EP4320618A4 - Zellfreies dna-sequenzdatenanalyseverfahren zur untersuchung des nukleosomschutzes und der chromatzugänglichkeit - Google Patents

Zellfreies dna-sequenzdatenanalyseverfahren zur untersuchung des nukleosomschutzes und der chromatzugänglichkeit

Info

Publication number
EP4320618A4
EP4320618A4 EP22785557.4A EP22785557A EP4320618A4 EP 4320618 A4 EP4320618 A4 EP 4320618A4 EP 22785557 A EP22785557 A EP 22785557A EP 4320618 A4 EP4320618 A4 EP 4320618A4
Authority
EP
European Patent Office
Prior art keywords
investigating
cell
dna sequence
data analysis
analysis method
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP22785557.4A
Other languages
English (en)
French (fr)
Other versions
EP4320618A2 (de
Inventor
Gavin Ha
David Macpherson
Peter S Nelson
Anna-Lisa Doebley
Joseph B Hiatt
Sarkar Navonil De
Robert Patton
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Fred Hutchinson Cancer Center
Original Assignee
Fred Hutchinson Cancer Center
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Fred Hutchinson Cancer Center filed Critical Fred Hutchinson Cancer Center
Publication of EP4320618A2 publication Critical patent/EP4320618A2/de
Publication of EP4320618A4 publication Critical patent/EP4320618A4/de
Withdrawn legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
    • G16H20/10—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance relating to drugs or medications, e.g. for ensuring correct administration to patients
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems

Landscapes

  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Medical Informatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Public Health (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Epidemiology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biomedical Technology (AREA)
  • Primary Health Care (AREA)
  • Databases & Information Systems (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • Software Systems (AREA)
  • Medicinal Chemistry (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
EP22785557.4A 2021-04-08 2022-04-08 Zellfreies dna-sequenzdatenanalyseverfahren zur untersuchung des nukleosomschutzes und der chromatzugänglichkeit Withdrawn EP4320618A4 (de)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202163172590P 2021-04-08 2021-04-08
US202163276378P 2021-11-05 2021-11-05
PCT/US2022/024082 WO2022217096A2 (en) 2021-04-08 2022-04-08 Cell-free dna sequence data analysis method to examine nucleosome protection and chromatin accessibility

Publications (2)

Publication Number Publication Date
EP4320618A2 EP4320618A2 (de) 2024-02-14
EP4320618A4 true EP4320618A4 (de) 2025-08-27

Family

ID=83545807

Family Applications (1)

Application Number Title Priority Date Filing Date
EP22785557.4A Withdrawn EP4320618A4 (de) 2021-04-08 2022-04-08 Zellfreies dna-sequenzdatenanalyseverfahren zur untersuchung des nukleosomschutzes und der chromatzugänglichkeit

Country Status (5)

Country Link
EP (1) EP4320618A4 (de)
JP (1) JP2024515565A (de)
AU (1) AU2022255198A1 (de)
CA (1) CA3214391A1 (de)
WO (1) WO2022217096A2 (de)

Families Citing this family (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN115376616B (zh) * 2022-10-24 2023-04-28 臻和(北京)生物科技有限公司 一种基于cfDNA多组学的多分类方法及装置
EP4665867A2 (de) * 2023-02-13 2025-12-24 Delfi Diagnostics, Inc. Delfi-abgeleitete zellfreie dna-fragmentierungsmuster zur differenzierung histologischer subtypen von lungenkrebs auf nichtinvasive weise
US20250101528A1 (en) * 2023-09-22 2025-03-27 Centre For Novostics Uses of cell-free dna fragmentation patterns associated with epigenetic modifications
AU2024357837A1 (en) * 2023-10-13 2026-04-23 Dana-Farber Cancer Institute, Inc. Methods, kits and systems for determining the status of lung cancer and methods for treating lung cancer based on same
WO2025081100A1 (en) * 2023-10-13 2025-04-17 Precede Biosciences, Inc. Methods, kits and systems for determining the her2 status of cancer and methods for treating cancer based on same
WO2025081094A2 (en) * 2023-10-13 2025-04-17 Precede Biosciences, Inc. Methods, kits and systems for determining the er status of cancer and methods for treating cancer based on same
WO2025213034A1 (en) * 2024-04-05 2025-10-09 Predicine, Inc. Systems and methods for multiple biomarker analysis in cancer
WO2025245302A1 (en) * 2024-05-22 2025-11-27 Precede Biosciences, Inc. Methods, kits and systems for determining er activity of cancer and methods for treating cancer based on same
WO2025250678A1 (en) * 2024-05-28 2025-12-04 Genecentric Therapeutics, Inc. Methods and systems for porting tissue-based classifiers into liquid biopsy samples

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150005176A1 (en) * 2013-06-21 2015-01-01 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US20200087710A1 (en) * 2017-03-17 2020-03-19 Sequenom, Inc. Methods and processes for assessment of genetic mosaicism

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8725422B2 (en) * 2010-10-13 2014-05-13 Complete Genomics, Inc. Methods for estimating genome-wide copy number variations
US10497461B2 (en) * 2012-06-22 2019-12-03 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
EP4358097A1 (de) * 2014-07-25 2024-04-24 University of Washington Verfahren zur bestimmung von gewebe- und/oder zelltypen zur entstehung von zellfreier dna und verfahren zur identifizierung einer krankheit oder störung damit
US20190287645A1 (en) * 2016-07-06 2019-09-19 Guardant Health, Inc. Methods for fragmentome profiling of cell-free nucleic acids
EP3635133A4 (de) * 2017-06-09 2021-03-03 Bellwether Bio, Inc. Bestimmung des krebstyps bei einer person durch probabilistische modellierung von zirkulierenden nukleinsäurefragment-endpunkten
CN112805563B (zh) * 2018-05-18 2025-06-13 约翰·霍普金斯大学 用于评估和/或治疗癌症的无细胞dna
JP7747524B2 (ja) * 2019-05-14 2025-10-01 テンパス エーアイ，インコーポレイテッド マルチラベルがん分類のためのシステムおよび方法

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150005176A1 (en) * 2013-06-21 2015-01-01 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US20200087710A1 (en) * 2017-03-17 2020-03-19 Sequenom, Inc. Methods and processes for assessment of genetic mosaicism

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
DOEBLEY ANNA-LISA ET AL: "A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA", NATURE COMMUNICATIONS, vol. 13, no. 1, 3 December 2022 (2022-12-03), UK, XP093292028, ISSN: 2041-1723, Retrieved from the Internet <URL:https://www.nature.com/articles/s41467-022-35076-w> DOI: 10.1038/s41467-022-35076-w *
Y. BENJAMINI ET AL: "Summarizing and correcting the GC content bias in high-throughput sequencing", NUCLEIC ACIDS RESEARCH, vol. 40, no. 10, 9 February 2012 (2012-02-09), pages 1 - 14, XP055162924, ISSN: 0305-1048, DOI: 10.1093/nar/gks001 *

Also Published As

Publication number Publication date
WO2022217096A3 (en) 2022-12-29
WO2022217096A2 (en) 2022-10-13
AU2022255198A1 (en) 2023-11-23
JP2024515565A (ja) 2024-04-10
CA3214391A1 (en) 2022-10-13
EP4320618A2 (de) 2024-02-14

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