR, or hybridization as
  • the molecular subtype is determined by detecting expression levels of at least five classifier biomarkers in Table 1 A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 at a nucleic acid level in a lung tissue sample by performing RT-PCR (or qRT-PCR) and comparing the detected expression levels to those of a reference sample or training set as described herein in order to determine if the molecular subtype of the lung tissue sample obtained from the patient is an adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype.
  • the neuroendocrine subtype can encompass small cell carcinoma and carcinoid.
  • the adenocarcinoma subtype can be further classified as being TRU, PI, or PP.
  • the RT-PCR can be performed with primers specific to the at least five classifier biomarkers.
  • the primers specific for the at least five classifier biomarkers are forward and reverse primers listed in Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6.
  • the molecular subtype is determined by probing the levels of at least five classifier biomarkers in Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 at a nucleic acid level in a lung tissue sample by mixing the sample with five or more oligonucleotides that are substantially complementary to portions of nucleic acid molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for hybridization of the five or more oligonucleotides to their complements or substantial complements, detecting whether hybridization occured between the five or more oligonucleotides to their complements or substantial complements, obtaining hybridization values of the at least five classifier biomarkers based on the detecting step and comparing the detected hybridization values to those of a reference sample or training set as described herein in order to determine if the molecular subtype of the lung tissue sample obtained from the patient is an
  • the morphological subtype of a tissue sample is a histological analysis. Histological analysis can be performed using any of the methods known in the art.
  • a lung tissue sample is assigned a histological subtype of adenocarcinoma, squamous, or neuroendocrine based on the histological analysis.
  • the histological subtype of a lung tissue sample obtained from a patient suffering from lung cancer is compared to the molecular subtype of the lung tissue sample, whereby the molecular subtype is determined by examining gene expression levels of classifier genes (e.g.
  • the histological subtype and molecular subtypes are in concordance, whereby the overall survival of the patient (as determined for example by using standard Kaplan-Meier plots as well as Cox proportional hazards modeling) is substantially similar to the overall survival of other patients with the same subtype of cancer.
  • the histological subtype and molecular subtype are discordant, whereby the overall survival of the patient (as determined for example by using standard Kaplan-Meier plots as well as Cox proportional hazards modeling) is substantially dissimilar to the overall survival of other patients with concordant molecular and histological subtype determinations of cancer.
  • the overall survival probability of patient's with discordant subtypes can be 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, 99.5%, or 99.9% less or lower than the overall survival probability of patient's with concordant subtypes of cancer (e.g., lung cancer).
  • cancer e.g., lung cancer
  • the patient upon determining a patient's lung cancer subtype, is selected for suitable therapy, for example chemotherapy or drug therapy with an angiogenesis inhibitor.
  • the therapy is angiogenesis inhibitor therapy
  • the angiogenesis inhibitor is a vascular endothelial growth factor (VEGF) inhibitor, a VEGF receptor inhibitor, a platelet derived growth factor (PDGF) inhibitor or a PDGF receptor inhibitor.
  • VEGF vascular endothelial growth factor
  • PDGF platelet derived growth factor
  • the angiogenesis inhibitor is an integrin antagonist, a selectin antagonist, an adhesion molecule antagonist (e.g., antagonist of intercellular adhesion molecule (ICAM)-l, ICAM-2, ICAM-3, platelet endothelial adhesion molecule (PCAM), vascular cell adhesion molecule (VCAM)), lymphocyte function-associated antigen 1 (LFA- 1)), a basic fibroblast growth factor antagonist, a vascular endothelial growth factor (VEGF) modulator, or a platelet derived growth factor (PDGF) modulator (e.g. , a PDGF antagonist).
  • an adhesion molecule antagonist e.g., antagonist of intercellular adhesion molecule (ICAM)-l, ICAM-2, ICAM-3, platelet endothelial adhesion molecule (PCAM), vascular cell adhesion molecule (VCAM)), lymphocyte function-associated antigen 1 (LFA- 1)
  • a basic fibroblast growth factor antagonist e.g.,
  • the integrin antagonist is a small molecule integrin antagonist, for example, an antagonist described by Paolillo et al. (Mini Rev Med Chem, 2009, volume 12, pp. 1439- 1446, incorporated by reference in its entirety), or a leukocyte adhesion-inducing cytokine or growth factor antagonist (e.g., tumor necrosis factor-a (TNF-a), interleukin- ⁇ ⁇ (IL- ⁇ ⁇ ), monocyte chemotactic protein-1 (MCP-1) and a vascular endothelial growth factor (VEGF)), as described in U.S. Patent No. 6,524,581, incorporated by reference in its entirety herein.
  • TNF-a tumor necrosis factor-a
  • IL- ⁇ ⁇ interleukin- ⁇ ⁇
  • MCP-1 monocyte chemotactic protein-1
  • VEGF vascular endothelial growth factor
  • the methods provided herein are also useful for determining whether a subject is likely to respond to one or more of the following angiogenesis inhibitors: interferon gamma 1 ⁇ , interferon gamma 1 ⁇ (Actimmune®) with pirfenidone, ACUHTR028, ⁇ 5, aminobenzoate potassium, amyloid P, ANG1122, ANG1170, ANG3062, ANG3281, ANG3298, ANG4011, anti-CTGF RNAi, Aplidin, astragalus membranaceus extract with salvia and schisandra chinensis, atherosclerotic plaque blocker, Azol, AZX100, BB3, connective tissue growth factor antibody, CT140, danazol, Esbriet, EXCOOl, EXC002, EXC003, EXC004, EXC005, F647, FG3019, Fibrocorin, Follistatin, FT011, a galectin-3 inhibitor, G
  • a method for determining whether a subject is likely to respond to one or more endogenous angiogenesis inhibitors.
  • the endogenous angiogenesis inhibitor is endostatin, a 20 kDa C-terminal fragment derived from type XVIII collagen, angiostatin (a 38 kDa fragment of plasmin), or a member of the thrombospondin (TSP) family of proteins.
  • the angiogenesis inhibitor is a TSP-1, TSP-2, TSP-3, TSP-4 and TSP-5.
  • soluble VEGFR-1 and neuropilin 1 NPR1
  • angiopoietin-1 angiopoietin-2
  • vasostatin calreticulin
  • platelet factor-4 a tissue inhibitor of metalloproteinase (TIMP)
  • TIMP1, TIMP2, TIMP 3, TIMP4 tissue inhibitor of metalloproteinase
  • cartilage- derived angiogenesis inhibitor e.g., peptide troponin I and chrondomodulin I
  • a disintegrin and metalloproteinase with thrombospondin motif 1 an interferon (IFN) (e.g. , IFN-a, IFN- ⁇ , IFN- ⁇ )
  • a chemokine e.g.
  • a chemokine having the C-X-C motif e.g., CXCLIO, also known as interferon gamma-induced protein 10 or small inducible cytokine B10
  • CXCLIO also known as interferon gamma-induced protein 10 or small inducible cytokine B10
  • an interleukin cytokine e.g. , IL-4, IL-12, IL-18
  • prothrombin e.g. IL-4, IL-12, IL-18
  • prothrombin antithrombin III fragment
  • prolactin the protein encoded by the TNFSF15 gene
  • osteopontin osteopontin
  • maspin canstatin
  • proliferin-related protein e.g., canstatin, proliferin-related protein.
  • a method for determining the likelihood of response to one or more of the following angiogenesis inhibitors is provided is angiopoietin-1, angiopoietin-2, angiostatin, endostatin, vasostatin, thrombospondin, calreticulin, platelet factor-4, TIMP, CDAI, interferon a, interferon p,vascular endothelial growth factor inhibitor (VEGI) meth-1, meth-2, prolactin, VEGI, SPARC, osteopontin, maspin, canstatin, proliferin- related protein (PRP), restin, TSP-1, TSP-2, interferon gamma 1 ⁇ , ACUHTR028, ⁇ 5, aminobenzoate potassium, amyloid P, ANG1122, ANG1170, ANG3062, ANG3281, ANG3298, ANG4011, anti-CTGF RNAi, Aplidin, astragalus membranaceus extract with sal
  • a methods for determining the likelihood of response to one or more of the following angiogenesis inhibitors is provided: pazopanib (Votrient), sunitinib (Sutent), sorafenib (Nexavar), axitinib (Inlyta), ponatinib (Iclusig), vandetanib (Caprelsa), cabozantinib (Cometrig), ramucirumab (Cyramza), regorafenib (Stivarga), ziv-aflibercept (Zaltrap), or a combination thereof.
  • the angiogenesis inhibitor is a VEGF inhibitor.
  • the PDGF antagonist is the anti-PDGF- ⁇ aptamer El 0030, sunitinib, axitinib, sorefenib, imatinib, imatinib mesylate, nintedanib, pazopanib HC1, ponatinib, MK-2461, dovitinib, pazopanib, crenolanib, PP-121, telatinib, imatinib, KRN 633, CP 673451, TSU-68, Ki8751, amuvatinib, tivozanib, masitinib, motesanib diphosphate, dovitinib dilactic acid, linifanib (ABT-869).
  • Table 10b A-833 dataset training gene centroids applied to data from 2 other publicly available lung cancer gene expression databases (TCGA & A-334) for a 3 class prediction of lung tumor type. LOO cross validation was performed for the A-833 dataset.
  • Table 10c A-833 dataset training gene centroids applied to data from 2 other publicly available lung cancer gene expression databases (TCGA & A-334) for a 4 class prediction of lung tumor type. LOO cross validation was performed for the A-833 dataset. Prediction
  • NCCN National Comprehensive Cancer Network
  • LSP Lung Subtype Panel
  • the datasets included several publically available lung cancer gene expression data sets, including 2,099 Fresh Frozen lung cancer samples (TCGA, NCI, UNC, Duke, Expo, Seoul, and France) as well as newly collected gene expression data from 78 FFPE samples. Data sources are provided in the Table 12 below.
  • the 78 FFPE samples were archived residual lung tumor samples collected at the University of North Carolina at Chapel Hill (UNC-CH) using an IRB approved protocol. Only samples with a definitive diagnosis of AD, carcinoid, Small Cell Carcinoma (SCC), or SQC were used in the analysis.
  • Affymetrix training gene centroids are provided in Table 14.
  • the training set gene centroids were tested in normalized TCGA RNAseq gene expression and Agilent microarray gene expression data sets. Due to missing data from the public Agilent dataset, the Agilent evaluations were performed with a 47 gene classifier, rather than a 52 gene panel with exclusion of the following genes: CIB1 FOXH1, LIPE, PCAM1, TUBAL
  • LGALS3 0.1805 -1.1435 -0.2305

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Abstract

Methods and compositions are provided for the molecular subtyping of lung cancer samples. Specifically, a method of assessing whether a patient's adenocarcinoma lung cancer subtype is terminal respiratory unit (TRU), proximal inflammatory (PI), or proximal proliferative (PP) is provided herein. The method entails detecting the levels of the classifier biomarkers of Table 1-Table 6 or a subset thereof at the nucleic acid level, in a lung cancer sample obtained from the patient. Based in part on the levels of the classifier biomarkers, the lung cancer sample is classified as a TRU, PI, or PP sample.

Description

METHODS FOR TYPING OF LUNG CANCER
CROSS REFERENCE TO U.S. NON-PROVISIONAL APPLICATONS
[0001] This application claims priority from U.S. Provisional Application Serial No. 62/147,547, filed April 14, 2015, which is incorporated by reference herein in its entirety for all purposes.
STATEMENT REGARDING SEQUENCE LISTING
[0002] The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is GNCN_007_01WO_ST25.txt. The text file is 17 KB, was created on April 14, 2016, and is being submitted electronically via EFS-Web.
BACKGROUND OF THE INVENTION
[0003] Lung cancer is the leading cause of cancer death in the United States and over 220,000 new lung cancer cases are identified each year. Lung cancer is a heterogeneous disease with subtypes generally determined by histology (small cell, non-small cell, carcinoid, adenocarcinoma, and squamous cell carcinoma). Differentiation among various morphologic subtypes of lung cancer is essential in guiding patient management and additional molecular testing is used to identify specific therapeutic target markers. Variability in morphology, limited tissue samples, and the need for assessment of a growing list of therapeutically targeted markers pose challenges to the current diagnostic standard. Studies of histologic diagnosis reproducibility have shown limited intra- pathologist agreement and inter-pathologist agreement.
[0004] While new therapies are increasingly directed toward specific subtypes of lung cancer (bevacizumab and pemetrexed), studies of histologic diagnosis reproducibility have shown limited intra-pathologist agreement and even less inter-pathologist agreement. Poorly differentiated tumors, conflicting immunohistochemistry results, and small volume biopsies in which only a limited number of stains can be performed continue to pose challenges to the current diagnostic standard (Travis and Rekhtman Sem Resp and Crit Care Med 2011 ; 32(1): 22-31; Travis et al. Arch Pathol Lab Med 2013; 137(5):668-84; Tang et al. J Thorac Dis 2014; 6(S5):S489-S501).
[0005] A recent example involving expert pathology re-review of lung cancer samples submitted to the TCGA Lung Cancer genome project led to the reclassification of 15-20% of lung tumors submitted, confirming the ongoing challenge of morphology-based diagnoses. (Cancer Genome Atlas Research Network. "Comprehensive genomic characterization of squamous cell lung cancers." Nature 489.7417 (2012): 519-525; Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature 511.7511 (2014): 543-550, each of which is incorporated by reference herein in its entirety). Thus a need exists for a more reliable means for determining lung cancer subtype. The present invention addresses this and other needs.
SUMMARY OF THE INVENTION
[0006] In one aspect, a method of assessing whether a patient's adenocarcinoma lung cancer subtype is squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative). In one embodiment, the method comprises probing the levels of at least five classifier biomarkers of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 at the nucleic acid level, in a lung cancer sample obtained from the patient. The probing step, in one embodiment, comprises mixing the sample with five or more oligonucleotides that are substantially complementary to portions of cDNA molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for hybridization of the five or more oligonucleotides to their complements or substantial complements; detecting whether hybridization occurs between the five or more
oligonucleotides to their complements or substantial complements; and obtaining
hybridization values of the at least five classifier biomarkers based on the detecting step. The hybridization values of the at least five classifier biomarkers are then compared to reference hybridization value(s) from at least one sample training set, wherein the at least one sample training set comprises, (i) hybridization value(s) of the at least five biomarkers from a sample that overexpresses the at least five biomarkers, or overexpresses a subset of the at least five biomarkers, (ii) hybridization values from a reference squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative) sample, or (iii) hybridization values from an adenocarcinoma free lung sample. The adenocarcinoma lung cancer sample is classified as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype based on the results of the comparing step. In one embodiment, the comparing step comprises determining a correlation between the hybridization values of the at least five classifier biomarkers and the reference hybridization values. In one embodiment, the comparing step further comprises determining an average expression ratio of the at least five biomarkers and comparing the average expression ratio to an average expression ratio of the at least five biomarkers, obtained from the references values in the sample training set. In one embodiment, the probing step comprises isolating the nucleic acid or portion thereof prior to the mixing step. In a further embodiment, the hybridization comprises hybridization of a cDNA to a cDNA, thereby forming a non-natural complex; or hybridization of a cDNA to an mRNA, thereby forming a non-natural complex. In even a further embodiment, the probing step comprises amplifying the nucleic acid in the sample. In one embodiment, the lung cancer sample comprises lung cells embedded in paraffin. In one embodiment, the lung cancer sample is a fresh frozen sample. In one embodiment, the lung cancer sample is selected from a formalin-fixed, paraffin-embedded (FFPE) lung tissue sample, fresh and a frozen tissue sample.
[0007] In another aspect, provided herein is a method for assessing whether a lung tissue sample from a human patient is a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative) adenocarcinoma lung cancer subtype. In one embodiment, the method comprises detecting expression levels of at least five of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 at the nucleic acid level by RNA-seq, a reverse transcriptase polymerase chain reaction (RT-PCR) or a hybridization assay with oligonucleotides specific to the classifier biomarkers; comparing the detected levels of expression of the at least five of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 to the expression levels of the at least five of the classifier biomarkers from at least one sample training set. In one embodiment, the at least one sample training set comprises, (i) expression levels(s) of the at least five biomarkers from a sample that overexpresses the at least five biomarkers, or overexpresses a subset of the at least five biomarkers, (ii) expression levels from a reference squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative) sample, or (iii) expression levels from an adenocarcinoma free lung sample; and classifying the lung tissue sample as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype based on the results of the comparing step. In one embodiment, the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the lung tissue sample and the expression data from the at least one training set(s); and classifying the lung tissue sample as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype based on the results of the statistical algorithm. In one embodiment, the comparing step further comprises determining an average expression ratio of the at least five biomarkers and comparing the average expression ratio to an average expression ratio of the at least five biomarkers, obtained from the references values in the sample training set. In one embodiment, the lung tissue sample is selected from a formalin-fixed, paraffin-embedded (FFPE) lung tissue sample, fresh and a frozen tissue sample.
[0008] In yet another aspect, provided herein is a method for determining a disease outcome for a patient suffering from lung cancer, the method comprising: determining a subtype of the lung cancer through gene expression analysis of a first sample obtained from the patient to produce a gene expression based subtype; determining the subtype of the lung cancer through a morphological analysis of a second sample obtained from the patient to produce a morphological based subtype; and comparing the gene expression based subtype to the morphological based subtype, wherein a presence or absence of concordance between the gene expression based subtype and the morphological based subtype is predictive of the disease outcome. In one embodiment, discordance between the gene expression based subtype and morphological based subtype is predictive of a poor disease outcome. In one embodiment, the disease outcome is overall survival. In one embodiment, the gene expression base subtype and/or morphological based subtype is adenocarcinoma, squamous cell carcinoma, or neuroendocrine. In one embodiment, the neuroendocrine encompasses small cell carcinoma and carcinoid. In one embodiment, the first sample and/or the second sample is a formalin-fixed, paraffin-embedded (FFPE) lung tissue sample, fresh, or a frozen tissue sample. In one embodiment, the first sample and the second sample are portions of an identical sample. In one embodiment, the gene expression analysis comprises determining expression levels of at least five classifier biomarkers in Table 1 A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 at a nucleic acid level in the first sample by performing RNA sequencing, reverse transcriptase polymerase chain reaction (RT-PCR) or hybridization based analyses. In one embodiment, the RT-PCR is quantitative real time reverse transcriptase polymerase chain reaction (qRT-PCR). In one embodiment, the RT- PCR is performed with primers specific to the at least five classifier biomarkers; comparing the detected levels of expression of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 to the expression of the at least five classifier biomarkers in at least one sample training set(s), wherein the at least one sample training set comprises expression data of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 from a reference adenocarcinoma sample, expression data of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 from a reference squamous cell carcinoma sample, expression data of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 from a reference neuroendocrine sample, or a combination thereof; and classifying the first sample as an adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype based on the results of the comparing step. In one embodiment, the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the first sample and the expression data from the at least one training set(s); and classifying the first sample as an adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype based on the results of the statistical algorithm. In one embodiment, the primers specific for the at least five classifier biomarkers are forward and reverse primers listed in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6. In one embodiment, the hybridization analysis comprises: (a) probing the levels of at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 in a lung cancer sample obtained from the patient at the nucleic acid level, wherein the probing step comprises; (i) mixing the sample with five or more oligonucleotides that are substantially complementary to portions of nucleic acid molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for hybridization of the five or more oligonucleotides to their complements or substantial complements; (ii) detecting whether hybridization occurs between the five or more oligonucleotides to their complements or substantial complements; (iii) obtaining hybridization values of the at least five classifier biomarkers based on the detecting step; (b) comparing the hybridization values of the at least five classifier biomarkers to reference hybridization value(s) from at least one sample training set, wherein the at least one sample training set comprises hybridization values from a reference adenocarcinoma sample, hybridization values from a reference squamous cell carcinoma sample, hybridization values from a reference neuroendocrine sample, or a combination thereof; and (c) classifying the lung cancer sample as a adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype based on the results of the comparing step. In one embodiment, the comparing step comprises determining a correlation between the hybridization values of the at least five classifier biomarkers and the reference hybridization values. In one embodiment, the comparing step further comprises determining an average expression ratio of the at least five biomarkers and comparing the average expression ratio to an average expression ratio of the at least five biomarkers, obtained from the references values in the sample training set. In one embodiment, the probing step comprises isolating the nucleic acid or portion thereof prior to the mixing step. In one embodiment, the hybridization comprises hybridization of a cDNA probe to a cDNA biomarker, thereby forming a non- natural complex. In one embodiment, the hybridization comprises hybridization of a cDNA probe to an mRNA biomarker, thereby forming a non-natural complex. In one embodiment, the morphological analysis of the second sample is a histological analysis.
[0009] In one embodiment, the at least five of the classifier biomarkers of any of the aspects provided above comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 1A, Table IB or Table 1C. In one embodiment, the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 2. In one embodiment, the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 3. In one embodiment, the at least five of the classifier biomarkers comprise the 6 biomarkers of Table 4. In one embodiment, the at least five of the classifier biomarkers comprise the 6 biomarkers of Table 5. In one embodiment, the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 6. In one embodiment, the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 1A, Table IB or Table 1C. In one embodiment, the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 2. In one embodiment, the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 3. In one embodiment, the at least five classifier biomarkers comprise from about 5 to about 30 classifier biomarkers, or from about 10 to about 30 classifier biomarkers of Table 6. In one embodiment, the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 1A, Table IB or Table 1C. In one embodiment, the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 2. In one embodiment, the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 3. In one embodiment, the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 6. In one embodiment, the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 1A. In one embodiment, the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table IB. In one embodiment, the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 1C.
BRIEF DESCRIPTION OF THE DRAWINGS
[0010] FIGs 1A-1D illustrate exemplary gene expression heatmaps for adenocarcinoma (FIG 1A), squamous cell carcinoma (FIG IB), small cell carcinoma (FIG 1C), and carcinoid (FIG ID).
[0011] FIG 2 illustrates a heatmap of gene expression hierarchical clustering for FFPE RT- PCR gene expression dataset.
[0012] FIG 3 illustrates a comparison of path review and LSP prediction for 77 FFPE samples. Each rectangle represents a single sample ordered by sample number. Arrows indicate 6 samples that disagreed with the original diagnosis by both pathology review and gene expression (for sample details see Table 18).
[0013] FIGs 4-7 illustrates Kaplan Meier plots showing the predicted lung cancer subtype
AD, SQ, or NE as a function of overall survival for 5 years for 3 independent AD datasets: Director's Challenge (Shedden et al; FIG. 4), TCGA R Aseq data (FIG. 5), Tomida et al. array data (FIG. 6) or pooled (FIG. 7) assigned a LSP gene expression subtype across all stages .
[0014] FIGs 8-11 illustrates Kaplan Meier plots showing the predicted lung cancer subtype
AD, SQ, or NE as a function of overall survival for 5 years for 3 independent AD datasets: Director's Challenge (Shedden et al; FIG. 8), TCGA RNAseq data (FIG. 9), Tomida et al. array data (FIG. 10) or pooled (FIG. ίί) assigned a LSP gene expression subtype across stages ί and II. [0015] FIG. 12 illustrates the proliferation score (11 gene PAM50 signature) is higher in AD-NE/SQ compared to AD- AD in all 3 datasets shown in FIGs. 4-6.
[0016] FIG, 13 illustrates gene mutation prevalence in histology-gene expression concordant (AD-AD) as compared to discordant (AD-NE/SQ) samples using Fisher's exact test.
[0017] FIG. 14 illustrates reduction in lung adenocarcinoma prognostic strength following exclusion of histologically defined adenocarcinoma samples that are NE or SQ by LSP gene expression (AD-NE/SQ).
[0018] FIG, IS illustrates the Cox proportional hazard models of overall survival (OS). Models in the hazard ratios table in FIG. 15 used binarized risk scores (at 0.67 quantile), calling one third of the samples high risk. Models in the p-values portion of the table left all risk scores continuous. All models adjusted for (T, N, Age).
DETAILED DESCRIPTION OF THE INVENTION
[0019] Gene expression based adenocarcinoma subtyping has been shown to classify adenocarcinoma tumors into 3 biologically distinct subtypes (Terminal Respiratory Unit (TRU; formerly referred to as Bronchioid), Proximal Inflammatory (PI; formerly referred to as Squamoid), and Proximal Proliferative (PP; formerly referred to as Magnoid)). These three subtypes vary in their prognosis, in their distribution of smokers vs. nonsmokers, in their prevalence of EGFR alterations, ALK rearrangements, TP53 mutations, and in their angiogenic features. The present invention addresses the need in the field for determining a prognosis or disease outcome for adenocarcinoma patient populations based in part on the adenocarcinoma subtype (Terminal Respiratory Unit (TRU), Proximal Inflammatory (PI), Proximal Proliferative (PP)) of the patient.
[0020] As used herein, an "expression profile" comprises one or more values corresponding to a measurement of the relative abundance, level, presence, or absence of expression of a discriminative gene. An expression profile can be derived from a subject prior to or subsequent to a diagnosis of lung cancer, can be derived from a biological sample collected from a subject at one or more time points prior to or following treatment or therapy, can be derived from a biological sample collected from a subject at one or more time points during which there is no treatment or therapy (e.g., to monitor progression of disease or to assess development of disease in a subject diagnosed with or at risk for lung cancer), or can be collected from a healthy subject. The term subject can be used interchangeably with patient. The patient can be a human patient.
[0021] As used herein, the term "determining an expression level" or "determining an expression profile" or "detecting an expression level" or "detecting an expression profile" as used in reference to a biomarker or classifier means the application of a biomarker specific reagent such as a probe, primer or antibody and/or a method to a sample, for example a sample of the subject or patient and/or a control sample, for ascertaining or measuring quantitatively, semi-quantitatively or qualitatively the amount of a biomarker or biomarkers, for example the amount of biomarker polypeptide or mRNA (or cDNA derived therefrom). For example, a level of a biomarker can be determined by a number of methods including for example immunoassays including for example immunohistochemistry, ELISA, Western blot, immunoprecipation and the like, where a biomarker detection agent such as an antibody for example, a labeled antibody, specifically binds the biomarker and permits for example relative or absolute ascertaining of the amount of polypeptide biomarker, hybridization and PCR protocols where a probe or primer or primer set are used to ascertain the amount of nucleic acid biomarker, including for example probe based and amplification based methods including for example microarray analysis, RT-PCR such as quantitative RT-PCR (qRT- PCR), serial analysis of gene expression (SAGE), Northern Blot, digital molecular barcoding technology, for example Nanostring Counter Analysis, and TaqMan quantitative PCR assays. Other methods of mRNA detection and quantification can be applied, such as mRNA in situ hybridization in formalin-fixed, paraffin-embedded (FFPE) tissue samples or cells. This technology is currently offered by the QuantiGene ViewRNA (Affymetrix), which uses probe sets for each mRNA that bind specifically to an amplification system to amplify the hybridization signals; these amplified signals can be visualized using a standard fluorescence microscope or imaging system. This system for example can detect and measure transcript levels in heterogeneous samples; for example, if a sample has normal and tumor cells present in the same tissue section. As mentioned, TaqMan probe-based gene expression analysis (PCR-based) can also be used for measuring gene expression levels in tissue samples, and this technology has been shown to be useful for measuring mRNA levels in FFPE samples. In brief, TaqMan probe-based assays utilize a probe that hybridizes specifically to the mRNA target. This probe contains a quencher dye and a reporter dye (fluorescent molecule) attached to each end, and fluorescence is emitted only when specific hybridization to the mRNA target occurs. During the amplification step, the exonuclease activity of the polymerase enzyme causes the quencher and the reporter dyes to be detached from the probe, and fluorescence emission can occur. This fluorescence emission is recorded and signals are measured by a detection system; these signal intensities are used to calculate the abundance of a given transcript (gene expression) in a sample.
[0022] The "biomarkers" or "classifier biomarkers" of the invention include genes and proteins, and variants and fragments thereof. Such biomarkers include DNA comprising the entire or partial sequence of the nucleic acid sequence encoding the biomarker, or the complement of such a sequence. The biomarker nucleic acids also include any expression product or portion thereof of the nucleic acid sequences of interest. A biomarker protein is a protein encoded by or corresponding to a DNA biomarker of the invention. A biomarker protein comprises the entire or partial amino acid sequence of any of the biomarker proteins or polypeptides.
[0023] A "biomarker" is any gene or protein whose level of expression in a tissue or cell is altered compared to that of a normal or healthy cell or tissue. The detection, and in some cases the level, of the biomarkers of the invention permits the differentiation of samples.
[0024] The biomarker panels and methods provided herein are used in various aspects, to assess, (i) whether a patient's NSCLC subtype is adenocarcinoma or squamous cell carcinoma; (ii) whether a patient's lung cancer subtype is adenocarcinoma, squamous cell carcinoma, or a neuroendocrine (encompassing both small cell carcinoma and carcinoid) and/or (iii) whether a patient's lung cancer subtype is adenocarcinoma, squamous cell carcinoma or small cell carcinoma. In one embodiment, as described herein, the methods provided herein further comprise characterizing a patient's lung cancer (adenocarcinoma) sample as proximal inflammatory (squamoid), proximal proliferative (magnoid) or terminal respiratory unit (bronchioid).
[0025] A biomarker capable of reliable classification can be one that is upregulated (e.g., expression is increased) or downregulated (e.g., expression is decreased) relative to a control. The control can be any control as provided herein. For example, the biomarker panels, or subsets thereof, as disclosed in Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 and Table 6 are used in various embodiments to assess and classify a patient's lung cancer subtype. [0026] In general, the methods provided herein are used to classify a lung cancer sample as a particular lung cancer subtype (e.g. subtype of adenocarcinoma). In one embodiment, the method comprises detecting or determining an expression level of at least five of the classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 in a lung cancer sample obtained from a patient or subject. In one embodiment, the detecting step is at the nucleic acid level by performing RNA-seq, a reverse transcriptase polymerase chain reaction (RT-PCR) or a hybridization assay with oligonucleotides that are substantially complementary to portions of cDNA molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for RNA-seq, RT-PCR or hybridization and obtaining expression levels of the at least five classifier biomarkers based on the detecting step. The expression levels of the at least five of the classifier biomarkers are then compared to reference expression levels ofthe at least five of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 from at least one sample training set. The at least one sample training set can comprise, (i) expression levels(s) of the at least five biomarkers from a sample that overexpresses the at least five biomarkers, or overexpresses a subset of the at least five biomarkers, (ii) expression levels from a reference squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative) sample, or (iii) expression levels from an adenocarcinoma free lung sample, and classifying the lung tissue sample as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype. The lung cancer sample can then be classified as an adenocarcinoma, squamous cell carcinoma, a neuroendocrine or small cell carcinoma or even a bronchioid, squamoid, or magnoid subtype of adenocarcinoma based on the results of the comparing step. In one embodiment, the comparing step can comprise applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the lung tissue or cancer sample and the expression data from the at least one training set(s); and classifying the lung tissue or cancer sample as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype based on the results of the statistical algorithm.
[0027] In one embodiment, the method comprises probing the levels of at least five of the classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 at the nucleic acid level, in a lung cancer sample obtained from the patient. The probing step, in one embodiment, comprises mixing the sample with five or more oligonucleotides that are substantially complementary to portions of cDNA molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for hybridization of the five or more oligonucleotides to their complements or substantial complements; detecting whether hybridization occurs between the five or more oligonucleotides to their complements or substantial complements; and obtaining hybridization values of the at least five classifier biomarkers based on the detecting step. The hybridization values of the at least five classifier biomarkers are then compared to reference hybridization value(s) from at least one sample training set. For example, the at least one sample training set comprises hybridization values from a reference adenocarcinoma, squamous cell carcinoma, a neuroendocrine sample, small cell carcinoma sample. The lung cancer sample is classified, for example, as an adenocarcinoma, squamous cell carcinoma, a neuroendocrine or small cell carcinoma based on the results of the comparing step.
[0028] The lung tissue sample can be any sample isolated from a human subject or patient. For example, in one embodiment, the analysis is performed on lung biopsies that are embedded in paraffin wax. This aspect of the invention provides a means to improve current diagnostics by accurately identifying the major histological types, even from small biopsies. The methods of the invention, including the RT-PCR methods, are sensitive, precise and have multianalyte capability for use with paraffin embedded samples. See, for example, Cronin et al. (2004) Am. J Pathol. 164(l):35-42, herein incorporated by reference.
[0029] Formalin fixation and tissue embedding in paraffin wax is a universal approach for tissue processing prior to light microscopic evaluation. A major advantage afforded by formalin-fixed paraffin-embedded (FFPE) specimens is the preservation of cellular and architectural morphologic detail in tissue sections. (Fox et al. (1985) J Histochem Cytochem 33 : 845-853). The standard buffered formalin fixative in which biopsy specimens are processed is typically an aqueous solution containing 37% formaldehyde and 10-15% methyl alcohol. Formaldehyde is a highly reactive dipolar compound that results in the formation of protein-nucleic acid and protein-protein crosslinks in vitro (Clark et al. (1986) J Histochem Cytochem 34: 1509-1512; McGhee and von Hippel (1975) Biochemistry 14: 1281 -1296, each incorporated by reference herein). [0030] In one embodiment, the sample used herein is obtained from an individual, and comprises fresh-frozen paraffin embedded (FFPE) tissue. However, other tissue and sample types are amenable for use herein (e.g., fresh tissue, or frozen tissue).
[0031] Methods are known in the art for the isolation of RNA from FFPE tissue. In one embodiment, total RNA can be isolated from FFPE tissues as described by Bibikova et al. (2004) American Journal of Pathology 165: 1799-1807, herein incorporated by reference. Likewise, the High Pure RNA Paraffin Kit (Roche) can be used. Paraffin is removed by xylene extraction followed by ethanol wash. RNA can be isolated from sectioned tissue blocks using the MasterPure Purification kit (Epicenter, Madison, Wis.); a DNase I treatment step is included. RNA can be extracted from frozen samples using Trizol reagent according to the supplier's instructions (Invitrogen Life Technologies, Carlsbad, Calif). Samples with measurable residual genomic DNA can be resubjected to DNasel treatment and assayed for DNA contamination. All purification, DNase treatment, and other steps can be performed according to the manufacturer's protocol. After total RNA isolation, samples can be stored at -80 °C until use.
[0032] General methods for mRNA extraction are well known in the art and are disclosed in standard textbooks of molecular biology, including Ausubel et al, ed., Current Protocols in Molecular Biology, John Wiley & Sons, New York 1987-1999. Methods for RNA extraction from paraffin embedded tissues are disclosed, for example, in Rupp and Locker (Lab Invest. 56:A67, 1987) and De Andres et al. (Biotechniques 18:42-44, 1995). In particular, RNA isolation can be performed using a purification kit, a buffer set and protease from commercial manufacturers, such as Qiagen (Valencia, Calif), according to the manufacturer's instructions. For example, total RNA from cells in culture can be isolated using Qiagen RNeasy mini-columns. Other commercially available RNA isolation kits include MasterPure. TM. Complete DNA and RNA Purification Kit (Epicentre, Madison, Wis.) and Paraffin Block RNA Isolation Kit (Ambion, Austin, Tex.). Total RNA from tissue samples can be isolated, for example, using RNA Stat-60 (Tel-Test, Friendswood, Tex.). RNA prepared from a tumor can be isolated, for example, by cesium chloride density gradient centrifugation. Additionally, large numbers of tissue samples can readily be processed using techniques well known to those of skill in the art, such as, for example, the single-step RNA isolation process of Chomczynski (U.S. Pat. No. 4,843,155, incorporated by reference in its entirety for all purposes). [0033] In one embodiment, a sample comprises cells harvested from a lung tissue sample, for example, an adenocarcinoma sample. Cells can be harvested from a biological sample using standard techniques known in the art. For example, in one embodiment, cells are harvested by centrifuging a cell sample and resuspending the pelleted cells. The cells can be resuspended in a buffered solution such as phosphate-buffered saline (PBS). After centrifuging the cell suspension to obtain a cell pellet, the cells can be lysed to extract nucleic acid, e.g, messenger RNA. All samples obtained from a subject, including those subjected to any sort of further processing, are considered to be obtained from the subject.
[0034] The sample, in one embodiment, is further processed before the detection of the biomarker levels of the combination of biomarkers set forth herein. For example, mRNA in a cell or tissue sample can be separated from other components of the sample. The sample can be concentrated and/or purified to isolate mRNA in its non-natural state, as the mRNA is not in its natural environment. For example, studies have indicated that the higher order structure of mRNA in vivo differs from the in vitro structure of the same sequence (see, e.g. , Rouskin et al. (2014). Nature 505, pp. 701-705, incorporated herein in its entirety for all purposes).
[0035] mRNA from the sample in one embodiment, is hybridized to a synthetic DNA probe, which in some embodiments, includes a detection moiety (e.g., detectable label, capture sequence, barcode reporting sequence). Accordingly, in these embodiments, a non-natural mRNA-cDNA complex is ultimately made and used for detection of the biomarker. In another embodiment, mRNA from the sample is directly labeled with a detectable label, e.g. , a fluorophore. In a further embodiment, the non-natural labeled-mRNA molecule is hybridized to a cDNA probe and the complex is detected.
[0036] In one embodiment, once the mRNA is obtained from a sample, it is converted to complementary DNA (cDNA) in a hybridization reaction or is used in a hybridization reaction together with one or more cDNA probes. cDNA does not exist in vivo and therefore is a non-natural molecule. Furthermore, cDNA-mRNA hybrids are synthetic and do not exist in vivo. Besides cDNA not existing in vivo, cDNA is necessarily different than mRNA, as it includes deoxyribonucleic acid and not ribonucleic acid. The cDNA is then amplified, for example, by the polymerase chain reaction (PCR) or other amplification method known to those of ordinary skill in the art. For example, other amplification methods that may be employed include the ligase chain reaction (LCR) (Wu and Wallace, Genomics, 4:560 (1989), Landegren et al., Science, 241 : 1077 (1988), incorporated by reference in its entirety for all purposes, transcription amplification (Kwoh et al., Proc. Natl. Acad. Sci. USA, 86: 1173 (1989), incorporated by reference in its entirety for all purposes), self-sustained sequence replication (Guatelli et al., Proc. Nat. Acad. Sci. USA, 87: 1874 (1990), incorporated by reference in its entirety for all purposes), incorporated by reference in its entirety for all purposes, and nucleic acid based sequence amplification (NASBA). Guidelines for selecting primers for PCR amplification are known to those of ordinary skill in the art. See, e.g., McPherson et al, PCR Basics: From Background to Bench, Springer-Verlag, 2000, incorporated by reference in its entirety for all purposes. The product of this amplification reaction, i.e. , amplified cDNA is also necessarily a non-natural product. First, as mentioned above, cDNA is a non-natural molecule. Second, in the case of PCR, the amplification process serves to create hundreds of millions of cDNA copies for every individual cDNA molecule of starting material. The number of copies generated are far removed from the number of copies of mRNA that are present in vivo.
[0037] In one embodiment, cDNA is amplified with primers that introduce an additional DNA sequence (e.g., adapter, reporter, capture sequence or moiety, barcode) onto the fragments (e.g., with the use of adapter-specific primers), or mRNA or cDNA biomarker sequences are hybridized directly to a cDNA probe comprising the additional sequence (e.g., adapter, reporter, capture sequence or moiety, barcode). Amplification and/or hybridization of mRNA to a cDNA probe therefore serves to create non-natural double stranded molecules from the non-natural single stranded cDNA, or the mRNA, by introducing additional sequences and forming non-natural hybrids. Further, as known to those of ordinary skill in the art, amplification procedures have error rates associated with them. Therefore, amplification introduces further modifications into the cDNA molecules. In one embodiment, during amplification with the adapter-specific primers, a detectable label, e.g. , a fluorophore, is added to single strand cDNA molecules. Amplification therefore also serves to create DNA complexes that do not occur in nature, at least because (i) cDNA does not exist in vivo, (i) adapter sequences are added to the ends of cDNA molecules to make DNA sequences that do not exist in vivo, (ii) the error rate associated with amplification further creates DNA sequences that do not exist in vivo, (iii) the disparate structure of the cDNA molecules as compared to what exists in nature and (iv) the chemical addition of a detectable label to the cDNA molecules. [0038] In some embodiments, the expression of a biomarker of interest is detected at the nucleic acid level via detection of non-natural cDNA molecules.
[0039] In some embodiments, the method for lung cancer subtyping includes detecting expression levels of a classifier biomarker set. In some embodiments, the detecting includes all of the classifier biomarkers of Table 1 (also characterized as a lung cancer subtype gene panel), Table 2, Table 3, Table 4, Table 5 or Table 6 at the nucleic acid level or protein level. In another embodiment, a single or a subset of the classifier biomarkers of Table 1 are detected, for example, from about five to about twenty. The detecting can be performed by any suitable technique including, but not limited to, RNA-seq, a reverse transcriptase polymerase chain reaction (RT-PCR), a microarray hybridization assay, or another hybridization assay, e.g., a NanoString assay for example, with primers and/or probes specific to the classifier biomarkers, and/or the like. In some cases, the primers useful for the amplification methods (e.g., RT-PCR or qRT-PCR) are the forward and reverse primers provided in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6. It should be noted however that the primers provided in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 and Table 6 are merely for illustrative purposes and should not be construed as limiting the invention.
[0040] The biomarkers described herein include RNA comprising the entire or partial sequence of any of the nucleic acid sequences of interest, or their non-natural cDNA product, obtained synthetically in vitro in a reverse transcription reaction. The term "fragment" is intended to refer to a portion of the polynucleotide that generally comprise at least 10, 15, 20, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 800, 900, 1,000, 1,200, or 1,500 contiguous nucleotides, or up to the number of nucleotides present in a full- length biomarker polynucleotide disclosed herein. A fragment of a biomarker polynucleotide will generally encode at least 15, 25, 30, 50, 100, 150, 200, or 250 contiguous amino acids, or up to the total number of amino acids present in a full-length biomarker protein of the invention.
[0041] In some embodiments, overexpression, such as of an RNA transcript or its expression product, is determined by normalization to the level of reference RNA transcripts or their expression products, which can be all measured transcripts (or their products) in the sample or a particular reference set of RNA transcripts (or their non-natural cDNA products). Normalization is performed to correct for or normalize away both differences in the amount of RNA or cDNA assayed and variability in the quality of the RNA or cDNA used. Therefore, an assay typically measures and incorporates the expression of certain normalizing genes, including well known housekeeping genes, such as, for example, GAPDH and/or β- Actin. Alternatively, normalization can be based on the mean or median signal of all of the assayed biomarkers or a large subset thereof (global normalization approach).
[0042] For example, in one embodiment, from about 5 to about 10, from about 5 to about 15, from about 5 to about 20, from about 5 to about 25, from about 5 to about 30, from about 5 to about 35, from about 5 to about 40, from about 5 to about 45, from about 5 to about 50 of the biomarkers in any of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 and Table 6 are detected in a method to determine the lung cancer subtype. In another embodiment, each of the biomarkers from any one of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, or from Table 6 are detected in a method to determine the lung cancer subtype.
Figure imgf000019_0001
Table 1A
Geiie symbol Gene name Forward primer SEQ Reverse primer SEQ n> IB
CDKN2C cyclin-dependent kinase TTTGGAAGGAC 8 TCG GTCTTTC AAA 65 inhibitor 2C (plS, TGCGCT TCGGGATTA
inhibits CDK4)
CIB1 calcium and integrin CACGTCATCTCC 9 CTGCTGTCACAG 66 binding 1 (calmyrin) CGTTC GACAAT 66
INSM1 insulinoma-associated 1 ATTGAACTTCCC 10 AAGGTAAAGCCA 67
ACACGA GACTCCA 67
LRP10 low density lipoprotein GGAACAGACTG 1 1 GGGAGCGTAGGG 68 receptor-related protein TCACCAT TTAAG
10
STMN1 stathmin TCAGAGTGTGTG 12 CAGTGTATTCTGC 69 i/oncoprotein 18 G ACAATCAAC
TCAGGC
CAPG capping protein (aciin GGGACAGCrrC 13 GTTCC AG GATGTT 70 filament), gelso!in-like AACACT GGA l Ti C
CHGA chromogranin A CCTGTGAACAG 14 GGAAAGTGTGTC 71
(parathyroid secretory CCCTATG GGAGAT
protein 1)
LGALS3 lectin, ga!acioside- TTCTGGGCACG 15 AGGCAACATCAT
binding, soluble, 3 GTGAAG TCCCTC
(galec!in 3)
MAPRE3 micro tubule-associated GGCCAAACTAG 16 GTCAACACCCAT 73 protein, RP/EB family, AGCACGAATA CTTCTTGAAA
member 3
SF stralifin TCAGCAAGAAG 17 CGTAGTGGAAGA 74
GAGATGCC CGGAAA
SNAP91 synaptosomal-associated GTGCTCCCTCTC 18 CTGGTGTAGAATT 75 protein, 91 kDa CATTAAGTA AGGAGACGTA
hornolog (mouse)
ABCC5 ΑΊΡ-binding cassette, CAAGTTCAGGA 19 GGCATCAAGAGA 76 sub-family C(CFTR RP), GAACTCGAC GAGGC
member 5
ALDH3BI aldehyde dehydrogenase GGCTGTGGTTA 20 GATAAAGAGTTA
3 TGCGATAG CAAGCTCCTCTG family, member Bl
ANTXR1 Anthrax toxin receptor 1 ACCCGAGGAAC 21 TCTAGGCCTTGAC 78
AACCTTA GGAT
BMP7 Bone morphogenetic CCCTCTCCATTCC 22 TTTGGGCAAACCTCGGTA 79 protein 7 (osteogenic CTACA A
protein 1)
CACNBl calcium channel, C AGA GCGCCAG 23 GCACAGCAAATG 80 voitage-dependent, beta GCATTA CCACT
1 subunit Table 1A
Geiie symbol Gene name Forward primer SEQ Reverse primer SEQ n> IB
CBX1 chromobox bomolog i CCACTGGCTGA 24 CTTGTCTTTCCCT 81
(HP1 beta homoiog GGTGTTA ACTGTCTTAC
Drosophila)
CYB5B cytochrome b5 type B TGGGCGAGTCT 25 CTTGTTCCAGCAG 82
(outer mitochondrial ACGATG AACCT
rnemerane)
DOK1 docking piotein 1, 62 CTTTCTGCCCTG 26 CAGTCCTCTGCAC 83 kDa (downstream oi' GAGATG CGTTA
tyrosine kinase I )
DSC3 desmocoliin 3 GCGCCATTTGCT 27 CATCCAGATCCCT 84
AGAGATA CACAT
FEN! flap structure-specific AGAGAAGATGG 28 CCAAGACACAGC 85 endo ucSease 1 GCAGAAAG CAGTAAT
FOXH1 forkhead box HI GCCCAGATCAT 29 TTTCCAGCCCTCG 86
CCGTCA TAGTC
GJB5 gap junction protein, ACCACAAGGAC 30 GGGACACAGGGA 87 beta ~ 5 (connexin 31.1) TTCGAC AGAAC
HOXD1 homeobox Dl GCTCCGCTGCT 31 GTCTGCCACTCTG 88
ATCTTT CAAC
HPN Hepsin (transmembrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1) GGATTA TTTGA
HYAL2 hyaluronoghicosam ATGGGC'I TGG 33 GAACAAGTCAGT 90 inidase 2 GAGCATA CTAGGGAATAC
ICA1 islet cell autoantigen GACCTGGATGC 34 TGCTTTCGATAAG 1
1, 69 kDa CAAGCTA TCCAGACA
1CAM5 intercellular adhesion CCGGCTCTTGG 35 CCTCTGAGGCTG 92 molecule 5, AAGTTG GAAACA
telencephalin
TTGA6 integrin, alpha 6 ACGCGGATCGA 36 ATCCACTGATCTT 93
GTTTGATAA CCTTGC
LiPE lipase, hormone-sensitive CGCAAGTCCCA 37 CAGTGCTGCTTCA 94
GAAGAT GACACA
ME3 malic enzyme 3, CGCGGATACGA 38 CCTTTCTTCAAGG 95
NADP(+)-dependent, TGTCAC GTAAAGGC
Mitochondrial
MGRN1 mahogunin, ring finger GAACTCGGCCT 39 TCGAATTTCTCTC 96
ATCGCT CTCCCAT
MYBPH myosin binding protein TCTGACCTCATC 40 CTGAGTCCACAC 97
H" ATCGGCAA AGGTTT
MY07A myosin VII A GAGGTGAAGCA 41 CCCATACTTGTTG 98
A ACT AC GG A ATGGCAATTA
NFIL3 nuclear factor, ACTCTCCACAA 42 TCCTGCGTGTGTT 99 interleukin 3 regulated AGCTCG CTACT Table 1A
Geiie symbol Gene aame Forward primer SEQ Reverse primer SEQ
IB IB
PI 3C2A phospboi no si is de -3 -kinase , GGATTTCAGCT 43 AGTCATCATGTAC 100 ci ss 2, alpha ACCAGTTA CTT CCAGCA
polypeptide
PLEKHA6 pleckstrin homology TTCGTCCTGGTG 44 CCCAGGATACTCT 101 domain containing, GATCG CTTCCTT
family A member 6
PSMD14 proteasome (prosome, AGTGATTGATG 45 CACTGGATCAAC 102 macropain) 26S subu 't, TGTTTGCTATG TGCCTC
non-ATPase, 14
SCD5 stearoyl-CoA desatarase CAAAGCCAAGC 46 CAGCTGTCACAC 103
5 CACTCACTC CCAGAGC
SSAH2 seven in absentia CTCGGCAGTCC 47 CGTATGGTGCAG 104 homolog 2 TGTTTC GGTCA
(Drosoph )
TCF2 transcription factor 2, ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic; LF-B3; variant GTCAGAA GTTGAAT
hepatic nuclear factor
TCP1 t-compiex 1 ATGCCCAAGAG 49 CCTGTACACCAA 106
AATCGTAAA GCTTCAT
T'S'FI th roid transcription ATGAGTCCAAA 50 CCATGCCCACTTT 107 factor 1 GCACACGA CTTGTA
TRSM29 tripartite motif-containing TGAGATTGAGG 51 CATTGGTGGTGA 108
29 ATGAAGCTGAG AGCTCTTG
TUBA1 tubulin, alpha 1 CCGACTCAACG 52 CGTGGACTGAGA 109
TGAGAC TGCATT
CFL1 cofilin 1 (non-muscle) GTGCCCTCTCCT 53 TTCATGTCGTTGA 110
TTTCG ACACCTTG
EEFiAl eukaryotic translation CGTTCTTTTTCG 54 CATTTTGGCTTTT 111 elongation factor 1 CAACGG AGGGGTAG
alpha 1
PL10 ribosomal protein L10 GGTGTGCCACT 55 GGCAGAAGCGAG 112
GAAGAT AC'fi f
RPL28 ribosomal protein L28 GTGTCGTGGTG 56 GCACATAGGAGG 113
GTCATT TGGCA
RPL37A ribosomal protem L37a GCATGAAGACA 57 GCGGACTTTACC 114
GTGGCT GTGAC
Figure imgf000022_0001
Table IB
Geiie symbol Gene aame Forward primer SEQ Reverse primer SEQ n> IB
CLEC3B C -type lecti n domain CCAGAAGCCCA 2 GCTCCTCAAACAT 5 family 3, member B AG A A GATTGT A CTTTGTGTTCA
PAICS phosphoribosylami AATCCTGGTGT 3 GACCACTGTGGG 60 noimidazoie CAAGGAAG TCATTATT
carboxylase,
phosphoribosylami
noimidazoie
succinocarboxamide
synthetase
PAKi p21/Cdc42/Racl~ GGACCGATTTT 4 GAAATCTCTGGC 61 activated kinase 1 (STE20 ACCGATCC CGCTC
homoiog, yeast)
PECAMI pSa!eiet/endotheSiai ceil ACAGTCCAGAT 5 ACTGGGCATCAT 62 adhesion molecule AGTCGTATGT AAGAAATCC
(CD31 antigen)
TFAP2A transcription factor AP- GTCTCCGCCATC 6 ACTGAACAGAAG 63
2 alpha (activating CCTAT ACTTCGT
enhancer binding
protein 2 alpha)
ACVR1 activin A receptor, ACTGGTGTAAC AACCTCCAAGTG 64 type 1 AG GA AC AT GAAATTCT
CDKN2C c clin-dependent kinase TTTGGAAGGAC 8 TCGGTCTTTCAAA 6 inhibitor 2C (pi 8, TGCGCT TCGGGATTA
inhibits CDK4)
CIB 1 calcium and integrin CACGTCATCTCC 9 CTGCTGTCACAG 66 binding 1 (caimyrin) CGTTC GACAAT 66
INSM1 insuiinoma-associated 1 ATTGAACTTCCC 10 AAGGTAA GCCA 67
ACACGA GACTCCA 67
LRP10 iow density lipoprotein GGAACAGACTG Π GGGAGCGTAGGG 68 receptor-related protein TCACCAT TTAAG
10
STMNi stathmin TCAGAGTGTGTG 12 CAGTGTATTCTGC 69 i/oncoprotein 18 G ACAATCAAC
TCAGGC
CAPG capping protein (actin GGGACAGCTTC 13 GTTCCAGGATGTT 70 filament), gelsoliti-like AACACT GGAC i Ti C
CHGA chromogranin A CCTGTGAACAG 14 GGAAAGTGTGTC 71
(parathyroid secretory CCCTATG GGAGAT
protein 1)
LGALS3 lectin, galacfoside- TTCTGGGCACG 15 AGGCAACATCAT
binding, soluble, 3 GTGAAG TCCCTC
(galectin 3)
MAPRE3 micro tubule-associated GGCCAAACTAG 16 GTCAACACCCAT 73 protein, RP EB family, AGCACGAATA CTTCTTGAAA
member 3
SF straiifin TCAGCAAGAAG 1? CGTAGTGGAAGA 74
GAGATGCC CGGAAA Table IB
Geiie symbol Gene name Forward primer SEQ Reverse primer SEQ
IB IB
5NAP91 sy iiap!oso!iiai- ssociated GTGCTCCCTCTC 18 CTGGTGTAGAATT 75 protein, 91 kDa CATTAAGTA AGGAGACGTA
homoiog (mouse)
ABCC5 ATP -binding cassette, CAAGTTCAGGA 19 GGCATCAAGAGA 76 sub-family C(CFTR/MRP), GAACTCGAC GAGGC
member 5
ALDH3B1 aldehyde dehydrogenase GGCTGTGGTTA 20 GATAAAGAGTTA 7
3 TGCGATAG CAAGCTCCTCTG family, member Bi
ANTXR1 Anthrax toxin receptor i ACCCGAGGAAC 2i TCTAGGCCTTGAC 78
AACCTTA GGAT
CACNB1 calcium channel, CAGAGCGCCAG 23 GCACAGCAAATG 80 voltaee-dependent. beta GCATTA CCACT
ί subunii
CBX1 chromobox homo!og i CCACTGGCTGA 24 CTTGTCTTTCCCT 81
(HP! beta homoiog GGTGTTA ACTGTCTTAC
Drosophila)
CYB5B cytochrome b5 type B TGGGCGAGTCT 2 CTTGTTCCAGCAG 82
(outer mitochondria! ACGATG AACCT
membrane)
DOK1 docking protein 1, 62 CTTTCTGCCCTG 26 CAGTCCTCTGCAC 83 kDa (downstream of GAGATG CGTTA
tyrosine kinase i )
DSC3 desmoco!Sin 3 GC GC C A TTTGCT CATCCAGATCCCT 84
AGAGATA CACAT
FE i flap structure-specific AGAGAAGATGG 28 C C A AG A C A C A G C 85 endonuclease 1 GCAGAAAG CAGTAAT
FOXH1 forkhead box HI GCCCAGATCAT 29 TTTCCAGCCCTCG 86
CCGTCA T GTC
GJB5 gap junction protein, ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (connexiti 31.1) TTCGAC AGAAC
HOXD1 hotneobox D GCTCCGCTGCT 31 GTCTGCCACTCTG 88
ATCTTT CAAC
HPN Hepsin (transmembrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1) GGATTA TTTGA
HYAL2 tiyaiuronoglucosam ATGGGCTTTGG 3 GAACAAGTCAGT 90 inidase 2 GAGCATA CTAGGGAATAC
ICAl islet ceil autoantigen GACCTGGATGC 34 TGCTTTCGATAAG 91
1, 69 kDa CAAGCTA TCCAGACA Table IB
Geiie symbol Gene name Forward primer SEQ Reverse primer SEQ n> IB
ICAM5 intercellular adhesion CCGGCTCTTGG 35 CCTCTGAGGCTG 92 molecule 5, AAGTTG GAAACA
telencephalon
ITGA6 integria alpha 6 ACGCGGATCGA 36 ATCC ACTG ATCTT 93
GTTTGATAA CCTTGC
LIFE lipase, hormone-sensitive CGCAAGTCCCA 37 CAGTGCTGCTTCA 94
GAAGAT GACACA
ME3 malic enzyme 3, CGCGGATACGA 38 CCTTTCTTCAAGG 95
NADP(+)-dependent, TGTCAC GTAAAGGC
Mitochondrial
GRN1 mahogunin, ring finger GAACTCGGCCT 39 TCGAATTTCTCTC 96
1 ATCGCT CTCCCAT
MYBPH myosin binding protein TCTGACCTCATC 40 CTGAGTCCA C AC 97
H ATCGGCAA AGGTTT
MY07A myosin VILA GAGGTGAAGCA 41 CCCATACTTGTTG 98
AACTACGGA ATGGCAATTA
NFIL3 nuclear factor, ACTCTCCACAA 42 TCCTGCGTGTGTT 99 interleukin 3 regulated AGCTCG CTACT
PSK3C2A phosphoinositide-3 -kinase, GGATTTCAGCT 43 AGTCATCATGTAC 100 class 2, alpha ACCAGTTACTT CCAGCA
polypeptide
PLEKHA6 pleckstrin homology TTCGTCCTGGTG 44 CCCAGGATACTCT 101 domain containing, GATCG crrccTT
family A member 6
PSMD14 proteasome (prosome, AGTGATTGATG 45 CACTGGATCAAC 102 macropaiti) 26S subunit, TGi i i'GCTATG TGCCTC
noti-ATPase, 14
SCD5 stearoyl-CoA desaturase C AAA GCCA AGC 46 CAGCTGTCA CAC 103
5 CACTCACTC CCAGAGC
SIAH2 seven in absentia CTCGGCAGTCC 47 CGTATGGTGCAG 104 homo!og 2 TGTTTC GGTCA
(Drosophi!a)
TCF2 transcriDtion factor 2, ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic; LF-B3; variant GTCAGAA GTTGAAT
hepatic nuclear factor
TCP! t-compiex 1 ATGCCCAAGAG 49 CCTGTACACCAA 106
AATCGTAAA GCTTCAT
TTF1 thyroid transcription ATGAGTCCAAA 50 CCATGCCCACTTT 107 factor 1 GCACACGA CTTGTA
TRIM29 tripartite motif -containing TG AG ATTGAGG 51 CATTGGTGGTGA 108
29 ATGAAGCTGAG AGCTCTTG
TUBA1 rabulia alpha 1 CCGACTCAACG 52 CGTGGACTGAGA 109
TGAGAC TGCATT
CFL1 cofflin 1 (non-muscle) GTGCCCTCTCCT 53 TTCATGTCGTTGA 110
TTTCG ACACCTTG Table IB
Geiie symbol Gene aame Forward primer SEQ Reverse primer SEQ
IB IB
EEFiAl eukaryotic translation CGTTCTTTTTCG 54 CATTTTGGCTTTT i ll eiotigation factor I CAACGG AGGGGTAG
aipha 1
RPL10 ribosomaJ protein L10 GGTGTGCCACT 55 GGCAGAAGCGAG 112
GAAGAT ACTTT
RPL28 ribosomal protein L28 GTGTCGTGGTG 56 GCACATAGGAGG 1 13
GTCATT TGGCA
RPL37A ribosomai protein L37a GCATGAAGACA 57 GCGGACTTTACC 114
GTGGCT GTGAC
Figure imgf000026_0001
Table 1C
Geiie symbol Gene aame Forward primer SEQ Reverse primer SEQ
IB IB
LRPIO iow density lipoprotein GGAACAGACTG 1 1 GGGAGCGTAGGG 68 receptor-related protein TCACCAT TTAAG
10
STMNl stathmin TC AG A GTGTGTG 12 CAGTGTATTCTGC 69 i/oncoprotein 18 G ACAATCAAC
TCAGGC
CAPG capping protein (actin GGGACAGCTTC 13 GTTCCAGGATGTT 70 filament), gelsolm-like AACACT GGACTTTC
CHGA chromogramn A CCTGTGAACAG 14 GGAAAGTGTGTC 71
(parathyroid secretory CCCTATG GGAGAT
protein 1)
LGALS3 lectin, gal acta side - TTCTGGGCACG 15 AGGCAACATCAT 72 binding, soluble, 3 GTGAAG TCCCTC
(galectin 3)
MAPRE3 microtubule-associated GGCCAAACTAG 16 GTCAACACCCAT 7"' protein, RP EB family, AGCACGAATA CTTCTTGAAA
member 3
SFN stratrfin TCAGCAAGAAG 17 CGTAGTGGAAGA 74
GAGATGCC CGGAAA
SNAP91 synaptosoma!-associated GTGCTCCCTCTC 18 CTGGTGTAGAATT 75 protein, 91 kDa CATTAAGTA AGGAGACGTA
homolog (mouse)
ABCC5 ATP-bindmg cassette, CAAGTTCAGGA 19 GGCATCAAGAGA 76 sub-family C(CFTR/ RP), GAACTCGAC GAGGC
member 5
ALDH3B1 aldehyde dehydrogenase GGCTGTGGTTA 20 G ATA A AGA GTTA 77
3 TGCGATAG CAAGCTCCTCTG family, member Bl
ANTXR1 Anthrax toxin receptor 1 ACCCGAGGAAC TCTAGGCCTTGAC 78
AACCTTA GGAT
BMP7 Bone morphogenetic CCCTCTCCATTCC 22 TTTGGGCAAACCTCGGTA 79 protein 7 (osteogenic CTACA A
protein !)
CACNB1 calcium cliannel, CAGAGCGCCAG 23 GCACAGCAAATG 80 voltage-dependent, beta GCATTA CCACT
i subtmit
CBX1 chromobox homolog ί CCACTGGCTGA 24 CTTGTCTTTCCCT 81
(HP! beta homolog GGTGTTA ACTGTCTTAC
Drosophila)
CYB5B cytochrome b5 type B TGGGCGAGTCT 2 CTTGTTCCAGCAG 82
(outer mitochondrial ACGATG AACCT
membrane) Table 1C
Geiie symbol Gene name Forward primer SEQ Reverse primer SEQ n> IB
DOKi docking protein i, 62 CTTTCTGCCCTG 26 CAGTCCTCTGCAC 83 kDa (downstream of GAGATG CGTTA
tyrosine kinase 1)
DSC3 desmocollin 3 GCGCCATTTGCT 27 CATCCAGATCCCT 84
AGAGATA CACAT
FEN 1 flap structure- specific AG AGA AG ATG G 28 CCAAGACACAGC 85 endomjcSease 1 GCAGAAAG CAGTAAT
FOXHl forkhead box Hi GCCCAGATCAT 29 TTTCCAGCCCTCG 86
CCGTCA TAGTC
GIBS gap junction protein, ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (conaexin 31.1) TTCGAC AGAAC
HOXD1 homeobox Dl GCTCCGCTGCT 31 GTCTGCCACTCTG 88
ATCTTT CAAC
HPN Hepsirt (transmembrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1) GGATTA TTTGA
HYAL2 hvaUiroiioghicosam ATGGGCTTTGG 33 G A AC A AGTC AGT 90 irridase 2 GAGCATA CTAGGGAATAC
ICA1 islet cell autoanligen GACCTGGATGC 34 TGCTTTCGATAAG 91 i, 69 kDa CAAGCTA TCCAGACA
ICAM5 intercellular adhesion CCGGCTCTTGG 35 CCTCTGAGGCTG 92 molecule 5, AAGTTG GAAACA
telencephalon
ITGA6 integria alpha 6 ACGCGGATCGA 36 ATCC ACTG ATCTT 93
GTTTGATAA CCTTGC
LIFE lipase, hormone-sensitive CGCAAGTCCCA 37 CAGTGCTGCTTCA 94
GAAGAT GACACA
MF.3 malic enzyme 3 , CGCGGATACGA 38 CCTTTCTTCAAGG 95
NADP(+)-dependent, TGTCAC GTAAAGGC
Mitochondrial
GRN1 mahogunia ring finger GAACTCGGCCT 39 TCGAATTTCTCTC 96
1 ATCGCT CTCCCAT
MYBPH myosin binding protein TCTGACCTCATC 40 CTGAGTCCACAC 97
ATCGGCAA AGGTTT
MY07A myosin VILA GAGGTGAAGCA 41 CCCATACTTGTf'G 98
AACTACGGA ATGGCAATTA
NFIL3 nuclear factor, ACTCTCCACAA 42 TCCTGCGTGTGTT 99 interieukin 3 regulated AGCTCG CTACT
PSK3C2A phosphoinositide-3 -kinase, GGATTTCAGCT 43 AGTCATCATGTAC 100 class 2, alpha ACCAGTTACTT CCAGCA
polypeptide
PLEKHA6 pleckstrin homology TTCGTCCTGGTG 44 CCCAGGATACTCT 101 domain containing, GATCG crrccTT
family A member 6 Table 1 C
Geiie symbol Gene aame Forward primer SEQ Reverse primer SEQ n> IB
P5MD14 pro!easome (prosome, AGTG ATTG ATG 45 CACTGGATCAAC 102 macropain) 26S subumt, TGTTTGCTATG TGCCTC
non-ATPase, i 1
SCD5 siearoyl-CoA desaturase CAAAGCCAAGC 46 CAGCTGTCACAC 103
5 CACTCACTC CCAGAGC
SIAH2 seven in absentia CTCGGCAGTCC 47 CGTATGGTGCAG 104 homoiog 2 TGTTTC GGTCA
(Drosophila)
TCF2 transcription factor 2, ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic; LF-B3; variant GTCAGAA GTTGAAT
hepatic nuclear factor
TCPi t-complex 1 ATGCCCAAGAG 49 CCTGTACACCAA 106
AATCGTAAA GCTTCAT
TTFi thyroid transcription ATGAGTCCAAA 50 CCATGCCCACTTT 107 factor 1 GCACACGA CTTGTA
TRIM29 tripartite motif-containing TGAGATTGAGG 51 CATTGGTGGTGA 108
29 ATGA A GCTGAG AGCTCTTG
TUBAl tubulin, alpha 1 CCGACTCAACG 52 CGTGGACTGAGA 109
TGAGAC TGCATT
Table 2
Gene name Forward priwier SEQ Reverse primer SEQ
Gene svmboi ID ID
CDH5 cadherin 5, type 2, AAGAGAGATTG I TTCTTGCGACTCACGCT 58
VE-cadherin GA TTTG G A A C C
(vascular epithelium)
PAICS phosphoribosy lami AATCCTGGTGT 3 GACCACTGTGGG 60 noimidazole CAAGGAAG TCATTATT
carboxylase,
phosphotibosyiami
noimidazole
succinocarboxamide
synthetase
PA i p21/Cde42/Racl- GGACCGATTTT 4 GAAATCTCTGGC 61 activated kinase I (STE20 ACCGATCC CGCTC
homolog, yeast)
PEC AMI platelet/endothelial cell ACAGTCCAGAT 5 ACTGGGCATCAT 62 adhesion molecule AGTCGTATGT A AG A AATC C
(CD31 antigen)
TFAP2A transcription factor AP- GTCTCCGCCATC 6 ACTGAACAGAAG 63
2 alpha (activating CCTAT ACTTCGT
enhancer binding
protein 2 alpha)
ACVR1 activin A receptor, ACTGGTGTAAC AACCTCCAAGTG 64 type 1 AGGAACAT GAAATTCT
CDKN2C cyclin-dependent kinase TTTGGAAGGAC 8 TCGGTCTTTCAAA 65 inhibitor 2C (pl8, TGCGCT TCGGGATTA
inhibits CDK4) Table 2
Gene name Forward primer SEQ Reverse primer SEQ
Geiie symbol n> IB
CJB1 calcium and integrin CACGTCATCTCC 9 CTGCTGTCA CAG 66 binding i (ca!myrin) CGTTC GACAAT 66
EN SMI insiilinoma-associated 1 ATTGAACTTCCC 10 AAGGTAAAGCCA 67
ACACGA GACTCCA 67
LRP10 low density lipoprotein GGAACAGACTG 11 GGGAGCGTAGGG 68 receptor-related protein TCACCAT TTAAG
10
STMN1 stathmin TCAGAGTGTGTG 12 CAGTGTATTCTGC 69
1/oncoprotein 18 G ACAATCAAC
TCAGGC
CAPG capping protein (actio GGGACAGCTTC 1 GTTCCAGGATGTT 70 filament), ge solin-like AACACT GGACTTTC
CHGA chroinogranin A CCTGTGAACAG 14 GGAAAGTGTGTC 71
(parathyroid secretory CCCTATG GGAGAT
protein 1)
LGALS3 lectin, galactoside- TTCTGGGCACG 15 AGGCAACATCAT 72 binding, soluble, 3 GTGAAG TCCCTC
(galectin 3)
MAPRE3 inicrotubule-associated GGCCAAACTAG 16 GTCAACACCCAT 73 protein, RP EB family, AGCACGAATA CTTCTTGAAA
member 3
SFN stratifiti TCAGCAAGAAG 17 CGT AGTGGA AG A 74
GAGATGCC CGGAAA
SNAP91 sy iiap!osomal- associated GTGCTCCCTCTC 18 CTGGTGTAGAATT 75 protein, 91 kDa CATTAAGTA AGGAGACGTA
homolog (mouse)
ABCC5 ATP -binding cassette, CAAGTTCAGGA 19 GGCATCAAGAGA 76 sub-family C(CFTR/MRP), GAACTCGAC GAGGC
member 5
ALDH3B1 aldehyde dehydrogenase GGCTGTGGTTA 20 GATAAAGAGTTA
3 TGCGATAG CAAGCTCCTCTG family, member Bl
ANTXR1 Anthrax toxin receptor i ACCCGAGGAAC TCTAGGCCTTGAC 78
AACCTTA GGAT
CACNB1 calcium channel, CAGAGCGCCAG 23 GCACAGCAAATG 80 voltaee-dependent. beta GCATTA CCACT
i siibimit
CBX1 chromobox homolog ί CCACTGGCTGA 24 CTTGTCTTTCCCT 81
(HP! beta homolog GGTGTTA ACTGTCTTAC
Drosophila) Table 2
Gene name Forw ard primer SEQ Reverse primer SEQ
Geiie symbol n> IB
CYB5B cytochrome b5 type B TGGGCGAGTCT 2 CTTGTTCCAGCAG 82
(outer mitochondrial ACGATG AACCT
membrane)
DOK1 docking protein 1 , 62 CTTTCTGCCCTG 26 CAGTCCTCTGCAC 83 kDa (downstream of GAGATG CGTTA
ty rosine kinase 1)
DSC3 desmocolSin 3 GC GC C A TTTGCT CATCCAGATCCCT 84
AGAGATA CACAT
FE i flap structure-specific AGAGAAGATGG 28 CCAAGACACAGC 85 endonuclease 1 GCAGAAAG CAGTAAT
FOXH1 forkhead box HI GCCCAGATCAT 29 TTTCCAGCCCTCG 86
CCGTCA TAGTC
GJB5 gap junction protein, ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (connexiti 31.1) TTCGAC AGAAC
HOXD1 homeobox D GCTCCGCTGCT 31 GTCTGCCACTCTG 88
ATCTTT CAAC
HPN He psin ( transme nibrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1) GGATTA TTTGA
HYAL2 hyaluronoglucosam ATGGGCTTTGG 3 GAACAAGTCAGT 90 inidase 2 GAGCATA CTAGGGAATAC
ICA1 islet eel! autoantigen GACCTGGATGC 34 TGCTTTCGATAAG 91
1 , 69 kDa CAAGCTA TCCAGACA
ICA 5 intercellular adhesion CCGGCTCTTGG 35 CCTCTGAGGCTG 92 molecule 5, AAGTTG GAAACA
telencephalo
ITGA6 integrin, alpha 6 ACGCGGATCGA 36 ATCCACTGATCTT 93
GT i'i'GATAA CCTTGC
LIFE lipase, hormone-sensitive CGCAAGTCCCA 37 CAGTGCTGCTTCA 94
GAAGAT GACACA
ME3 malic enzyme 3, CGCGGATACGA 38 CCTTTCTTCAAGG 95
ADP(+)-dependent. TGTCAC GTAAAGGC
Mitochondrial
MGRN1 mahogunin, ring finger GAACTCGGCCT 39 TCGAATTTCTCTC 96
ATCGCT CTCCCAT YBPH myosin binding protein TCTGACCTCATC 40 CTGAGTCCACAC 97
H" ATCGGCAA AGGTTT
MY07A myosin VILA GAGGTGAAGCA 41 CCCATACTTGTTG 98
AACTACGGA ATGGCAATTA
NFIL3 nuclear factor, ACTCTCCACAA 42 TCCTGCGTGTGTT 99 interleukin 3 regulated AGCTCG CTACT
PI 3C2A phosphoi no si ti de -3 -kinase , GGATTTCAGCT 43 AGTCATCATGTAC 100 class 2, alpha ACCAGTTA CTT CCAGCA
polypeptide Table 2
Gene name Forw ard primer SEQ Reverse primer SEQ
Geiie symbol IB IB
PLEKHA6 pleckstrin homology' TTCGTCCTGGTG 44 CCC AGGATA CTCT 101 domain containing, GATCG CTTCCTT
family A member 6
PSMD14 proteasome prosome, A GTGATTG ATG 45 CACTGGATCAAC 102 maeropain.) 26 S subunit, TGTTTGCTATG TGCCTC
non-ATPase, 14
SCD5 steaioyl-CoA desaturase CAAAGCCAAGC 46 C AG CTGTCAC AC 103
5 CACTCACTC CCAGAGC
SIAH2 seven in absentia CTCGGCAGTCC 47 CGTATGGTGCAG 104 bomolog 2 TGiTi'C GGTCA
(Drosophila)
TCF2 transcription factor 2, ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic, LF-B3; variant GTCAGAA GTTGAAT
hepatic nuclear factor
TTFi thyroid transcription ATGAGTCCAAA 50 CCATGCCCACTTT 1.07 factor .1 GCACACGA CTTGTA
TRIM29 tripartite motif-containing TGAGATTGAGG 51 CATTGGTGGTGA 108
29 ATGA A GCTGAG AGCTCTTG
TUBAl tubulin, alpha 1 CCGACTCAACG 52 CGTGGACTGAGA 109
TGAGAC TGCATT
CFL1 coiilin 1 (non-muscle) GTGCCCTCTCCT 53 TTCATGTCGTTGA 1 10
TTTCG ACACCTTG
EEF1A1 ikar otic translation CGTTCTTTTTCG 54 CATTTTGGCTTTT 111 elongation factor 1 CAACGG AGGGGTAG
alpha 1
RPL10 ribosomal protein L10 GGTGTGCCACT 55 GGCAGAAGCGAG 1 12
GAAGAT ACTTT
RPL28 ribosomai protein L28 GTGTCGTGGTG 56 GCACATAGGAGG 1 13
GTCATT TGGCA
RPL37A ribosomal protein L37a GCATGAAGACA 57 GCGGACTTTACC 1 14
GTGGCT GTGAC
TabSe 3
Gene name Forward primer SEQ Reverse primer SEQ
Gene symbol ID IB
CDH5 cadlierin 5, type 2, AAGAGAGATTG 1 TTCTTGCGACTCACGCT 58
VE-cadherin GATTTGGAACC
(vascular epithelium)
CLEC3B C - type lec ti n domain CCAGAAGC:CCA 2 GCTCCTCAAACAT 59 family 3, member B AG A A GATTGT A CTTTGTGTTCA Table 3
Gene name Forw ard primer SEQ Reverse primer SEQ
Geiie symbol IB IB
P JCS phosphoribois lami AATCCTGGTGT 3 GACCACTGTGGG 60 noimidazoie CAAGGAAG TCATTATT
carboxylase,
phosphoribosy!ami
noimidazoie
succinocarboxarnide
synthetase
PAK1 p21/Cdc42/Racl- GGACCGATTTT 4 GAAATCTCTGGC 61 activated kinase 1 (STE20 ACCGATCC CGCTC
homolog, yeast)
TFAP2A transcription factor AP- GTCTCCGCCATC 6 ACTGAACAGAAG 63
2 alpha (activating CCTAT ACTTCGT
enhancer binding
protein 2 alpha)
ACVR1 activin A receptor, ACTGGTGTAAC AACCTCCAAGTG 64 type 1 AGGAACAT GAAATTCT
CDKN2C cyclin-dependent kinase TTTGGAAGGAC 8 TCGGTCTTTCAAA 65 inhibitor 2C (pl8, TGCGCT TCGGGATTA
inhibits CDK4)
INSM1 insulinoma-associated 1 ATTGAACTTCCC 10 AAGGTAAAGCCA
ACACGA GACTCCA 67
LRP10 low density lipoprotein GGAACAGACTG 11 GGGAGCGTAGGG 68 receptor-related protein TCACCAT TTAAG
10
STMN1 stathmin TCAGAGTGTGTG 12 CAGTGTATTCTGC 69 l/oncoprotein 18 G ACAATCAAC
TCAGGC
CAPG capping protein (actio GGGACAGCTTC 13 GTTCCAGGATGTT 70 filament), gelsolin-iike AACACT GGACTTTC
CHGA chromogranin A CCTGTGAACAG 1.4 GGAAAGTGTGTC 71
(parathy ro id sec eto ry CCCTATG GGAGAT
protein 1)
LGALS3 lectin, galactoside- TTCTGGGCACG 15 AGGCAACATCAT 72 binding, soluble, 3 GTGAAG TCCCTC
(galectin 3)
MAPRE3 microtubule -associated GGCCAAACTAG 16 GTCAACACCCAT 73 protein, RP EB family, AGCACGAATA CTTCTTGAAA
member 3
SFN stratifiti TCAGCAAGAAG 17 CGT AGTGGA AG A 74
GAGATGCC CGGAAA
SNAP 1 syiiaptosonLai-associated GTGCTCCCTCTC 18 CTGGTGTAGAATT 75 protein., 91 kDa CATTAAGTA AGGAGACGTA
homolog (mouse)
ABCC5 ATP -binding cassette, CAAGTTCAGGA 19 GGCATCAAGAGA 76 sub-family C(CFTR/MRP), GAACTCGAC GAGGC
member 5 Table 3
Gene name Forward primer SEQ Reverse primer SEQ
Geiie symbol IB IB
ALDH3B1 aldehyde dehydrogenase GGCTGTGGTTA 20 GATA A AG AGTTA
3 TGCGATAG CAAGCTCCTCTG family, member Bl
ANTXR1 Anthrax toxm receptor ! ACCCGAGGAAC 2! TCTAGGCCTTGAC 78
AACCTTA GGAT
CACNB1 calcium channel, CAGAGCGCCAG 23 GCACAGCAAATG 80 voltage-dependent, beta GCATTA CCACT
1 subunit
CBX1 chromobox homoiog ! CCACTGGCTGA 24 CTTGTCTTTCCCT 81
(HP I beta homo!og GGTGTTA ACTGTCTTAC
Drosophila)
CYB5B cytochrome b5 type B TGGGCGAGTCT 25 CTTGTTCCA GCAG 82
(outer mitochondrial ACGATG AACCT
e bra e)
DOK1 docking protein i, 62 CTTTCTGCCCTG 26 CAGTCCTCTGCAC 83 kDa (downstream of GAGATG CGTTA
tyrosine kinase 1)
DSC3 desmocollin 3 GCGCCATTTGCT 27 CATCCAGATCCCT 84
AGAGATA CACAT
FEN 1 flap structure- pecific AGAGAAGATGG 28 CCAAGACACAGC 85 endonuciease 1 GCAGAAAG CAGTAAT
GJB5 gap junction protein, ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (connexin 31.1) TTCGAC AGAAC
HOXD1 homeobox Dl GCTCCGCTGCT 31 GTCTGCCACTCTG 88
ATCTTT CAAC
HPN Hepsin (transmembrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1) GGATTA TTTGA
HYAL2 hyalurotio rucosam ATGGGCTTTGG 33 GAACAAGTCAGT 90 inidase 2 GAGCATA CTAGGGAATAC iCAl is lei cell autoanligen GA CCTGGATGC 34 TGCTTTCGATAAG 91
1, 69 kDa CAAGCTA TCCAGACA
ICA 5 intercellular adhesion CCGGCTCTTGG 35 CCTCTGAGGCTG 92 molecule 5, AAGTTG GAAACA
telencephaSin
ITGA6 integrin, alpha 6 ACGCGGATCGA 36 ATCCACTGATCTT 93
GTTTGATAA CCTTGC
ME3 malic enzyme 3, CGCGGATACGA 38 CCTTTCTTCAAGG 95
NADP(+)-dependent. TGTCAC GTAAAGGC
Mitochondrial
MGRN1 niahogunin, ring finger GAACTCGGCCT 39 TCGAATTTCTCTC 96
1 ATCGCT CTCCCAT
MYBPH myosin binding protein TCTGACCTCATC 40 CTGAGTCCACAC 97
H" ATCGGCAA AGGTTT Table 3
Gene name Forw ard primer SEQ Reverse primer SEQ
Geiie symbol n> IB Y07A myosin A G AGGTGA A GC A 41 CCCATACTTGTTG 98
AACTACGGA ATGGCAATTA FIL3 nuclear factor, ACTCTCCACAA 42 TCCTGCGTGTGTT 99 iiiterleukin 3 regulated AGCTCG CTACT
PJK3C2A phosphoinositide-3 -kinase, GGATTTCAGCT 43 AGTCATCATGTAC too class 2, alpha ACCAGTTACTT CCAGCA
polypeptide
PLEKHA6 piecksirin homology TTCGTCCTGGTG 44 CCCAGGATACTCT 101 domain containing, GATCG CTTCCTT
family A member 6
P5MD14 pro!easome (prosome, AGTGATTGATG 45 CACTGGATCAAC 102 macropain) 26S submit, TGTTTGCTATG TGCCTC
non-ATPase, i 1
SCD5 stearoyl-CoA desaturass CAAAGCCAAGC 46 CAGCTGTCACAC 103
5 CACTCACTC CCAGAGC
SIAH2 seven in absentia CTCGGCAGTCC 47 CGTATGGTGCAG 1.04 homoiog 2 TGTTTC GGTCA
(Drosop ila)
TCF2 transcription factor 2, ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic; LF-B3; variant GTCAGAA GTTGAAT
hepatic nuclear factor
TCPi t-complex 1 ATGCCCAAGAG 49 CCTGTACACCAA 106
AATCGTAAA GCTTCAT
TTFi thyroid transcription ATGAGTCCAAA 50 CCATGCCCACTTT 107 factor .1 GCACACGA CTTGTA
TRIM29 tripartite motif-containing TGAGATTGAGG 51 CATTGGTGGTGA 108
29 ATGAAGCTGAG AGCTCTTG
CFL1 cofilin 1 (non-muscle) GTGCCCTCTCCT 53 TTCATGTCGTTGA 110
TTTCG ACACCTTG
EEFlAl eukaryo!ic translation CGTTCTTTTTCG 54 CATTTTGGCTTl'T 11 1 elongation factor 1 CAACGG AGGGGTAG
alpha I
RPL10 ribosomal protein L10 GGTGTGCCACT 55 GGCAGAAGCGAG 112
GAAGAT ACTTT
RPL28 ribosomal protein L2S GTGTCGTGGTG 56 GCACATAGGAGG 133
GTCATT TGGCA
RPL37A ribosomal protein L37a GCATGAAGACA 57 GCGGACTTTACC 114
GTGGCT GTGAC
Table 4
Gene symbol Gene name Forward primer SEQ Reverse primer SEQ
ID ID
ACVR1 activin A receptor, ACTGGTGTAAC AACCTCCAAGTG 64 type 1 AG GA AC AT GAAATTCT Table 4
Gene symbol Gene name Forward primer SEQ Reverse primer SEQ
ID ID
CDKN2C cyclin-dependent kinase TTTGGAAGGAC 8 TCG GTCTTTC AAA 65 inhibitor 2C (plS, TGCGCT TCGGGATTA
inhibits CDK4)
CIB1 calcium and integrin CACGTCATCTCC 9 CTGCTGTCACAG 66 binding 1 (caimyrin) CGTTC GACAAT 66
1NSM1 insuiinoma-associated 1 ATTGAACTTCCC 10 AAGGTAAAGCCA 67
ACACGA GACTCCA 67
LRP10 low density lipoprotein GGAACAGACTG 1 1 GGGAGCGTAGGG 68 receptor-related protein TCACCAT TTAAG
10
STMNI stathmin TCAGAGTGTGTG 12 CAGTGTATTCTGC 69 i/oncoprotein 18 G ACAATCAAC
TCAGGC
Table 5
Gene name Forward primer SEQ Reverse primer SEQ
Gene symbol IB IB
CAPG capping protein (actin GGGACAGCTTC 13 GTTCCAGGATGTT 70 filament), geisoSin-iike AACACT GGACTTTC
CHGA chromogranin A CCTGTGAACAG 14 GGAAAGTGTGTC 71
(parathy ro id sec reto ty CCCTATG GGAGAT
protein 1)
LGALS3 lectin, gaiactoside- TTCTGGGCACG 15 AGGCAACATCAT 72 binding, soluble, 3 GTGAAG TCCCTC
(galectin 3)
MAPRE3 microtubule -associated GGCCAAACTAG 16 GTCAACACCCAT 73 protein, RP/EB family, AGCACGAATA CTTCTTGAAA
member 3
SFN siratiiiti TCAGCAAGAAG 17 CGTAGTGGAAGA 74
GAGATGCC CGGAAA
SNAP 1 GTGCTCCCTCTC 18 CTGGTGTAGAATT 75 protein, 91 kDa CATTAAGTA AGGAGACGTA
homolog (mouse)
Table 6
Gene symbol Gene name Forward primer SEQ Reverse primer SEQ
IB IB
ABCC5 ΑΊΡ-bmding casseue, CAAGTTCAGGA 19 GGCATCAAGAGA 76 sub-famiiy C(CFTR/ RP), GAACTCGAC GAGGC
member 5
ALDH3BI aldehyde dehydrogenase GGCTGTGGTTA 20 GATAAAGAGTTA
3 TGCGATAG CAAGCTCCTCTG family, member Bl Table 6
Geiie symbol Gene name Forward primer SEQ Reverse primer SEQ n> IB
ANTXR 1 Anthrax toxin receptor i ACCCGAGGAAC 21 TCTAGGCCTTGAC 78
AACCTTA GGAT
BMP7 bone morphogenetic CCCTCTCCATTC 22 TTTGGGCAAACCT 79 protein 7 (osteogenic CCTACA CGGTAA
protein 1)
CACNB 1 calcium channel, CAGAGCGCCAG 23 GCACAGCAAATG 80 voltage-dependent, beta GCATTA CCACT
1 subunit
CBX1 chromobox homoiog ! CCACTGGCTGA 24 CTTGTCTTTCCCT 81
(HP I beta homo!og GGTGTTA ACTGTCTTAC
Drosophila)
CYB5B cytochrome b5 type B TGGGCGAGTCT CTTGTTCCA GCAG 82
(outer mitochondrial ACGATG AACCT
memb ane)
DOK1 docking protein i, 62 CTTTCTGCCCTG 26 CAGTCCTCTGCAC 83 kDa (downstream of GAGATG CGTTA
tyrosine kinase 1)
DSC3 desmocollin 3 GCGCCATTTGCT 27 CATCCAGATCCCT 84
AGAGATA CACAT
FEN 1 flap structure- specific AGAGAAGATGG 28 CCAAGACACAGC 85 endonvjcJease 1 GCAGAAAG CAGTAAT
Foxm forkhead box Hi GCCCAGATCAT 29 TTTCCAGCCCTCG 86
CCGTCA TAGTC
GJB5 gap junction protein, ACCACAAGGAC 30 GGGACACAGGGA 87 beta 5 (connexin 31.1) TTCGAC AGAAC
HOXD1 homeobox Dl GCTCCGCTGCT 31 GTCTGCCACTCTG 88
ATCTTT CAAC
HPN Hepsin (transmembrane AGCGGCCAGGT 32 GTCGGCTGACGC 89 protease, serine 1) GGATTA TTTGA
HYAL2 hvai ronogiucosam ATGGGCTTTGG 33 G A AC A AGTC AGT 90 inidase 2 GAGCATA CTAGGGAATAC
ICA1 islet cell autoan!igen GACCTGGATGC 34 TGCTTTCGATAAG 91
1, 69 kDa CAAGCTA TCCAGACA
ICAM5 intercellular adhesion CCGGCTCTTGG 35 CCTCTGAGGCTG 92 molecule 5, AAGTTG GAAACA
telencephalin
ITGA6 integrin, alpha 6 ACGCGGATCGA 36 ATCC ACTG ATCTT 93
GTTTGATAA CCTTGC
LiPE lipase, hormone-sensitive CGCAAGTCCCA 37 CAGTGCTGCTTCA 94
GAAGAT GACACA
ME3 malic enzyme 3, CGCGGATACGA 38 CCTTTCTTCAAGG 95
NADP(+)-dependent, TGTCAC GTAAAGGC
Mitochondrial Table 6
Geiie symbol Gene name Forw ard primer SEQ Reverse primer SEQ n> IB GRN1 mahogunin, ring finger GAACTCGGCCT 39 TCGAATTTCTCTC 96
ATCGCT CTCCCAT
MYBPH myosin binding protein TCTGACCTCATC 40 CTGAGTCCA C AC 97
H ATCGGCAA AGGTTT
MY07A myosin VILA GAGGTGAAGCA 41 CCCATACTTGTf'G 98
AACTACGGA ATGGCAATTA
NFIL3 nuclear factor, ACTCTCCACAA 42 TCCTGCGTGTGTT 99 interieukin 3 regulated AGCTCG CTACT
PSK3C2A phospho ino sifide■ 3 -Id nase , GGATTTCAGCT 43 AGTCATCATGTAC 100 class 2, alpha ACCAGTTACTT CCAGCA
polypeptide
PLEKHA6 plecksirin homology TTCGTCCTGGTG 44 CCCAGGATACTCT 101 domain containing, GATCG crrccTT
family A member 6
PSMD14 proteasome (prosome, AGTGATTGATG 45 CACTGGATCAAC 102 maciopaiti) 26S subunit, TGi i i'GCTATG TGCCTC
non-ATPase, 14
SCD5 stearoyl-CoA desaturase C AAA GCCA AGC 46 CAGCTGTCA CAC 103
5 CACTCACTC CCAGAGC
SIAH2 seven in absentia CTCGGCAGTCC 47 CGTATGGTGCAG 104 homolog 2 TGTTTC GGTCA
(Drosophi'a)
TCF2 transcription factor 2, ACACCTGGTAC 48 TCTGGACTGTCTG 105 hepatic; LF-B3; variant GTCAGAA GTTGAAT
hepatic nuclear factor
TCP! t-complex 1 ATGCCCAAGAG 49 CCTGTACACCAA 106
AATCGTAAA GCTTCAT
TTF1 thyroid transcription ATGAGTCCAAA 50 CCATGCCCACTTT 107 factor 1 GCACACGA CTTGTA
TRIM29 tripartite motif -containing TG AG ATTGAGG 51 CATTGGTGGTGA 108
29 ATGAAGCTGAG AGCTCTTG
TUBA1 tubulin, alpha 1 CCGACTCAACG 52 CGTGGACTGAGA 109
TGAGAC TGCATT
[0043] Isolated mRNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, PCR analyses and probe arrays, NanoString Assays. One method for the detection of mRNA levels involves contacting the isolated mRNA or synthesized cDNA with a nucleic acid molecule (probe) that can hybridize to the mRNA encoded by the gene being detected. The nucleic acid probe can be, for example, a cDNA, or a portion thereof, such as an oligonucleotide of at least 7, 15, 30, 50, 100, 250, or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to the non-natural cDNA or mRNA biomarker of the present invention.
[0044] As explained above, in one embodiment, once the mRNA is obtained from a sample, it is converted to complementary DNA (cDNA) in a hybridization reaction. Conversion of the mRNA to cDNA can be performed with oligonucleotides or primers comprising sequence that is complementary to a portion of a specific mRNA. Conversion of the mRNA to cDNA can be performed with oligonucleotides or primers comprising random sequence. Conversion of the mRNA to cDNA can be performed with oligonucleotides or primers comprising sequence that is complementary to the poly(A) tail of an mRNA. cDNA does not exist in vivo and therefore is a non-natural molecule. In a further embodiment, the cDNA is then amplified, for example, by the polymerase chain reaction (PCR) or other amplification method known to those of ordinary skill in the art. PCR can be performed with the forward and/or reverse primers provided in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, or Table 6. The product of this amplification reaction, i.e. , amplified cDNA is necessarily a non-natural product. As mentioned above, cDNA is a non-natural molecule. Second, in the case of PCR, the amplification process serves to create hundreds of millions of cDNA copies for every individual cDNA molecule of starting material. The number of copies generated is far removed from the number of copies of mRNA that are present in vivo.
[0045] In one embodiment, cDNA is amplified with primers that introduce an additional DNA sequence (adapter sequence) onto the fragments (with the use of adapter-specific primers). The adaptor sequence can be a tail, wherein the tail sequence is not complementary to the cDNA. For example, the forward and/or reverse primers provided in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, or Table 6 can comprise tail sequence. Amplification therefore serves to create non-natural double stranded molecules from the non- natural single stranded cDNA, by introducing barcode, adapter and/or reporter sequences onto the already non-natural cDNA. In one embodiment, during amplification with the adapter-specific primers, a detectable label, e.g., a fluorophore, is added to single strand cDNA molecules. Amplification therefore also serves to create DNA complexes that do not occur in nature, at least because (i) cDNA does not exist in vivo, (i) adapter sequences are added to the ends of cDNA molecules to make DNA sequences that do not exist in vivo, (ii) the error rate associated with amplification further creates DNA sequences that do not exist in vivo, (iii) the disparate structure of the cDNA molecules as compared to what exists in nature and (iv) the chemical addition of a detectable label to the cDNA molecules.
[0046] In one embodiment, the synthesized cDNA (for example, amplified cDNA) is immobilized on a solid surface via hybridization with a probe, e.g., via a microarray. In another embodiment, cDNA products are detected via real-time polymerase chain reaction (PCR) via the introduction of fluorescent probes that hybridize with the cDNA products. For example, in one embodiment, biomarker detection is assessed by quantitative fluorogenic RT-PCR (e.g., with TaqMan® probes). For PCR analysis, well known methods are available in the art for the determination of primer sequences for use in the analysis.
[0047] Biomarkers provided herein in one embodiment, are detected via a hybridization reaction that employs a capture probe and/or a reporter probe. For example, the hybridization probe is a probe derivatized to a solid surface such as a bead, glass or silicon substrate. In another embodiment, the capture probe is present in solution and mixed with the patient's sample, followed by attachment of the hybridization product to a surface, e.g., via a biotin- avidin interaction (e.g., where biotin is a part of the capture probe and avidin is on the surface). The hybridization assay, in one embodiment, employs both a capture probe and a reporter probe. The reporter probe can hybridize to either the capture probe or the biomarker nucleic acid. Reporter probes e.g., are then counted and detected to determine the level of biomarker(s) in the sample. The capture and/or reporter probe, in one embodiment contain a detectable label, and/or a group that allows functionalization to a surface.
[0048] For example, the nCounter gene analysis system (see, e.g., Geiss et al. (2008) Nat. Biotechnol. 26, pp. 317-325, incorporated by reference in its entirety for all purposes, is amenable for use with the methods provided herein.
[0049] Hybridization assays described in U.S. Patent Nos. 7,473,767 and 8,492,094, the disclosures of which are incorporated by reference in their entireties for all purposes, are amenable for use with the methods provided herein, i.e., to detect the biomarkers and biomarker combinations described herein.
[0050] Biomarker levels may be monitored using a membrane blot (such as used in hybridization analysis such as Northem, Southem, dot, and the like), or microwells, sample tubes, gels, beads, or fibers (or any solid support comprising bound nucleic acids). See, for example, U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, each incorporated by reference in their entireties.
[0051] In one embodiment, microarrays are used to detect biomarker levels. Microarrays are particularly well suited for this purpose because of the reproducibility between different experiments. DNA microarrays provide one method for the simultaneous measurement of the expression levels of large numbers of genes. Each array consists of a reproducible partem of capture probes attached to a solid support. Labeled RNA or DNA is hybridized to complementary probes on the array and then detected by laser scanning Hybridization intensities for each probe on the array are determined and converted to a quantitative value representing relative gene expression levels. See, for example, U.S. Pat. Nos. 6,040,138, 5,800,992 and 6,020,135, 6,033,860, and 6,344,316, each incorporated by reference in their entireties. High-density oligonucleotide arrays are particularly useful for determining the gene expression profile for a large number of RNAs in a sample.
[0052] Techniques for the synthesis of these arrays using mechanical synthesis methods are described in, for example, U.S. Pat. No. 5,384,261. Although a planar array surface is generally used, the array can be fabricated on a surface of virtually any shape or even a multiplicity of surfaces. Arrays can be nucleic acids (or peptides) on beads, gels, polymeric surfaces, fibers (such as fiber optics), glass, or any other appropriate substrate. See, for example, U.S. Pat. Nos. 5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992, each incorporated by reference in their entireties. Arrays can be packaged in such a manner as to allow for diagnostics or other manipulation of an all-inclusive device. See, for example, U.S. Pat. Nos. 5,856,174 and 5,922,591, each incorporated by reference in their entireties.
[0053] Serial analysis of gene expression (SAGE) in one embodiment is employed in the methods described herein. SAGE is a method that allows the simultaneous and quantitative analysis of a large number of gene transcripts, without the need of providing an individual hybridization probe for each transcript. First, a short sequence tag (about 10-14 bp) is generated that contains sufficient information to uniquely identify a transcript, provided that the tag is obtained from a unique position within each transcript. Then, many transcripts are linked together to form long serial molecules, that can be sequenced, revealing the identity of the multiple tags simultaneously. The expression partem of any population of transcripts can be quantitatively evaluated by determining the abundance of individual tags, and identifying the gene corresponding to each tag. See, Velculescu et al. Science 270:484-87, 1995; Cell 88:243-51, 1997, incorporated by reference in its entirety.
[0054] An additional method of biomarker level analysis at the nucleic acid level is the use of a sequencing method, for example, RNAseq, next generation sequencing, and massively parallel signature sequencing (MPSS), as described by Brenner et al. (Nat. Biotech. 18:630- 34, 2000, incorporated by reference in its entirety). This is a sequencing approach that combines non-gel-based signature sequencing with in vitro cloning of millions of templates on separate 5 μηι diameter microbeads. First, a microbead library of DNA templates is constructed by in vitro cloning. This is followed by the assembly of a planar array of the template-containing microbeads in a flow cell at a high density (typically greater than 3.0 X 106 microbeads/cm2). The free ends of the cloned templates on each microbead are analyzed simultaneously, using a fluorescence-based signature sequencing method that does not require DNA fragment separation. This method has been shown to simultaneously and accurately provide, in a single operation, hundreds of thousands of gene signature sequences from a yeast cDNA library.
[0055] Another method if biomarker level analysis at the nucleic acid level is the use of an amplification method such as, for example, RT-PCR or quantitative RT-PCR (qRT-PCR). Methods for determining the level of biomarker mRNA in a sample may involve the process of nucleic acid amplification, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88: 189-193), self-sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87: 1874-1878), transcriptional amplification system (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86: 1173-1177), Q-Beta Replicase (Lizardi et al. (1988) Bio/Technology 6: 1197), rolling circle replication (Lizardi et al, U.S. Pat. No. 5,854,033) or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. Numerous different PCR or qRT-PCR protocols are known in the art and can be directly applied or adapted for use using the presently described compositions for the detection and/or quantification of expression of discriminative genes in a sample. See, for example, Fan et al. (2004) Genome Res. 14:878-885, herein incorporated by reference. Generally, in PCR, a target polynucleotide sequence is amplified by reaction with at least one oligonucleotide primer or pair of oligonucleotide primers. The primer(s) hybridize to a complementary region of the target nucleic acid and a DNA polymerase extends the primer(s) to amplify the target sequence. Under conditions sufficient to provide polymerase-based nucleic acid amplification products, a nucleic acid fragment of one size dominates the reaction products (the target polynucleotide sequence which is the amplification product). The amplification cycle is repeated to increase the concentration of the single target polynucleotide sequence. The reaction can be performed in any thermocycler commonly used for PCR.
[0056] Quantitative RT-PCR (qRT-PCR) (also referred as real-time RT-PCR) is preferred under some circumstances because it provides not only a quantitative measurement, but also reduced time and contamination. As used herein, "quantitative PCR (or "real time qRT- PCR") refers to the direct monitoring of the progress of a PCR amplification as it is occurring without the need for repeated sampling of the reaction products. In quantitative PCR, the reaction products may be monitored via a signaling mechanism (e.g., fluorescence) as they are generated and are tracked after the signal rises above a background level but before the reaction reaches a plateau. The number of cycles required to achieve a detectable or "threshold" level of fluorescence varies directly with the concentration of amplifiable targets at the beginning of the PCR process, enabling a measure of signal intensity to provide a measure of the amount of target nucleic acid in a sample in real time. A DNA binding dye (e.g., SYBR green) or a labeled probe can be used to detect the extension product generated by PCR amplification. Any probe format utilizing a labeled probe comprising the sequences of the invention may be used.
[0057] Immunohistochemistry methods are also suitable for detecting the levels of the biomarkers of the present invention. Samples can be frozen for later preparation or immediately placed in a fixative solution. Tissue samples can be fixed by treatment with a reagent, such as formalin, gluteraldehyde, methanol, or the like and embedded in paraffin. Methods for preparing slides for immunohistochemical analysis from formalin-fixed, paraffin-embedded tissue samples are well known in the art.
[0058] In one embodiment, the levels of the biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 (or subsets thereof, for example 5 to 20, 5 to 30, 5 to 40 biomarkers), are normalized against the expression levels of all RNA transcripts or their non-natural cDNA expression products, or protein products in the sample, or of a reference set of RNA transcripts or a reference set of their non-natural cDNA expression products, or a reference set of their protein products in the sample. [0059] As provided throughout, the methods set forth herein provide a method for determining the lung cancer subtype of a patient. Once the biomarker levels are determined, for example by measuring non-natural cDNA biomarker levels or non-natural mRNA-cDNA biomarker complexes, the biomarker levels are compared to reference values or a reference sample, for example with the use of statistical methods or direct comparison of detected levels, to make a determination of the lung cancer molecular subtype. Based on the comparison, the patient's lung cancer sample is classified, e.g., as neuroendocrine, squamous cell carcinoma, adenocarcinoma. In another embodiment, based on the comparison, the patient's lung cancer sample is classified as squamous cell carcinoma, adenocarcinoma or small cell carcinoma. In yet another embodiment, based on the comparison, the patient's lung cancer sample is classified as squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative).
[0060] In one embodiment, expression level values of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 are compared to reference expression level value(s) from at least one sample training set, wherein the at least one sample training set comprises expression level values from a reference sample(s). In a further embodiment, the at least one sample training set comprises expression level values of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 from an adenocarcinoma sample, a squamous cell carcinoma sample, a neuroendocrine sample, a small cell lung carcinoma sample, a proximal inflammatory (squamoid), proximal proliferative (magnoid), a terminal respiratory unit (bronchioid) sample, or a combination thereof.
[0061] In a separate embodiment, hybridization values of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 are compared to reference hybridization value(s) from at least one sample training set, wherein the at least one sample training set comprises hybridization values from a reference sample(s). In a further embodiment, the at least one sample training set comprises hybridization values of the at least five classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 from an adenocarcinoma sample, a squamous cell carcinoma sample, a neuroendocrine sample, a small cell lung carcinoma sample, a proximal inflammatory (squamoid), proximal proliferative (magnoid), a terminal respiratory unit (bronchioid) sample, or a combination thereof. In another embodiment, the at least one sample training set comprises hybridization values of the at least five classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, Table 6 from the reference samples provided in Table A below.
Figure imgf000045_0001
[0062] Methods for comparing detected levels of biomarkers to reference values and/or reference samples are provided herein. Based on this comparison, in one embodiment a correlation between the biomarker levels obtained from the subject's sample and the reference values is obtained. An assessment of the lung cancer subtype is then made.
[0063] Various statistical methods can be used to aid in the comparison of the biomarker levels obtained from the patient and reference biomarker levels, for example, from at least one sample training set.
[0064] In one embodiment, a supervised pattern recognition method is employed. Examples of supervised partem recognition methods can include, but are not limited to, the nearest centroid methods (Dabney (2005) Bioinformatics 21(22):4148-4154 and Tibshirani et al. (2002) Proc. Natl. Acad. Sci. USA 99(10):6576-6572); soft independent modeling of class analysis (SIMCA) (see, for example, Wold, 1976); partial least squares analysis (PLS) (see, for example, Wold, 1966; Joreskog, 1982; Frank, 1984; Bro, R., 1997); linear descriminant analysis (LDA) (see, for example, Nillson, 1965); K-nearest neighbour analysis (KNN) (sec, for example, Brown et al, 1996); artificial neural networks (ANN) (see, for example, Wasserman, 1989; Anker et al., 1992; Hare, 1994); probabilistic neural networks (PNNs) (see, for example, Parzen, 1962; Bishop, 1995; Speckt, 1990; Broomhead et al, 1988; Patterson, 1996); rule induction (RI) (see, for example, Quinlan, 1986); and, Bayesian methods (see, for example, Bretthorst, 1990a, 1990b, 1988). In one embodiment, the classifier for identifying tumor subtypes based on gene expression data is the centroid based method described in Mullins et al. (2007) Clin Chem. 53(7): 1273-9, each of which is herein incorporated by reference in its entirety.
[0065] In other embodiments, an unsupervised training approach is employed, and therefore, no training set is used.
[0066] Referring to sample training sets for supervised learning approaches again, in some embodiments, a sample training set(s) can include expression data of all of the classifier biomarkers (e.g., all the classifier biomarkers of any of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, Table 6) from an adenocarcinoma sample. In some embodiments, a sample training set(s) can include expression data of all of the classifier biomarkers (e.g., all the classifier biomarkers of any of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5, Table 6) from a squamous cell carcinoma sample, an adenocarcinoma sample and/or a neuroendocrine sample. In some embodiments, the sample training set(s) are normalized to remove sample-to-sample variation.
[0067] In some embodiments, comparing can include applying a statistical algorithm, such as, for example, any suitable multivariate statistical analysis model, which can be parametric or non-parametric. In some embodiments, applying the statistical algorithm can include determining a correlation between the expression data obtained from the human lung tissue sample and the expression data from the adenocarcinoma and squamous cell carcinoma training set(s). In some embodiments, cross-validation is performed, such as (for example), leave-one-out cross-validation (LOOCV). In some embodiments, integrative correlation is performed. In some embodiments, a Spearman correlation is performed. In some embodiments, a centroid based method is employed for the statistical algorithm as described in Mullins et al. (2007) Clin Chem. 53(7): 1273-9, and based on gene expression data, which is herein incorporated by reference in its entirety. [0068] Results of the gene expression performed on a sample from a subject (test sample) may be compared to a biological sample(s) or data derived from a biological sample(s) that is known or suspected to be normal ("reference sample" or "normal sample", e.g., non- adenocarcinoma sample). In some embodiments, a reference sample or reference gene expression data is obtained or derived from an individual known to have a particular molecular subtype of adenocarcimona, i.e., squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative). In another embodiment, a reference sample or reference biomarker level data is obtained or derived from an individual known to have a lung cancer subtype, e.g. , adenocarcinoma, squamous cell carcinoma, neuroendocrine or small cell carcinoma.
[0069] The reference sample may be assayed at the same time, or at a different time from the test sample. Alternatively, the biomarker level information from a reference sample may be stored in a database or other means for access at a later date.
[0070] The biomarker level results of an assay on the test sample may be compared to the results of the same assay on a reference sample. In some cases, the results of the assay on the reference sample are from a database, or a reference value(s). In some cases, the results of the assay on the reference sample are a known or generally accepted value or range of values by those skilled in the art. In some cases the comparison is qualitative. In other cases the comparison is quantitative. In some cases, qualitative or quantitative comparisons may involve but are not limited to one or more of the following: comparing fluorescence values, spot intensities, absorbance values, chemiluminescent signals, histograms, critical threshold values, statistical significance values, expression levels of the genes described herein, mRNA copy numbers.
[0071] In one embodiment, an odds ratio (OR) is calculated for each biomarker level panel measurement. Here, the OR is a measure of association between the measured biomarker values for the patient and an outcome, e.g. , lung cancer subtype. For example, see, J. Can. Acad. Child Adolesc. Psychiatry 2010; 19(3): 227-229, which is incorporated by reference in its entirety for all purposes.
[0072] In one embodiment, a specified statistical confidence level may be determined in order to provide a confidence level regarding the lung cancer subtype. For example, it may be determined that a confidence level of greater than 90% may be a useful predictor of the lung cancer subtype. In other embodiments, more or less stringent confidence levels may be chosen. For example, a confidence level of about or at least about 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, 99.5%, or 99.9% may be chosen. The confidence level provided may in some cases be related to the quality of the sample, the quality of the data, the quality of the analysis, the specific methods used, and/or the number of gene expression values (i.e. , the number of genes) analyzed. The specified confidence level for providing the likelihood of response may be chosen on the basis of the expected number of false positives or false negatives. Methods for choosing parameters for achieving a specified confidence level or for identifying markers with diagnostic power include but are not limited to Receiver Operating Characteristic (ROC) curve analysis, binormal ROC, principal component analysis, odds ratio analysis, partial least squares analysis, singular value decomposition, least absolute shrinkage and selection operator analysis, least angle regression, and the threshold gradient directed regularization method.
[0073] Determining the lung cancer subtype in some cases can be improved through the application of algorithms designed to normalize and or improve the reliability of the gene expression data. In some embodiments of the present invention, the data analysis utilizes a computer or other device, machine or apparatus for application of the various algorithms described herein due to the large number of individual data points that are processed. A "machine learning algorithm" refers to a computational-based prediction methodology, also known to persons skilled in the art as a "classifier," employed for characterizing a gene expression profile or profiles, e.g., to determine the lung cancer subtype. The biomarker levels, determined by, e.g., microarray-based hybridization assays, sequencing assays, NanoString assays, etc., are in one embodiment subjected to the algorithm in order to classify the profile. Supervised learning generally involves "training" a classifier to recognize the distinctions among classes (e.g., adenocarcinoma positive, adenocarcinoma negative, squamous positive, squamous negative, neuroendocrine positive, neuroendocrine negative, small cell positive, small cell negative, squamoid (proximal inflammatory) positive, bronchoid (terminal respiratory unit) positive or magnoid (proximal proliferative) positive, and then "testing" the accuracy of the classifier on an independent test set. For new, unknown samples the classifier can be used to predict, for example, the class (e.g. , adenocarcinoma vs. squamous cell carcinoma vs. neuroendocrine) in which the samples belong. [0074] In some embodiments, a robust multi-array average (RMA) method may be used to normalize raw data. The RMA method begins by computing background-corrected intensities for each matched cell on a number of microarrays. In one embodiment, the background corrected values are restricted to positive values as described by Irizarry et al. (2003). Biostatistics April 4 (2): 249-64, incorporated by reference in its entirety for all purposes. After background correction, the base-2 logarithm of each background corrected matched-cell intensity is then obtained. The background corrected, log-transformed, matched intensity on each microarray is then normalized using the quantile normalization method in which for each input array and each probe value, the array percentile probe value is replaced with the average of all array percentile points, this method is more completely described by Bolstad et al. Bioinformatics 2003, incorporated by reference in its entirety. Following quantile normalization, the normalized data may then be fit to a linear model to obtain an intensity measure for each probe on each microarray. Tukey's median polish algorithm (Tukey, J. W., Exploratory Data Analysis. 1977, incorporated by reference in its entirety for all purposes) may then be used to determine the log-scale intensity level for the normalized probe set data.
[0075] Various other software programs may be implemented. In certain methods, feature selection and model estimation may be performed by logistic regression with lasso penalty using glmnet (Friedman et al. (2010). Journal of statistical software 33(1): 1-22, incorporated by reference in its entirety). Raw reads may be aligned using TopHat (Trapnell et al. (2009). Bioinformatics 25(9): 1105-11, incorporated by reference in its entirety). In methods, top features (N ranging from 10 to 200) are used to train a linear support vector machine (SVM) (Suykens JAK, Vandewalle J. Least Squares Support Vector Machine Classifiers. Neural Processing Letters 1999; 9(3): 293-300, incorporated by reference in its entirety) using the el 071 library (Meyer D. Support vector machines: the interface to libsvm in package el071. 2014, incorporated by reference in its entirety). Confidence intervals, in one embodiment, are computed using the pROC package (Robin X, Turck N, Hainard A, et al. pROC: an open- source package for R and S+ to analyze and compare ROC curves. BMC bioinformatics 2011; 12: 77, incorporated by reference in its entirety).
[0076] In addition, data may be filtered to remove data that may be considered suspect. In one embodiment, data derived from microarray probes that have fewer than about 4, 5, 6, 7 or 8 guanosine+cytosine nucleotides may be considered to be unreliable due to their aberrant hybridization propensity or secondary structure issues. Similarly, data deriving from microarray probes that have more than about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 guanosine+cytosine nucleotides may in one embodiment be considered unreliable due to their aberrant hybridization propensity or secondary structure issues.
[0077] In some embodiments of the present invention, data from probe-sets may be excluded from analysis if they are not identified at a detectable level (above background).
[0078] In some embodiments of the present disclosure, probe-sets that exhibit no, or low variance may be excluded from further analysis. Low-variance probe-sets are excluded from the analysis via a Chi-Square test. In one embodiment, a probe-set is considered to be low- variance if its transformed variance is to the left of the 99 percent confidence interval of the Chi-Squared distribution with (N-l) degrees of freedom. (N-l)*Probe-set Variance/(Gene Probe-set Variance), about. Chi-Sq(N-l) where N is the number of input CEL files, (N-l) is the degrees of freedom for the Chi-Squared distribution, and the "probe-set variance for the gene" is the average of probe-set variances across the gene. In some embodiments of the present invention, probe-sets for a given mRNA or group of mRNAs may be excluded from further analysis if they contain less than a minimum number of probes that pass through the previously described filter steps for GC content, reliability, variance and the like. For example in some embodiments, probe-sets for a given gene or transcript cluster may be excluded from further analysis if they contain less than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or less than about 20 probes.
[0079] Methods of biomarker level data analysis in one embodiment, further include the use of a feature selection algorithm as provided herein. In some embodiments of the present invention, feature selection is provided by use of the LIMMA software package (Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397-420, incorporated by reference in its entirety for all purposes).
[0080] Methods of biomarker level data analysis, in one embodiment, include the use of a pre-classifier algorithm. For example, an algorithm may use a specific molecular fingerprint to pre-classify the samples according to their composition and then apply a correction/normalization factor. This data/information may then be fed in to a final classification algorithm which would incorporate that information to aid in the final diagnosis.
[0081] Methods of biomarker level data analysis, in one embodiment, further include the use of a classifier algorithm as provided herein. In one embodiment of the present invention, a diagonal linear discriminant analysis, k-nearest neighbor algorithm, support vector machine (SVM) algorithm, linear support vector machine, random forest algorithm, or a probabilistic model-based method or a combination thereof is provided for classification of microarray data. In some embodiments, identified markers that distinguish samples (e.g., of varying biomarker level profiles, of varying lung cancer subtypes, and/or varying molecular subtypes of adenocarcinoma (e.g., squamoid, bronchoid, magnoid)) are selected based on statistical significance of the difference in biomarker levels between classes of interest. In some cases, the statistical significance is adjusted by applying a Benjamin Hochberg or another correction for false discovery rate (FDR).
[0082] In some cases, the classifier algorithm may be supplemented with a meta-analysis approach such as that described by Fishel and Kaufman et al. 2007 Bioinformatics 23(13): 1599-606, incorporated by reference in its entirety for all purposes. In some cases, the classifier algorithm may be supplemented with a meta-analysis approach such as a repeatability analysis.
[0083] Methods for deriving and applying posterior probabilities to the analysis of biomarker level data are known in the art and have been described for example in Smyth, G. K. 2004 Stat. Appi. Genet. Mol. Biol. 3: Article 3, incorporated by reference in its entirety for all purposes. In some cases, the posterior probabilities may be used in the methods of the present invention to rank the markers provided by the classifier algorithm.
[0084] A statistical evaluation of the results of the biomarker level profiling may provide a quantitative value or values indicative of one or more of the following: the lung cancer subtype (adenocarcinoma, squamous cell carcinoma, neuroendocrine); molecular subtype of adenocarcinoma (squamoid, bronchoid or magnoid); the likelihood of the success of a particular therapeutic intervention, e.g., angiogenesis inhibitor therapy or chemotherapy. In one embodiment, the data is presented directly to the physician in its most useful form to guide patient care, or is used to define patient populations in clinical trials or a patient population for a given medication. The results of the molecular profiling can be statistically evaluated using a number of methods known to the art including, but not limited to: the students T test, the two sided T test, Pearson rank sum analysis, hidden Markov model analysis, analysis of q-q plots, principal component analysis, one way ANOVA, two way ANOVA, LIMMA and the like.
[0085] In some cases, accuracy may be determined by tracking the subject over time to determine the accuracy of the original diagnosis. In other cases, accuracy may be established in a deterministic manner or using statistical methods. For example, receiver operator characteristic (ROC) analysis may be used to determine the optimal assay parameters to achieve a specific level of accuracy, specificity, positive predictive value, negative predictive value, and/or false discovery rate.
[0086] In some cases the results of the biomarker level profiling assays, are entered into a database for access by representatives or agents of a molecular profiling business, the individual, a medical provider, or insurance provider. In some cases, assay results include sample classification, identification, or diagnosis by a representative, agent or consultant of the business, such as a medical professional. In other cases, a computer or algorithmic analysis of the data is provided automatically. In some cases the molecular profiling business may bill the individual, insurance provider, medical provider, researcher, or govemment entity for one or more of the following: molecular profiling assays performed, consulting services, data analysis, reporting of results, or database access.
[0087] In some embodiments of the present invention, the results of the biomarker level profiling assays are presented as a report on a computer screen or as a paper record. In some embodiments, the report may include, but is not limited to, such information as one or more of the following: the levels of biomarkers (e.g. , as reported by copy number or fluorescence intensity, etc.) as compared to the reference sample or reference value(s); the likelihood the subject will respond to a particular therapy, based on the biomarker level values and the lung cancer subtype and proposed therapies.
[0088] In one embodiment, the results of the gene expression profiling may be classified into one or more of the following: adenocarcinoma positive, adenocarcinoma negative, squamous cell carcinoma positive, squamous cell carcinoma negative, neuroendocrine positive, neuroendocrine negative, small cell carcinoma positive, small cell carcinoma negative, squamoid (proximal inflammatory) positive, bronchoid (terminal respiratory unit) positive, magnoid (proximal proliferative) positive, squamoid (proximal inflammatory) negative, bronchoid (terminal respiratory unit) negative, magnoid (proximal proliferative) negative; likely to respond to angiogenesis inhibitor or chemotherapy; unlikely to respond to angiogenesis inhibitor or chemotherapy; or a combination thereof.
[0089] In some embodiments of the present invention, results are classified using a trained algorithm. Trained algorithms of the present invention include algorithms that have been developed using a reference set of known gene expression values and/or normal samples, for example, samples from individuals diagnosed with a particular molecular subtype of adenocarcinoma. In some cases a reference set of known gene expression values are obtained from individuals who have been diagnosed with a particular molecular subtype of adenocarcinoma, and are also known to respond (or not respond) to angiogenesis inhibitor therapy.
[0090] Algorithms suitable for categorization of samples include but are not limited to k- nearest neighbor algorithms, support vector machines, linear discriminant analysis, diagonal linear discriminant analysis, updown, naive Bayesian algorithms, neural network algorithms, hidden Markov model algorithms, genetic algorithms, or any combination thereof.
[0091] When a binary classifier is compared with actual true values (e.g., values from a biological sample), there are typically four possible outcomes. If the outcome from a prediction is p (where "p" is a positive classifier output, such as the presence of a deletion or duplication syndrome) and the actual value is also p, then it is called a true positive (TP); however if the actual value is n then it is said to be a false positive (FP). Conversely, a true negative has occurred when both the prediction outcome and the actual value are n (where "n" is a negative classifier output, such as no deletion or duplication syndrome), and false negative is when the prediction outcome is n while the actual value is p. In one embodiment, consider a test that seeks to determine whether a person is likely or unlikely to respond to angiogenesis inhibitor therapy. A false positive in this case occurs when the person tests positive, but actually does respond. A false negative, on the other hand, occurs when the person tests negative, suggesting they are unlikely to respond, when they actually are likely to respond. The same holds true for classifying a lung cancer subtype.
[0092] The positive predictive value (PPV), or precision rate, or post-test probability of disease, is the proportion of subjects with positive test results who are correctly diagnosed as likely or unlikely to respond, or diagnosed with the correct lung cancer subtype, or a combination thereof. It reflects the probability that a positive test reflects the underlying condition being tested for. Its value does however depend on the prevalence of the disease, which may vary. In one example the following characteristics are provided: FP (false positive); TN (true negative); TP (true positive); FN (false negative). False positive rate (□)=FP/(FP+TN)-specificity; False negative rate (D)=FN/(TP+FN)-sensitivity; Power= sensitivity = 1-D D ; Likelihood-ratio positive=sensitivity/(l-specificity); Likelihood-ratio negative=( 1 -sensitivity )/specificity. The negative predictive value (NPV) is the proportion of subjects with negative test results who are correctly diagnosed.
[0093] In some embodiments, the results of the biomarker level analysis of the subject methods provide a statistical confidence level that a given diagnosis is correct. In some embodiments, such statistical confidence level is at least about, or more than about 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% 99.5%, or more.
[0094] In some embodiments, the method further includes classifying the lung tissue sample as a particular lung cancer subtype based on the comparison of biomarker levels in the sample and reference biomarker levels, for example present in at least one training set. In some embodiments, the lung tissue sample is classified as a particular subtype if the results of the comparison meet one or more criterion such as, for example, a minimum percent agreement, a value of a statistic calculated based on the percentage agreement such as (for example) a kappa statistic, a minimum correlation (e.g., Pearson's correlation) and/or the like.
[0095] It is intended that the methods described herein can be performed by software (stored in memory and/or executed on hardware), hardware, or a combination thereof. Hardware modules may include, for example, a general-purpose processor, a field programmable gate array (FPGA), and/or an application specific integrated circuit (ASIC). Software modules (executed on hardware) can be expressed in a variety of software languages (e.g., computer code), including Unix utilities, C, C++, Java™, Ruby, SQL, SAS®, the R programming language/software environment, Visual Basic™, and other object-oriented, procedural, or other programming language and development tools. Examples of computer code include, but are not limited to, micro-code or micro-instructions, machine instructions, such as produced by a compiler, code used to produce a web service, and files containing higher-level instructions that are executed by a computer using an interpreter. Additional examples of computer code include, but are not limited to, control signals, encrypted code, and compressed code.
[0096] Some embodiments described herein relate to devices with a non-transitory computer- readable medium (also can be referred to as a non-transitory processor-readable medium or memory) having instructions or computer code thereon for performing various computer- implemented operations and/or methods disclosed herein. The computer-readable medium (or processor-readable medium) is non-transitory in the sense that it does not include transitory propagating signals per se (e.g., a propagating electromagnetic wave carrying information on a transmission medium such as space or a cable). The media and computer code (also can be referred to as code) may be those designed and constructed for the specific purpose or purposes. Examples of non-transitory computer-readable media include, but are not limited to: magnetic storage media such as hard disks, floppy disks, and magnetic tape; optical storage media such as Compact Disc/Digital Video Discs (CD/DVDs), Compact Disc- Read Only Memories (CD-ROMs), and holographic devices; magneto-optical storage media such as optical disks; carrier wave signal processing modules; and hardware devices that are specially configured to store and execute program code, such as Application-Specific Integrated Circuits (ASICs), Programmable Logic Devices (PLDs), Read-Only Memory (ROM) and Random-Access Memory (RAM) devices. Other embodiments described herein relate to a computer program product, which can include, for example, the instructions and/or computer code discussed herein.
[0097] In some embodiments, a single biomarker, or from about 5 to about 10, from about 5 to about 15, from about 5 to about 20, from about 5 to about 25, from about 5 to about 30, from about 5 to about 35, from about 5 to about 40, from about 5 to about 45, from about 5 to about 50 biomarkers (e.g., as disclosed in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 and Table 6) is capable of classifying types and/or subtypes of lung cancer with a predictive success of at least about 70%, at least about 71%, at least about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, up to 100%, and all values in between. In some embodiments, any combination of biomarkers disclosed herein (e.g., in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 and Table 6 and sub-combinations thereof) can used to obtain a predictive success of at least about 70%, at least about 71%, at least about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, up to 100%, and all values in between.
[0098] In some embodiments, a single biomarker, or from about 5 to about 10, from about 5 to about 15, from about 5 to about 20, from about 5 to about 25, from about 5 to about 30, from about 5 to about 35, from about 5 to about 40, from about 5 to about 45, from about 5 to about 50 biomarkers (e.g., as disclosed in Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 and Table 6) is capable of classifying lung cancer types and/or subtypes with a sensitivity or specificity of at least about 70%, at least about 71%, at least about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, up to 100%, and all values in between. In some embodiments, any combination of biomarkers disclosed herein can be used to obtain a sensitivity or specificity of at least about 70%, at least about 71%, at least about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, up to 100%, and all values in between.
[0099] In some embodiments, one or more kits for practicing the methods of the invention are further provided. The kit can encompass any manufacture (e.g., a package or a container) including at least one reagent, e.g., an antibody, a nucleic acid probe or primer, and/or the like, for detecting the biomarker level of a classifier biomarker. The kit can be promoted, distributed, or sold as a unit for performing the methods of the present invention. Additionally, the kits can contain a package insert describing the kit and methods for its use.
[00100] In one embodiment, a method is provided herein for determining a disease outcome or prognosis for a patient suffering from cancer. In some cases, the cancer is lung cancer. The method can comprise determining a disease outcome or prognosis for the patient by comparing a molecular subtype of the patient's cancer with a morphological subtype of the patient's cancer, whereby the presence or absence of concordance between the molecular and morphological subtypes predicts the disease outcome or prognosis of the patient. In one embodiment, discordance between the molecular subtype and the morphological subtype indicates a poor prognosis or poor disease outcome. The poor prognosis or disease outcome can be in comparison to a patient suffering from the same type of cancer (e.g., lung cancer) whose molecular and morphological subtype determinations are concordant. The disease outcome or prognosis can be measured by examining the overall survival for a period of time or intervals (e.g., 0 to 36 months or 0 to 60 months). In one embodiment, survival is analyzed as a function of subtype (e.g., for lung cancer, adenocarcinoma (TRU, PI, and PP), neuroendocrine (small cell carcinoma and carcinoid), or squamous). Relapse-free and overall survival can be assessed using standard Kaplan-Meier plots (see FIGs. 4-11) as well as Cox proportional hazards modeling.
[00101] In one embodiment, the molecular subtype is determined by detecting expression levels of classifier biomarkers, thereby obtaining an expression profile. The expression profile can be determined using any of the methods provided herein. In some cases, the patient is suffering from lung cancer and the molecular subtype of a lung tissue sample obtained from the patient is determined by detecting the levels of a single biomarker, or from about 5 to about 10, from about 5 to about 15, from about 5 to about 20, from about 5 to about 25, from about 5 to about 30, from about 5 to about 35, from about 5 to about 40, from about 5 to about 45, from about 5 to about 50 classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 using any of the methods provided herein for detecting the expression levels (e.g., RNA-seq, RT-PCR, or hybridization assay such as, for example, microarray hybridization assay).
[00102] In one embodiment, the molecular subtype is determined by detecting expression levels of at least five classifier biomarkers in Table 1 A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 at a nucleic acid level in a lung tissue sample by performing RT-PCR (or qRT-PCR) and comparing the detected expression levels to those of a reference sample or training set as described herein in order to determine if the molecular subtype of the lung tissue sample obtained from the patient is an adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype. The neuroendocrine subtype can encompass small cell carcinoma and carcinoid. The adenocarcinoma subtype can be further classified as being TRU, PI, or PP. The RT-PCR can be performed with primers specific to the at least five classifier biomarkers. The primers specific for the at least five classifier biomarkers are forward and reverse primers listed in Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6.
[00103] In one embodiment, the molecular subtype is determined by probing the levels of at least five classifier biomarkers in Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 at a nucleic acid level in a lung tissue sample by mixing the sample with five or more oligonucleotides that are substantially complementary to portions of nucleic acid molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for hybridization of the five or more oligonucleotides to their complements or substantial complements, detecting whether hybridization occured between the five or more oligonucleotides to their complements or substantial complements, obtaining hybridization values of the at least five classifier biomarkers based on the detecting step and comparing the detected hybridization values to those of a reference sample or training set as described herein in order to determine if the molecular subtype of the lung tissue sample obtained from the patient is an adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype. The neuroendocrine subtype can encompass small cell carcinoma and carcinoid. The adenocarcinoma subtype can be further classified as being TRU, PI, or PP.
[00104] In one embodiment, the morphological subtype of a tissue sample (e.g., lung tissue sample) is a histological analysis. Histological analysis can be performed using any of the methods known in the art. In one embodiment, a lung tissue sample is assigned a histological subtype of adenocarcinoma, squamous, or neuroendocrine based on the histological analysis. In one embodiment, the histological subtype of a lung tissue sample obtained from a patient suffering from lung cancer is compared to the molecular subtype of the lung tissue sample, whereby the molecular subtype is determined by examining gene expression levels of classifier genes (e.g. from Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6). In one embodiment, the histological subtype and molecular subtypes are in concordance, whereby the overall survival of the patient (as determined for example by using standard Kaplan-Meier plots as well as Cox proportional hazards modeling) is substantially similar to the overall survival of other patients with the same subtype of cancer. In one embodiment, the histological subtype and molecular subtype are discordant, whereby the overall survival of the patient (as determined for example by using standard Kaplan-Meier plots as well as Cox proportional hazards modeling) is substantially dissimilar to the overall survival of other patients with concordant molecular and histological subtype determinations of cancer. The overall survival probability of patient's with discordant subtypes can be 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, 99.5%, or 99.9% less or lower than the overall survival probability of patient's with concordant subtypes of cancer (e.g., lung cancer).
[00105] In one embodiment, upon determining a patient's lung cancer subtype, the patient is selected for suitable therapy, for example chemotherapy or drug therapy with an angiogenesis inhibitor. In one embodiment, the therapy is angiogenesis inhibitor therapy, and the angiogenesis inhibitor is a vascular endothelial growth factor (VEGF) inhibitor, a VEGF receptor inhibitor, a platelet derived growth factor (PDGF) inhibitor or a PDGF receptor inhibitor.
[00106] In another embodiment, the angiogenesis inhibitor is an integrin antagonist, a selectin antagonist, an adhesion molecule antagonist (e.g., antagonist of intercellular adhesion molecule (ICAM)-l, ICAM-2, ICAM-3, platelet endothelial adhesion molecule (PCAM), vascular cell adhesion molecule (VCAM)), lymphocyte function-associated antigen 1 (LFA- 1)), a basic fibroblast growth factor antagonist, a vascular endothelial growth factor (VEGF) modulator, or a platelet derived growth factor (PDGF) modulator (e.g. , a PDGF antagonist). In one embodiment of determining whether a subject is likely to respond to an integrin antagonist, the integrin antagonist is a small molecule integrin antagonist, for example, an antagonist described by Paolillo et al. (Mini Rev Med Chem, 2009, volume 12, pp. 1439- 1446, incorporated by reference in its entirety), or a leukocyte adhesion-inducing cytokine or growth factor antagonist (e.g., tumor necrosis factor-a (TNF-a), interleukin-ΐ β (IL-Ι β), monocyte chemotactic protein-1 (MCP-1) and a vascular endothelial growth factor (VEGF)), as described in U.S. Patent No. 6,524,581, incorporated by reference in its entirety herein.
[00107] The methods provided herein are also useful for determining whether a subject is likely to respond to one or more of the following angiogenesis inhibitors: interferon gamma 1β, interferon gamma 1β (Actimmune®) with pirfenidone, ACUHTR028, ανβ5, aminobenzoate potassium, amyloid P, ANG1122, ANG1170, ANG3062, ANG3281, ANG3298, ANG4011, anti-CTGF RNAi, Aplidin, astragalus membranaceus extract with salvia and schisandra chinensis, atherosclerotic plaque blocker, Azol, AZX100, BB3, connective tissue growth factor antibody, CT140, danazol, Esbriet, EXCOOl, EXC002, EXC003, EXC004, EXC005, F647, FG3019, Fibrocorin, Follistatin, FT011, a galectin-3 inhibitor, GKT137831, GMCTOl, GMCT02, GRMDOl, GRMD02, GRN510, Heberon Alfa R, interferon α-2β, ITMN520, JKB119, JKB121, JKB122, KRX168, LPA1 receptor antagonist, MGN4220, MIA2, microRNA 29a oligonucleotide, MMI0100, noscapine, PBI4050, PBI4419, PDGFR inhibitor, PF-06473871, PGN0052, Pirespa, Pirfenex, pirfenidone, plitidepsin, PRM151, Pxl02, PYN17, PYN22 with PYN17, Relivergen, rhPTX2 fusion protein, RXI109, secretin, STX100, TGF-β Inhibitor, transforming growth factor, β- receptor 2 oligonucleotide, VA999260, XV615, or a combination thereof.
[00108] In another embodiment, a method is provided for determining whether a subject is likely to respond to one or more endogenous angiogenesis inhibitors. In a further embodiment, the endogenous angiogenesis inhibitor is endostatin, a 20 kDa C-terminal fragment derived from type XVIII collagen, angiostatin (a 38 kDa fragment of plasmin), or a member of the thrombospondin (TSP) family of proteins. In a further embodiment, the angiogenesis inhibitor is a TSP-1, TSP-2, TSP-3, TSP-4 and TSP-5. Methods for determining the likelihood of response to one or more of the following angiogenesis inhibitors are also provided a soluble VEGF receptor, e.g. , soluble VEGFR-1 and neuropilin 1 (NPR1), angiopoietin-1, angiopoietin-2, vasostatin, calreticulin, platelet factor-4, a tissue inhibitor of metalloproteinase (TIMP) (e.g., TIMP1, TIMP2, TIMP 3, TIMP4), cartilage- derived angiogenesis inhibitor (e.g., peptide troponin I and chrondomodulin I), a disintegrin and metalloproteinase with thrombospondin motif 1, an interferon (IFN) (e.g. , IFN-a, IFN-β, IFN-γ), a chemokine, e.g. , a chemokine having the C-X-C motif (e.g., CXCLIO, also known as interferon gamma-induced protein 10 or small inducible cytokine B10), an interleukin cytokine (e.g. , IL-4, IL-12, IL-18), prothrombin, antithrombin III fragment, prolactin, the protein encoded by the TNFSF15 gene, osteopontin, maspin, canstatin, proliferin-related protein.
[00109] In one embodiment, a method for determining the likelihood of response to one or more of the following angiogenesis inhibitors is provided is angiopoietin-1, angiopoietin-2, angiostatin, endostatin, vasostatin, thrombospondin, calreticulin, platelet factor-4, TIMP, CDAI, interferon a, interferon p,vascular endothelial growth factor inhibitor (VEGI) meth-1, meth-2, prolactin, VEGI, SPARC, osteopontin, maspin, canstatin, proliferin- related protein (PRP), restin, TSP-1, TSP-2, interferon gamma 1β, ACUHTR028, ανβ5, aminobenzoate potassium, amyloid P, ANG1122, ANG1170, ANG3062, ANG3281, ANG3298, ANG4011, anti-CTGF RNAi, Aplidin, astragalus membranaceus extract with salvia and schisandra chinensis, atherosclerotic plaque blocker, Azol, AZX100, BB3, connective tissue growth factor antibody, CT140, danazol, Esbriet, EXCOOl, EXC002, EXC003, EXC004, EXC005, F647, FG3019, Fibrocorin, Follistatin, FT011, a galectin-3 inhibitor, GKT137831, GMCTOl, GMCT02, GRMDOl, GRMD02, GRN510, Heberon Alfa R, interferon α-2β, ITMN520, JKB119, JKB121, JKB122, KRX168, LPA1 receptor antagonist, MGN4220, MIA2, microRNA 29a oligonucleotide, MMI0100, noscapine, PBI4050, PBI4419, PDGFR inhibitor, PF-06473871, PGN0052, Pirespa, Pirfenex, pirfenidone, plitidepsin, PRM151, Pxl02, PYN17, PYN22 with PYN17, Relivergen, rhPTX2 fusion protein, RXI109, secretin, STX100, TGF-β Inhibitor, transforming growth factor, β- receptor 2 oligonucleotide, VA999260, XV615 or a combination thereof.
[00110] In yet another embodiment, a methods for determining the likelihood of response to one or more of the following angiogenesis inhibitors is provided: pazopanib (Votrient), sunitinib (Sutent), sorafenib (Nexavar), axitinib (Inlyta), ponatinib (Iclusig), vandetanib (Caprelsa), cabozantinib (Cometrig), ramucirumab (Cyramza), regorafenib (Stivarga), ziv-aflibercept (Zaltrap), or a combination thereof. In yet another embodiment, the angiogenesis inhibitor is a VEGF inhibitor. In a further embodiment, the VEGF inhibitor is axitinib, cabozantinib, aflibercept, brivanib, tivozanib, ramucirumab or motesanib. In yet a further embodiment, the angiogenesis inhibitor is motesanib.
[00111] In one embodiment, the methods provided herein relate to determining a subject's likelihood of response to an antagonist of a member of the platelet derived growth factor (PDGF) family, for example, a drug that inhibits, reduces or modulates the signaling and/or activity of PDGF-receptors (PDGFR). For example, the PDGF antagonist, in one embodiment, is an anti-PDGF aptamer, an anti-PDGF antibody or fragment thereof, an anti- PDGFR antibody or fragment thereof, or a small molecule antagonist. In one embodiment, the PDGF antagonist is an antagonist of the PDGFR-a or PDGFR-β. In one embodiment, the PDGF antagonist is the anti-PDGF-β aptamer El 0030, sunitinib, axitinib, sorefenib, imatinib, imatinib mesylate, nintedanib, pazopanib HC1, ponatinib, MK-2461, dovitinib, pazopanib, crenolanib, PP-121, telatinib, imatinib, KRN 633, CP 673451, TSU-68, Ki8751, amuvatinib, tivozanib, masitinib, motesanib diphosphate, dovitinib dilactic acid, linifanib (ABT-869). EXAMPLES
[00112] The present invention is further illustrated by reference to the following
Examples. However, it should be noted that these Examples, like the embodiments described above, is illustrative and is not to be construed as restricting the scope of the invention in any way.
Example 1- Methods to validate a 57 gene expression Lung Subtype Panel (LSP)
[00113] Several publically available lung cancer gene expression data sets including 2,168 lung cancer samples (TCGA, NCI, UNC, Duke, Expo, Seoul, Tokyo, and France) were assembled to validate a 57 gene expression Lung Subtype Panel (LSP) developed to complement morphologic classification of lung tumors. LSP included 52 lung tumor classifying genes plus 5 housekeeping genes. Data sets with both gene expression data and lung tumor morphologic classification were selected. Three categories of genomic data were represented in the data sets: Affymetrix U133+2 (n=883) (also referred to as "A-833"), Agilent 44K (n=334) (also referred to as "A-334"), and Illumina RNAseq (n=951) (also referred to as "1-951"). Data sources are provided in Table 7 and normalization methods in Table 8. Samples with a definitive diagnosis of adenocarcinoma, carcinoid, small cell, and squamous cell carcinoma were used in the analysis.
Figure imgf000062_0001
Table 7. Data sources for publicly available lung cancer gene expression data
Source Platform(s) N Subtype Ref
Sci Transl Med all histology
French8 HG-U133+2 307 (2013)
subtypes
PMID: 23698379 adenocarcinoma and Nature (2006)
Duke9 HG-U133+2 118
squamous PMID: 16273092
PLoS One (2012)
Tokyo10 HG-U133+2 246 adenocarcinomas PMID: 22080568,
23028479
'https ://tcga-data.nci.nih.gov/tcgafiles/ftp auth/distro ftpusers/anonymous/tumor/luad/cgcc/unc.edu/ illuminahiseq_rnaseqv2/ rnaseqv2/? C= S ; 0= A
2https ://tcga-data.nci.nih.gov/tcgafiles/fitp auth/distro ftpusers/anonymous/tumor/lusc/cgcc/unc.edu/ illuminahiseq^rnaseqv2/rnaseqv2/
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17710
4http://www.ncbi. nlm.nih.gov/geo/queiy/acc. cgi?acc=GSE26939
5http : //re search, agendia. com/
6http://www.ncbi. nlm.nih.gov/geo/queiy/acc. cgi?acc=GSE8894
7http://www. ncbi. nlm.nih.gov/geo/queiy/acc. cgi?acc=GSE2109
8http://www.ncbi.nlm.nih.gov/geo/queiy/acc.cgi?acc=GSE30219
http://www. ncbi. nlm.nih.gov/geo/queiy/acc.cgi?acc=GSE3141
10http://www.ncbi. nlm.nih.gov/geo/query/acc. cgi?acc=GSE31210
Figure imgf000063_0001
[00114] The A-833 dataset was used as training for calculation of adenocarcinoma, carcinoid, small cell carcinoma, and squamous cell carcinoma gene centroids according to methods described previously. Gene centroids trained on the A-833 data were then applied to the normalized TCGA and A-334 datasets to investigate LSP's ability to classify lung tumors using publicly available gene expression data. For the application of A-833 training centroids to the A-833 dataset, evaluation was performed using Leave One Out (LOO) cross validation. Spearman correlations were calculated for tumor sample gene expression results to the A-833 gene expression training centroids. Tumors were assigned a genomic-defined histologic type (carcinoid, small cell, adenocarcinoma and squamous cell carcinoma) corresponding to the maximally correlated centroids. A 2 class, 3 class, and 4 class prediction was explored. Correct predictions were defined as LSP calls matching the tumor's histologic diagnosis. Percent agreement was defined as the number of correct predictions divided by the number of all predictions and an agreement kappa statistic was calculated.
[00115] Ten lung tumor RNA expression datasets were combined into three platform specific data sets (A-833, A-334, and 1-951). The patient population was diverse and included smokers and nonsmokers with tumors ranging from Stage 1 - Stage IV. Sample characteristics and lung cancer diagnoses of the three datasets are included in Table 9.
Table 9: Sample Characteristics
Figure imgf000065_0001
II 146 NA NA
III 119 NA NA
IV 26 NA NA
Stage not available 305 322 770
Smoking
Smoker 386 NA NA
Nonsmoker 39 NA NA
Smoking status not 526 322 770
available
[00116] Predicted tumor type for a 2 class, 3 class, and 4 class predictor were compared with tumor morphologic classification and percent agreement and Fleiss' kappa was calculated for each predictor (Tables lOa-c).
Table 10a. A-833 dataset training gene centroids applied to 2 other publicly available lung cancer gene expression databases (TCGA & A-334) for a 2 class prediction of lung tumor type. LOO cross validation was performed for the A-833 dataset.
Figure imgf000066_0001
Figure imgf000067_0001
Table 10b. A-833 dataset training gene centroids applied to data from 2 other publicly available lung cancer gene expression databases (TCGA & A-334) for a 3 class prediction of lung tumor type. LOO cross validation was performed for the A-833 dataset.
Figure imgf000068_0001
Table 10c. A-833 dataset training gene centroids applied to data from 2 other publicly available lung cancer gene expression databases (TCGA & A-334) for a 4 class prediction of lung tumor type. LOO cross validation was performed for the A-833 dataset. Prediction
Histology TCGA RNAseq Agilent Affymetrix LOO Diagnosis
AD CA SC SQ Sum AD CA SC SQ Sum AD CA SC SQ Su m
Adeno- 428 2 20 18 468 138 2 5 29 174 389 1 3 97 490 carcinom
a (AD)
Carcinoi NA NA NA NA NA NA NA NA NA NA 1 22 0 0 23 d (CA)
Small NA NA NA NA NA NA NA NA NA NA 1 1 20 2 24 Cell (SC)
Squamou 23 2 15 443 483 27 0 3 118 148 27 1 5 194 227 s cell
carcinom
a (SQ)
Sum 451 4 35 461 951 165 2 8 147 322 418 25 28 293 764
% 92% 80% 82%
Agreeme
nt kappa 0.84 0.60 0.65
[00117] Evaluation of inter-observer reproducibility of lung cancer diagnosis based on morphologic classification alone has previously been published. Overall inter-observer agreement improved with simplification of the typing scheme. Using the comprehensive 2004 World Health Organization classification system inter-observer agreement was low (k = 0.25). Agreement improved with simplification of the diagnosis to the therapeutically relevant 2 type differentiation of squamous/non-squamous (k = 0.55). Agreement of inter- observer diagnosis is compared to agreement of 2, 3 and 4 class LSP diagnosis in this validation study (Table 1 1).
Table 11. Inter-observer agreement (3) measured using kappa statistic and LSP agreement with histologic diagnosis in multiple gene expression datasets.
Figure imgf000071_0001
[00118] Differentiation among various morphologic subtypes of lung cancer is increasingly important as therapeutic development and patient management become more specifically targeted to unique features of each tumor. Histologic diagnosis can be challenging and several studies have demonstrated limited reproducibility of morphologic diagnoses. The addition of several immunohistochemistry markers, such as p63 and TTF-1 improves diagnostic precision but many lung cancer biopsies are limited in size and/or cellularity precluding full characterization using multiple IHC markers. Agreement was markedly better for all the classifiers (2,3, and 4 type) in the TCGA RNAseq dataset (% agreement range 91%-94%) as compared to the other datasets possibly due to the greater accuracy of the histologic diagnosis and/or the greater precision of the RNA expression results. Despite several limitations described below, this study demonstrates that LSP, can be a valuable adjunct to histology in typing lung tumors.
[00119] In multiple datasets with hundreds of lung cancer samples, molecular profiling using the Lung Subtype Panel (LSP) compared favorably to light microscopic derived diagnoses, and showed a higher level of agreement than pathologist reassessments. RNA- based tumor subtyping can provide valuable information in the clinic, especially when tissue is limiting and the morphologic diagnosis remains unclear. [00120] The disclosures of the following references are incorporated herein by reference in their entireties for all purposes: a. American Cancer Society. Cancer Facts and Figures, 2014.
b. National Comprehensive Cancer Network (NCCN) Clinical Practice Guideline in Oncology. Non-Small Cell Lung Cancer. Version 2.2013.
c. Grilley Olson JE, Hayes DN, Moore DT, et al. Arch Pathol Lab Med 2013; 137: 32- 40
d. Thunnissen E, Boers E, Heideman DA, et al. Virchows Arch 2012; 461 :629-38.
e. Wilkerson MD, Schallheim JM, Hayes DN, et al. J Molec Diagn 2013; 15:485-497. f. Li B, Dewey CN. BMC Bioinformatics 2011, 12:323 doi: 10.1186/1471-2105-12-323 g. Yang YH, Dudoit S, Luu P, et al. Nucleic Acids Research 2002, 30:el5.
h. Hubbell E, Liu, W, Mei R. Bioinformatics (2002) 18 (12): 1585-1592. doi: 10.1093/bioinformatics/l 8.12.1585.
i. Travis WD, Brambilla E, Muller-Hermelink HK, Harris CC. Pathology and Genetics of Tumors of the Lung, Pleura, Thymus, and Heart. 3rd ed. Lyon, France: IARC Press; 2004. World Health Organization Classification of Tumors: vol 10.
j. Travis WD and Rekhtman N.. Sem Resp and Crit Care Med 2011; 32(1): 22-31.
Example 2 - Lung Cancer Subtyping of Multiple Fresh Frozen and Formalin Fixed Paraffin Embedded Lung Tumor Gene Expression Datasets
[00121] Multiple datasets comprising 2,177 samples were assembled to evaluate a Lung Subtype Panel (LSP) gene expression classifier. The datasets included several publically available lung cancer gene expression data sets, including 2,099 Fresh Frozen lung cancer samples (TCGA, NCI, UNC, Duke, Expo, Seoul, and France) as well as newly collected gene expression data from 78 FFPE samples. Data sources are provided in the Table 12 below. The 78 FFPE samples were archived residual lung tumor samples collected at the University of North Carolina at Chapel Hill (UNC-CH) using an IRB approved protocol. Only samples with a definitive diagnosis of AD, carcinoid, Small Cell Carcinoma (SCC), or SQC were used in the analysis. A total of 4 categories of genomic data were available for analysis: Affymetrix U133+2 (n=693), Agilent 44K (n=344), Illumina® RNAseq (n=l,062) and newly collected qRT-PCR (n=78) data. [00122] Archived FFPE lung tumor samples (n=78) were analyzed using a qRT-PCR gene expression assay as previously described (Wilkerson et al. J Molec Diagn 2013; 15:485-497, incorporated by reference herein in its entirety for all purposes) with the following modifications. RNA was extracted from one 10 μιτι section of FFPE tissue using the High Pure RNA Paraffin Kit (Roche Applied Science, Indianapolis, IN). Extracted RNA was diluted to 5 ng/μΕ and first strand cDNA was synthesized using gene specific 3' primers in combination with random hexamers (Superscript III®, Invitrogen®, Thermo Fisher Scientific Corp, Waltham, MA). An ABI 7900 (Applied Biosystems, Thermo Fisher Scientific Corp, Waltham, MA) was used for qRT-PCR with continuous SYBR green fluorescence (530nm) monitoring. ABI 7900 quantitation software generated amplification curves and associated threshold cycle (Ct) values. Original clinical diagnoses gathered with the samples is in Table 13
Table 12
Figure imgf000073_0001
2 squamous cell intensities are 2 based log GSE8894 carcinoma transformed, data matrix is row
Expo HG-U133 + 130 All histology (gene) median centered, column Ref 24
2 subtypes (sample) standardized30 GSE2109
French HG-U133 + 307 All histology Ref 25
2 subtypes GSE3021
9
Duke HG-U133 + 118 Adenocarcinoma, Ref 26
2 squamous cell GSE3141 carcinoma
U C FFPE tissue 78 Adenocarcinoma, FFPE sample gene expression Ref 27 RT-PCR squamous cell data was scaled to align gene Supplment carcinoma, small variance with Wilkerson et al. al File #1 cell & carcinoid data21. A gene-specific scaling
factor was calculated that took
into account label frequency
differences between the data sets.
Table 13
Sample Label
VELO001 Squamous.Cell.Carcinoma
VELO002 Squamous.Cell.Carcinoma
VELO004 Adenocarcinoma
VELO006 Squamous.Cell.Carcinoma
VELO007 Squamous.Cell.Carcinoma
VELO008 Squamous.Cell.Carcinoma
VELO010 Squamous.Cell.Carcinoma
VELO011 Squamous.Cell.Carcinoma
VELO012 Squamous.Cell.Carcinoma
VELO013 Squamous.Cell.Carcinoma
VELO014 Squamous.Cell.Carcinoma
VELO015 Adenocarcinoma
VELO016 Squamous.Cell.Carcinoma
VELO017 Squamous.Cell.Carcinoma
VELO018 Squamous.Cell.Carcinoma
VELO019 Squamous.Cell.Carcinoma
VELO020 Adenocarcinoma
VELO021 Adenocarcinoma
VELO022 Adenocarcinoma
VELO023 Adenocarcinoma
VELO024 Adenocarcinoma
VELO025 Adenocarcinoma
VELO026 Adenocarcinoma
VELO027 Adenocarcinoma
VELO028 Adenocarcinoma
VELO029 Adenocarcinoma
VELO030 Adenocarcinoma
VELO031 Adenocarcinoma
VELO032 Adenocarcinoma
VELO033 Adenocarcinoma
VELO034 Adenocarcinoma
VELO035 Adenocarcinoma
VELO036 Adenocarcinoma
VELO037 Adenocarcinoma
VELO038 Squamous.Cell.Carcinoma
VELO039 Squamous.Cell.Carcinoma
VELO040 Squamous.Cell.Carcinoma
VELO042 Squamous.Cell.Carcinoma
VELO044 Squamous.Cell.Carcinoma
VELO046 Squamous.Cell.Carcinoma
VELO048 Squamous.Cell.Carcinoma
VELO049 Squamous.Cell.Carcinoma Table 13
VELO050 Adenocarcinoma
VELO041 Squamous. Cell. Carcinoma
VELO043 Squamous. Cell. Carcinoma
VELO045 Squamous. Cell. Carcinoma
VELO055 Neuroendocrine
VELO056 Neuroendocrine
VELO057 Neuroendocrine
VELO058 Neuroendocrine
VELO059 Neuroendocrine
VELO060 Neuroendocrine
VELO061 Neuroendocrine
VELO062 Neuroendocrine
VELO063 Neuroendocrine
VELO064 Neuroendocrine
VELO065 Neuroendocrine
VELO066 Neuroendocrine
VELO067 Neuroendocrine
VELO068 Neuroendocrine
VELO069 Neuroendocrine
VELO070 Neuroendocrine
VELO071 Neuroendocrine
VELO072 Neuroendocrine
VELO073 Neuroendocrine
VELO074 Neuroendocrine
VELO075 Neuroendocrine
VELO076 Neuroendocrine
VELO077 Neuroendocrine
VELO078 Neuroendocrine
VELO079 Neuroendocrine
VELO080 Neuroendocrine
VELO081 Neuroendocrine
VELO082 Neuroendocrine
VELO083 Neuroendocrine
VELO084 Neuroendocrine
VELO085 Neuroendocrine
[00123] Pathology review was only possible for the FFPE lung tumor cohort in which additional sections were collected and imaged. Two contiguous sections from each sample were Hematoxylin & Eosin (H&E) stained and scanned using an Aperio™ ScanScope® slide scanner (Aperio Technologies, Vista, CA). Virtual slides were viewable at magnifications equivalent to 32 to 320 objectives (340 magnifier). Pathologist review was blinded to the original clinical diagnosis and to the gene expression-based subtype classification. Pathology review-based histological subtype calls were compared to the original diagnosis (n=78). Agreement of pathology review was defined as those samples for which both slides were assigned the same subtype as the original diagnosis.
[00124] All statistical analyses were conducted using R 3.0.2 software (http://cran.R- project.org). Data analyses were conducted separately for FF and for FFPE tumor samples.
[00125] Fresh Fro zen Palai et Anal)' sis : Datasets were normalized as described in Table 12. The Affymetrix dataset served as the training set for calculation of AD, carcinoid, SCC, and SQC gene centroids according to methods described previously (Wilkerson et al. PLoS ONE. 2012; 7(5) e36530. Doi: 10.1371/journal.pone.0036530; Wilkerson et al. J Molec Diagn 2013; 15:485-497, each of which is incorporated by reference herein in its entirety for all purposes)
[00126] Affymetrix training gene centroids are provided in Table 14. The training set gene centroids were tested in normalized TCGA RNAseq gene expression and Agilent microarray gene expression data sets. Due to missing data from the public Agilent dataset, the Agilent evaluations were performed with a 47 gene classifier, rather than a 52 gene panel with exclusion of the following genes: CIB1 FOXH1, LIPE, PCAM1, TUBAL
Table 14.
Gene Adenocarcinoma Neuroendocrine Squamous. Cell. Carcinoma
ABCC5 -0.453 0.3715 1.1245
ACVR1 0.0475 0.3455 -0.0465
ALDH3B1 0.4025 -0.638 -0.401
ANTXR1 -0.0705 -0.478 0.014
BMP7 -0.532 -0.6265 0.6245
CACNB1 0.024 0.157 -0.039
CAPG 0.109 -1.9355 -0.0605
CBX1 -0.2045 0.745 0.187
CDH5 0.391 0.145 -0.352
CDKN2C -0.0045 1.496 0.004
CHGA -0.143 5.7285 0.1075
CIB1 0.1955 -0.261 -0.065
CLEC3B 0.449 0.6815 -0.3085
CYB5B 0.058 1.487 -0.03
DOK1 0.233 -0.355 -0.183
DSC3 -0.781 -0.8175 4.3445 Table 14.
Gene Adenocarcinoma Neuroendocrine Squamous. Cell. Carcinoma
FEN1 -0.5025 -0.0195 0.4035
FOX HI -0.0405 0.1315 -0.0105
GJB5 -1.388 -1.5505 0.7685
HOXD1 0.17 -0.462 -0.288
HPN 0.5335 0.444 -0.736
HYAL2 0.1775 0.073 -0.143
ICA1 0.3455 1.048 -0.233
ICAM5 0.13 -0.145 -0.12
INSM1 0.0705 7.5695 -0.0245
ITGA6 -0.709 0.029 1.074
LGALS3 0.1805 -1.1435 -0.2305
LIPE 0.0065 0.5225 -0.0015
LRP10 0.2565 -0.087 -0.16
MAPRE3 -0.0245 0.6445 -0.0025
ME3 0.3085 0.3415 -0.2915
MGRN1 0.429 0.8075 -0.3775
MYBPH 0.04 -0.193 -0.054
MY07A 0.083 -0.287 -0.109
NFIL3 -0.332 -1.0425 0.3095
PAICS -0.2145 0.3915 0.2815
PAK1 -0.112 0.6095 0.0965
PCAM1 0.232 -0.256 -0.144
PIK3C2A 0.1505 0.597 -0.021
PLEKHA6 0.4465 2.0785 -0.2615
PSMD14 -0.251 0.5935 0.1635
SCD5 -0.1615 0.06 0.13
SFN -0.789 -3.026 0.91
SIAH2 -0.5795 0.1895 0.7175
SNAP91 -0.0255 3.818 0.003
STMN 1 -0.0995 1.2095 0.1405
TCF2 0.2835 -0.5175 -0.4665
TCP1 -0.1685 0.9815 0.1985
TFAP2A -0.374 -0.5075 0.3645
TITF1 1.482 0.1525 -1.2755
TRIM29 -1.0485 -1.318 1.379
TUBA1 0.155 1.71 -0.07
Table 15.
Gene Adenocarcinoma Neuroendocrine Squamous. Cell. Carcinoma
ABCC5 -1.105993 0.53584995 0.28498017
ACVR1 -0.1780792 0.27746814 -0.1331305 Table 15.
Gene Adenocarcinoma Neuroendocrine Squamous. Cell. Carcinoma
ALDH3B1 2.21915126 -1.0930042 0.82709803
ANTXR1 0.14704523 -0.0027417 -0.1000265
CACNB1 -0.2032444 0.36015235 -0.7588385
CAPG 0.52784999 -0.6495988 -0.0218352
CBX1 -0.5905845 -0.0461076 -0.2776489
CDH5 -0.1546498 0.53564677 -0.9166437
CDKN2C -1.8382992 -0.1614815 -0.7501799
CHGA -6.2702431 8.18090411 -7.4497926
CIB1 0.29948877 -0.1804507 0.06141265
CLEC3B 0.1454466 0.86221597 -0.6686516
CYB5B -0.1957799 0.13060667 -0.2393801
D0K1 0.03629227 0.03029676 -0.2861762
DSC3 0.76811006 -2.2230482 4.45353398
FEN1 -0.4100344 -0.774919 0.19244803
FOX HI 1.36365962 -1.1539159 1.86758359
GJB5 2.19942372 -3.2908475 4.00132739
HOXD1 -0.069692 -0.3296808 0.50430984
HPN 0.62232864 -0.0416111 -0.5391064
HYAL2 0.47459315 -0.2332929 -0.0080073
ICA1 -0.8108302 1.25305275 -2.1742476
ICAM5 2.12506546 -2.2078991 2.89691121
INSM1 -2.4346556 1.92393374 -1.9749654
ITGA6 -0.7881662 0.36443897 0.54978058
LGALS3 -0.8270046 0.79512054 -0.9453521
LIPE -0.2519692 0.29291064 -0.2216243
LRP10 0.09504093 0.14082188 -0.4042101
MAPRE3 -0.6806204 1.2417945 -0.5496704
ME3 0.17668171 0.67674964 -1.581183
MGRN1 -0.0839601 0.35069923 -0.6885404
MYBPH 0.73519429 -0.9569161 1.14344753
MY07A 0.58098661 -0.2096425 0.0488886
NFIL3 0.22274434 -0.337858 0.66234639
PAICS -0.2423309 -0.1863934 0.39037381
PAK1 -0.3803406 0.15627507 0.0677904
PCAM1 0.03655586 0.32457357 -0.6957339
PIK3C2A -0.3868824 0.56861416 -0.6629455
PLEKHA6 -0.4007847 1.31002812 -1.9802266
PSMD14 -0.5115938 0.27513479 -0.2847234
SCD5 -0.4770619 -0.4338812 0.56043153
SFN 0.35719248 -1.4361124 2.34498532
SIAH2 -0.4222382 -0.3853078 0.43237756
SNAP91 -5.5499562 4.65742276 -2.5441741 Table 15.
Gene Adenocarcinoma Neuroendocrine Squamous. Cell. Carcinoma
STMN 1 -1.4075058 0.49776156 -1.017481
TCF2 1.96819785 -0.4121173 -0.6555613
TCP1 -2.9255287 2.322428 -2.3059797
TFAP2A 2.02528144 -2.9053184 3.62844763
TITF1 0.46476685 -9.82E-05 -1.7079242
TRIM29 -1.6554559 -0.6463626 2.94818107
TUBA1 1.77126501 -2.0395783 1.58902579
[00127] Evaluation of the Affymetrix data was performed using Leave One Out (LOO) cross validation. Spearman correlations were calculated for tumor test sample to the Affymetrix gene expression training centroids. Tumors were assigned a genomic-defined histologic type (AD, SQC, or NE) corresponding to the maximally correlated centroids. Correct predictions were defined as LSP calls matching the tumor's original histologic diagnosis. Percent agreement was defined as the number of correct predictions divided by the number of total predictions and an agreement kappa statistic was calculated.
[00128] qRT-PCR from FFPE sample analysis: Previously published training centroids (Wilkerson et al. J Molec Diagn 2013; 15:485-497, incorporated by reference herein), calculated from qRT-PCR data of FFPE lung tumor samples, were cross-validated in this new sample set of qRT-PCR gene expression from FFPE lung tumor tissue. Wilkerson et al. AD and SQC centroids were used as published (Wilkerson et al. J Molec Diagn 2013; 15:485- 497, incorporated by reference herein). Neuroendocrine gene centroids were calculated similarly using published gene expression data (n=130) (Wilkerson et al. J Molec Diagn 2013; 15:485-497, incorporated by reference herein). The Wilkerson et al. gene centroids (Wilkerson et al. J Molec Diagn 2013; 15:485-497, incorporated by reference herein) for the FFPE tissue evaluation are included in Table 15. FFPE sample gene expression data was scaled to align gene variance with Wilkerson et al. data. A gene-specific scaling factor was calculated that took into account label frequency differences between the data sets. Gene expression data was then median centered, sign flipped (high Ct = low abundance), and scaled using the gene specific scaling factor. Subtype was predicted by correlating each sample with the 3 subtype centroids and assignment of the subtype with the highest correlation centroid (Spearman correlation). [00129] Ten iung tumor gene expression daiasets including nine FF plus one new FFPE qRT-PCR gene expression dataset were combined into four platform-specific data sets (Affymetrix, Agilent, lilumina RNAseq, and qRT-PCR). For the datasets where clinical information was available, the patient population was diverse and included smokers and nonsmokers with tumors ranging from Stage 1 - Stage IV. Sample characteristics and lung cancer diagnoses of the datasets used in this study are included in Table 16. After exclusion of samples without a definitive diagnosis of AD, SQC, SCC, or carcinoid, and exclusion of 1 FFPE sample that failed qRT-PCR analysis, the following samples were available for further data analysis: Affymetrix (n=538), Agilent (n=322), lilumina RNAseq (n=951) and qRT- PCR (n=77).
Figure imgf000081_0001
[00130] As a means of de novo evaluation of the new FFPE data set, we performed hierarchical clustering of LSP gene expression from the FFPE archived samples (n=77); as expected, this analysis demonstrated three clusters/subtypes corresponding to AD, SQC, and NE (FIG. 2). The predetermined LSP 3-subtype centroid predictor was then applied to all 4 datasets, and results were compared with tumor morphologic classifications. Percent agreement and Fleiss' kappa were calculated for each dataset (Table 17). The percent agreement ranged from 78% - 91% and kappa's from 0.57 - 0.85.
[00131] As another means of assessing independent pathology agreement, the agreement of blinded pathology review of the 77 FFPE lung tumors with the original morphologic diagnosis was found to be 82% (63/77). In 12/77 cases, blinded duplicate slides provided conflicting results and in 10/77 cases, at least one of the duplicates had a non-definitive pathological subtype classification of "Adenosquamous", "Large Cell", or "High grade poorly differentiated carcinoma". Comparison of the original morphologic diagnosis, blinded pathology review, and gene expression LSP subtype call for each of the 77 samples is shown in FIG. 3. Details of discordant sample overlap (i.e., 6 samples where tumor subtype disagreed with original morphology diagnosis by both path review and gene expression LSP call) are provided in Table 18. Overall, these concordance values of LSP relative to the original pathology calls were at least as great as the concordance between any two pathologists (Grilley et al. Arch Pathol Lab Med 2013; 137: 32-40; Thunnissen et al.
Virchows Arch 2012; 461(6):629-38. Doi: 10.1007/s00428-012-1234-x. Epub 2012 Oct 12; Thunnissen et al. Mod Pathol 2012; 25(12): 1574-83. Doi: 10.1038/modpathol.2012.106; each of which is incorporated by reference herein for all purposes) thus suggesting that the assay described herein performs at least as well as a trained pathologist.
[00132] In this study, LSP provided reliable subtype classifications, validating its performance across multiple gene expression platforms, and even when using FFPE specimens. Hierarchical clustering of the newly assayed FFPE samples demonstrated good separation of the 3 subtypes (AC, SQC, and NE) based on the levels of 52 classifier biomarkers. Concordance with morphology diagnosis when using the LSP centroids was greatest in the TCGA RNAseq dataset (agreement = 91%), possibly due to the very extensive pathology review and accuracy of the histologic diagnosis associated with TCGA samples as compared to other datasets. Agreement was lowest (78%) in the Agilent dataset, which may have been affected by the reduced number of genes that were available for that analysis. Overall, the LSP assay displayed a higher concordance with the original morphology diagnosis than the pathology review in all datasets except in the Agilent dataset, in which only 47 genes, rather than 52, were present for the analysis.
[00133] In the FFPE samples where blinded pathology re-review was possible, results suggested that pathology calls were not always consistent with the original diagnosis, nor were they necessarily consistent in the duplicate slides provided from each sample. For a subset of samples (n=6), both the pathology re-review and the LSP gene expression analysis suggested the same alternate diagnosis, leading one to question the accuracy of the original morphologic diagnosis, which was our "gold standard".
[00134] In this study, there were a low number of NE tumor samples in the Affymetrix dataset, and an absence of NE samples in both the Agilent and TCGA datasets. This was partially overcome by a relatively high number of NE samples in the FFPE sample set (31/77), thus providing a good test of the LSP signature's ability to identify NE samples. Another limitation of the study relates to the blinded pathology re-review. The blinded pathology review was based on two imaged sections and did not reflect usual histology standard practice where multiple sections/blocks and potentially IHC stains would have been available to make a diagnosis.
Incorporation by reference
[00135] The following references are incorporated by reference in their entireties for all purposes.
1. American Cancer Society. Cancer Facts and Figures, 2014.
2. National Comprehensive Cancer Network (NCCN) Clinical Practice Guideline in Oncology. Non-Small Cell Lung Cancer. Version 1.2015.
3. AVASTIN® (Bevacizumab) Genetech Inc, San Francisco, CA prescribing
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Thunnissen E, Beasley MB, Borczuk AC, et al. Reproducibility of histopathological subtypes and invasion in pulmonary adenocarcinoma. An international interobserver study. Mod Pathol 2012; 25(12): 1574-83. Doi: 10.1038/modpathol.2012.106.
Rekhtman N, Ang DC, Sima CS, Travis WD, Moreira AL. Immunnohistochemical algorithm for differentiation of lung adenocarcinoma and squamous cell carcinoma based on large series of whole-tissue sections with validation in small specimens. Modern Path. 2011; 24: 1348-1359.
Travis WD, BrambillaE, Riley GJ, New pathologic classification of lung cancer: relevance for clinical practice and clinical trials. J Clin Oncol 2013; 31 :992-1001. Thunnissen E, Noguchi M, Aisner S, et al. Reproducibility of histopathological diagnosis in poorly differentiated NSCLC: an international multiobserver study. J Thorac Oncol 2014; 9(9): 1354-62. doi: 10. 1097/JTO.0000000000000264.
Travis WD and Rekhtman N. Pathological diagnosis and classification of lung cancer in small biopsies and cytology: strategic management of tissue for molecular testing. Sem Resp and Crit Care Med 2011; 32(1): 22-31.
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Shedden K, Taylor JMG, Enkemann SA, et al. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study: director's challenge consortium for the molecular classification of lung adenocarcinoma. Nat Med 2008. 14(8): 822-827. doi: 10.1038/nm. l790.
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Roepman P, et al. An immune response enriched 72-gene prognostic profile for early- stage non-small-cell lung cancer. Clinical Cancer Research 15.1 (2009): 284-290. Lee ES, et al. Prediction of recurrence-free survival in postoperative non-small cell lung cancer patients by using an integrated model of clinical information and gene expression." Clinical Cancer Research 14.22 (2008): 7397-7404.
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Faruki H, Miglarese M, Mayhew G, et al. Validation of a RT-PCR Gene Expression Assay for Subtyping Lung Tumor Samples. Abstract #4222. Presented at the Association of Molecular Pathology Annual Meeting in Baltimore, MD. Nov 12-15, 2014. 28. Li B, and Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011, 12:323
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31. Rekhtman N, Tafe LJ, Chaft JE, et al. Distinct profile of driver mutations and clinical features in immunomarker-defined subsets of pulmonary large-cell carcinoma. Mod Pathol 2013; 26(4): 511-22. doi: 10.1038/modpathol.2012.195.
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Table 17. Subtype prediction and agreement with morphologic diagnosis for multiple validation datasets analyzed by the gene expression LSP gene signature. (Results shown below were in part based upon data generated by the TCGA Research Network:
http://cancergenome.nih.gov/).
Figure imgf000086_0001
endocrine
(NE)*
Squamous 22 II 11 II 450 || 483 27 II 1 II 120 II 148 26 II 0 II 201 II 227 1 II 1 II 23 II 25 cell (SQ)
Sum 441 II 32 II 478 || 951 158 II 7 II 157 II 322 276 II 43 || 219 || 538 15 II 32 II 30 || 77
% 91% (869/951) 78% (251/322) 91% (492/538) 84% (65/77)
Agreemen
t
Kappa 0.83 0.57 0.85 0.76
includes small cell carcinoma and carcinoid
Table 18. Original morphology diagnosis, blinded path review, and LSP subtype result details for 6 FFPE samples, in which both path review and LSP predicted subtype disagreed with the original morphologic diagnosis.
Figure imgf000087_0001
EXAMPLE 3 - Survival Differences of Adenocarcinoma Lung Tumors with Squamous Cell Carcinoma or Neuroendocrine Profiles by Gene Expression Subtyping.
[00136] As shown in FIGs. 4-7, the Lung Subtype Panel (LSP) 3-ciass (Adenocarcinoma (AD), Squamous Cell Carcinoma(SQ), and Neuroendocrine (NE)) nearest centroid predictor developed in array data and described herein was applied to histology defined AD samples of all stages in the Director's Challenge (Shedden et al., Affy array, n=442, FIG. 4), TCGA
(RNAseq, n=492, FIG. 5), and Tomida et al. (Agilent array, n=l 17, FIG. 6) datasets. Each histology defined AD sample was predicted as AD, SQ, or NE based on the LSP nearest centroid predictor. Kaplan Meier plots (FIGs. 4-7) and log rank tests for each dataset (FIGs. 4-6) and the pooled datasets (FIG. 7) were used to assess and compare 5-year overall survival in two groups, those that were histologically and gene expression (GE) concordant (AD-AD) and those that were histologically and GE discordant (AD predicted SQ or NE (AD-NE/SQ). Cox proportional Hazard Models were used to assess survival differences while controlling for T stage, N stage, and proliferation (as measured by the PAM 50 score: FIG. 12). The distribution of samples among the AD subtypes (Terminal Respiratory Unit(TRU), Proximal Proliferative(PP), and Proximal Inflammatory(PI)) was investigated.
[00137] For the analysis performed on the histology defined AD samples of all stages, the predictor confirmed AD subtype by GE in 80% of the histological AD samples, while the histological AD samples were called as GE subtypes of SQ and NE in 12% and 8% of cases, respectively. FThe AD-NE/SQ group (AD by histology and SQ or NE by gene expression LSP) had poorer survival than the AD-AD group (AD by both histology and LSP) in each data set (iogrank p- value in RNAseq, Director's, and Tomida were 1.17e-06, 0.0009, and 0.0001, respectively). Pooling the 3 data sets and using a stratified cox model that allowed for different baseline hazards in each study, the hazard ratio comparing AD-NE/SQ to AD- AD was 1 .84 (95% CI 1.48-2.30). When we fit the model adjusting for T stage, N stage, and proliferation score, the HR was 1.58 (95%> CI 1.22-2.04). Adenosubtype profiling of AD- NE/SQ samples indicated that tumors were overwhelmingly of the PP or PI AD subtypes (209/213).
[00138] Overall, --20% histologic-defmed lung adenocarcinoma (AD) differ in gene expression profiles. Histoiogy-GE discordant AD tumors show worse survival than concordant cases. Survival differences may be partially explained by elevated proliferation score (see FIG. 12). Survival differences may be due to tumor biology and/or to variable response to standard AD management regimens. Further, gene expression tumor subtyping may provide valuable clinical information identifying a subset of AD samples with poor prognosis. Poor prognosis adenocarcinoma samples belong to the PI and PP adenocarcinoma subtypes, and demonstrate elevated proliferation scores. This subset of AD tumors may be less responsive to standard adenocarcinoma management.
Incorporation by reference
[00139] The following references are incorporated by reference in their entireties for all purposes.
1. Shedden K, et al. Nat Med 2008. 14(8): 822-827.
2. TCGA Cancer Nature 2014: 511(7511): 543-550
3. Tomida S, J Clin Oncol 2009; 27(17): 2793-99.
4. Neilsen TO. Clin Cancer Res 2010.
EXAMPLE 4 - Survival Differences of Adenocarcinoma Lung Tumors with Squamous Cell Carcinoma or Neuroendocrine Profiles by Gene Expression Subtyping
[00140] As shown in FIGs. 8-11, the Lung Subtype Panel (LSP) 3-class (Adenocarcinoma (AD), Squamous Cell Carcinoma(SQ), and Neuroendocrine (NE)) nearest centroid predictor developed in array data and described herein was applied to histology defined AD samples of stages 1 and II in the Director's Challenge (Shedden et al, Affy array, n=371, FIG. 8), TCGA (RNAseq, n 384. FIG, 9), and Tomida et al. (Agilent array, n=92, FIG, 10) datasets. Each histology defined AD sample was predicted as AD, SQ, or NE based on the LSP nearest centroid predictor. Kaplan Meier plots (FIGs. 8-11) and log rank tests for each dataset (FIGs. 8-10) and the pooled datasets (FIG. 11) were used to assess and compare 5-year overall survival in two groups, those that were histologically and gene expression (GE) concordant (AD-AD) and those that were histologically and GE discordant (AD predicted SQ or NE (AD-NE/SQ). Cox proportional Hazard Models were used to examine the LSP hazard ratio and to compare it with several other prognostic panels, Wilkerson et al (506 genes) Wistuba et al (31 genes), Kratz et al (11 genes) and Zhu et al (15 genes). For Wistuba et al. , genes were weighted equally. For Kratz et al, genes were weighted according to the coefficients in the publication. For Zhu et al., genes were weighted -1 to +1 according to the direction of effect on OS in the TCGA AD data set. For Wilkerson et al., the risk score was calculated as distance to the TRU (bronchioid) centroid. Gene mutation prevalence was examined for significantly associated mutations of lung AD and SQ. The predictor confirmed AD subtype by GE in 81% of the histological AD samples, while the histological AD samples were called as GE subtypes of SQ and E in 12% and 7% of cases, respectively. The AD-NE/SQ group (AD by histology and SQ or NE by gene expression LSP) had poorer survival than the AD-AD group (AD by both histology and LSP) in each data set (see logrank p-value in FIGs. 8-10). Pooling the 3 data sets and using a stratified cox model that allowed for different baseline hazards in each study, the hazard ratio comparing AD-NE/SQ to AD- AD was 2.27 (95% CI 1.71 to 3) as shown in FIG. 11.
[00141] In agreement with the conclusions from Example 3, this analysis showed that -20% of histologically defined lung AD differ by gene expression subtype. Further, histology-GE discordant AD tumors demonstrate worse survival and are responsible for much of the prognostic risk in multiple prognostic gene signatures as shown in FIGs. 14 and 15. As shown in FIG. 13, mutation frequencies in Histology-GE discordant samples differ significantly from concordant samples for 9/48 genes evaluated. Finally, survival differences may be attributable to tumor biology and/or to variable response to standard AD
management.
Incorporation by reference
[00142] The following references are incorporated by reference in their entireties for all purposes.
1. Wilkerson MD et al, J Molec Diag 2013; 15:485-497.
2. Faruki H, et al. Archives Path & Lab Med. October 2015.
3. Shedden K, et al. Nat Med 2008. 14(8): 822-827.
4. TCGA Lung AdenoC. Nature 2014: 511(7511): 543-550
5. Tomida S, J Clin Oncol 2009; 27(17): 2793-99.
6. Wilkerson MD et al. Clin Cancer Res 2013; 19(22): 6261-6271.
7. Kratz JR, et al. Lancet 2012: 379 (9818): 823-832.
8. Zhu CQ, et al. J Clin Oncol 2010; 28(29); 4417-4424.
9. TCGA Lung SQCC. Nature 2012; 489(7417): 519-525. [00143] The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent application, foreign patents, foreign patent application and non-patent publications referred to in this specification and/or listed in the Application Data Sheet are incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary to employ concepts of the various patents, application and publications to provide yet further embodiments.
[00144] These and other changes can be made to the embodiments in light of the above- detailed description. In general, in the following claims, the terms used should not be construed to limit the claims to the specific embodiments disclosed in the specification and the claims, but should be construed to include all possible embodiments along with the full scope of equivalents to which such claims are entitled. Accordingly, the claims are not limited by the disclosure.

Claims

What is claimed is;
1. A method of assessing whether a patient's adenocarcinoma lung cancer subtype is squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative), the method comprising:
(a) probing levels of at least five classifier biomarkers of the classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 at in a lung cancer sample obtained from the patient at a nucleic acid level, wherein the probing step comprises ;
(i) mixing the sample with five or more oligonucleotides that are substantially complementary to portions of nucleic acid molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for hybridization of the five or more oligonucleotides to their complements or substantial complements;
(ii) detecting whether hybridization occurs between the five or more oligonucleotides to their complements or substantial complements;
(iii) obtaining hybridization values of the at least five classifier biomarkers based on the detecting step;
(b) comparing the hybridization values of the at least five classifier biomarkers to reference hybridization value(s) from at least one sample training set, wherein the at least one sample training set comprises, (i) hybridization value(s) of the at least five biomarkers from a sample that overexpresses the at least five biomarkers, or overexpresses a subset of the at least five biomarkers, (ii) hybridization values from a reference squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative) sample, or (iii) hybridization values from an adenocarcinoma free lung sample, and
(c) classifying the adenocarcinoma sample as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype based on the results of the comparing step.
2. The method of claim 1, wherein the comparing step comprises determining a
correlation between the hybridization values of the at least five classifier biomarkers and the reference hybridization values.
3. The method of claim 1, wherein the comparing step further comprises determining an average expression ratio of the at least five biomarkers and comparing the average expression ratio to an average expression ratio of the at least five biomarkers, obtained from the references values in the sample training set.
4. The method of any one of claims 1-3, wherein the probing step comprises isolating the nucleic acid or portion thereof prior to the mixing step.
5. The method of any one of claims 1 -4, wherein the hybridization comprises
hybridization of a cDNA probe to a cDNA biomarker, thereby forming a non-natural complex.
6. The method of any one of claims 1 -4, wherein the hybridization comprises
hybridization of a cDNA probe to an mRNA biomarker, thereby forming a non- natural complex.
7. The method of any one of claims 1-5, wherein the probing step comprises amplifying the nucleic acid in the sample.
8. The method of any one of claims 1 -7, wherein the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 1A, Table IB or Table 1C.
9. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 2.
10. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 3.
1 1. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise the 6 biomarkers of Table 4.
12. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise the 6 biomarkers of Table 5.
13. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 6.
14. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 1A, Table IB or Table 1 C.
15. The method of any one of claims 1 -7, wherein the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 2.
16. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 3.
17. The method of any one of claims 1 -7, wherein the at least five classifier biomarkers comprise from about 5 to about 30 classifier biomarkers, or from about 10 to about 30 classifier biomarkers of Table 6.
18. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise each of the classifier biomarkers set forth in Table 1A, Table IB or Table 1 C.
19. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise each of the classifier biomarkers set forth in Table 2.
20. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise each of the classifier biomarkers set forth in Table 3.
21. The method of any one of claims 1 -7, wherein the at least five of the classifier
biomarkers comprise each of the classifier biomarkers set forth in Table 6.
22. The method of any one of claims 1 -21, wherein the sample comprises lung cells embedded in paraffin.
23. The method of any one of claims 1-21 , wherein the sample is a fresh frozen sample.
24. The method according to any one of claims 1-21 , wherein the lung tissue sample is selected from a formalin-fixed, paraffin-embedded (FFPE) lung tissue sample, fresh and a frozen tissue sample.
25. The method of claim 18, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table 1 A.
26. The method of claim 18, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table IB.
27. The method of claim 18, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table 1 C.
28. A method for determining a disease outcome for a patient suffering from lung cancer, the method comprising: determining a subtype of the lung cancer through gene expression analysis of a first sample obtained from the patient to produce a gene expression based subtype; determining the subtype of the lung cancer through a morphological analysis of a second sample obtained from the patient to produce a morphological based subtype; and comparing the gene expression based subtype to the morphological based subtype, wherein a presence or absence of concordance between the gene expression based subtype and the morphological based subtype is predictive of the disease outcome.
29. The method of claim 28, wherein discordance between the gene expression based subtype and morphological based subtype is predictive of a poor disease outcome.
30. The method of claim 28 or 29, wherein the disease outcome is overall survival.
31. The method of any of claims 28-30, wherein the gene expression base subtype and/or morphological based subtype is adenocarcinoma, squamous cell carcinoma, or neuroendocrine.
32. The method claim 31, wherein the neuroendocrine encompasses small cell carcinoma and carcinoid.
33. The method of any one of claims 28-32, wherein the first sample and/or the second sample is a formalin-fixed, paraffin-embedded (FFPE) lung tissue sample, fresh, or a frozen tissue sample.
34. The method of any one of claims 28-33, wherein the first sample and the second sample are portions of an identical sample.
35. The method of any one of claims 28-34, wherein the gene expression analysis
comprises determining expression levels of at least five classifier biomarkers in Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 at a nucleic acid level in the first sample by performing RNA sequencing, reverse transcriptase polymerase chain reaction (RT-PCR) or hybridization based analyses.
36. The method of claim 35, wherein the RT-PCR is quantitative real time reverse
transcriptase polymerase chain reaction (qRT-PCR).
37. The method of claim 35, wherein the RT-PCR is performed with primers specific to the at least five classifier biomarkers; comparing the detected levels of expression of the at least five classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 to the expression of the at least five classifier biomarkers in at least one sample training set(s), wherein the at least one sample training set comprises expression data of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 from a reference adenocarcinoma sample, expression data of the at least five classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 from a reference squamous cell carcinoma sample, expression data of the at least five classifier biomarkers of Table 1A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6 from a reference neuroendocrine sample, or a combination thereof; and classifying the first sample as an adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype based on the results of the comparing step.
38. The method of claim 37, wherein the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the first sample and the expression data from the at least one training set(s); and classifying the first sample as an adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype based on the results of the statistical algorithm.
39. The method of claim 37 or 38 , wherein the primers specific for the at least five
classifier biomarkers are forward and reverse primers listed in Table 1 A, Table IB, Table 1 C, Table 2, Table 3, Table 4, Table 5 or Table 6.
40. The method of claim 35, wherein the hybridization based analysis comprises:
(a) probing the levels of at least five classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 in a lung cancer sample obtained from the patient at the nucleic acid level, wherein the probing step comprises;
(i) mixing the sample with five or more oligonucleotides that are substantially complementary to portions of nucleic acid molecules of the at least five classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 under conditions suitable for hybridization of the five or more
oligonucleotides to their complements or substantial complements;
(ii) detecting whether hybridization occurs between the five or more
oligonucleotides to their complements or substantial complements;
(iii) obtaining hybridization values of the at least five classifier biomarkers based on the detecting step;
(b) comparing the hybridization values of the at least five classifier biomarkers to
reference hybridization value(s) from at least one sample training set, wherein the at least one sample training set comprises hybridization values from a reference adenocarcinoma sample, hybridization values from a reference squamous cell carcinoma sample, hybridization values from a reference neuroendocrine sample, or a combination thereof; and
(c) classifying the lung cancer sample as a adenocarcinoma, squamous cell carcinoma, or a neuroendocrine subtype based on the results of the comparing step.
41. The method of claim 40, wherein the comparing step comprises determining a
correlation between the hybridization values of the at least five classifier biomarkers and the reference hybridization values.
42. The method of claim 40, wherein the comparing step further comprises determining an average expression ratio of the at least five biomarkers and comparing the average expression ratio to an average expression ratio of the at least five biomarkers, obtained from the references values in the sample training set.
43. The method of any one of claims 40-42, wherein the probing step comprises isolating the nucleic acid or portion thereof prior to the mixing step.
44. The method of any one of claims 40 -43, wherein the hybridization comprises
hybridization of a cDNA probe to a cDNA biomarker, thereby forming a non-natural complex.
45. The method of any one of claims 40 -43, wherein the hybridization comprises
hybridization of a cDNA probe to an mRNA biomarker, thereby forming a non- natural complex.
46. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 1A, Table IB or Table 1 C.
47. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 2.
48. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 3.
49. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise the 6 biomarkers of Table 4.
50. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise the 6 biomarkers of Table 5.
51. The method of claim 35, wherein the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 6.
52. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 1A, Table IB or Table 1 C.
53. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 2.
54. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 3.
55. The method of claim 35, wherein the at least five classifier biomarkers comprise from about 5 to about 30 classifier biomarkers, or from about 10 to about 30 classifier biomarkers of Table 6.
56. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table 1A, Table IB or Table 1C.
57. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table 2.
58. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table 3.
59. The method of claim 35, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table 6.
60. The method of claim 56, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table 1A.
61. The method of claim 56, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table IB.
62. The method of claim 56, wherein the at least five of the classifier biomarkers
comprise each of the classifier biomarkers set forth in Table 1 C.
63. The method of any one of claims 28-62, wherein the morphological analysis of the second sample is a histological analysis.
64. A method of assessing whether a lung tissue sample from a human patient is a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative) adenocarcinoma lung cancer subtype, the method comprising: detecting expression levels of at least five of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 at the nucleic acid level by RNA-seq, a reverse transcriptase polymerase chain reaction (RT-PCR) or a hybridization assay with oligonucleotides specific to the classifier biomarkers;
comparing the detected levels of expression of the at least five of the classifier biomarkers of Table 1A, Table IB, Table 1C, Table 2, Table 3, Table 4, Table 5 or Table 6 to the expression levels of the at least five of the classifier biomarkers from at least one sample training set, wherein the at least one sample training set comprises, (i) expression levels(s) of the at least five biomarkers from a sample that
overexpresses the at least five biomarkers, or overexpresses a subset of the at least five biomarkers, (ii) expression levels from a reference squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or magnoid (proximal proliferative) sample, or (iii) expression levels from an adenocarcinoma free lung sample; and
classifying the lung tissue sample as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype based on the results of the comparing step.
65. The method of claim 64, wherein the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the lung tissue sample and the expression data from the at least one training set(s); and classifying the lung tissue sample as a squamoid (proximal inflammatory), bronchoid (terminal respiratory unit) or a magnoid (proximal proliferative) subtype based on the results of the statistical algorithm.
66. The method of claim 64 or 65, wherein the lung tissue sample is selected from a
formalin-fixed, paraffin-embedded (FFPE) lung tissue sample, fresh and a frozen tissue sample.
67. The method of claim 64, wherein the comparing step further comprises determining an average expression ratio of the at least five biomarkers and comparing the average expression ratio to an average expression ratio of the at least five biomarkers, obtained from the references values in the sample training set.
68. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 1A, Table IB or Table 1C.
69. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 2.
70. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 3.
71. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise the 6 biomarkers of Table 4.
72. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise the 6 biomarkers of Table 5.
73. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise at least 10 biomarkers, at least 20 biomarkers or at least 30 biomarkers of Table 6.
74. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 1A, Table IB or Table 1 C.
75. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 2.
76. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise from about 10 to about 30 classifier biomarkers, or from about 15 to about 40 classifier biomarkers of Table 3.
77. The method of any one of claims 64-67, wherein the at least five classifier biomarkers comprise from about 5 to about 30 classifier biomarkers, or from about 10 to about 30 classifier biomarkers of Table 6.
78. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 1A, Table IB or Table 1 C.
79. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 2.
80. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 3.
81. The method of any one of claims 64-67, wherein the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 6.
82. The method of claim 78, wherein the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 1 A.
83. The method of claim 78, wherein the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table IB.
84. The method of claim 78, wherein the at least five of the classifier biomarkers comprise each of the classifier biomarkers set forth in Table 1 C.
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