AU2019339511A1 - Methods and systems for assessing microsatellite instability - Google Patents

Methods and systems for assessing microsatellite instability Download PDF

Info

Publication number
AU2019339511A1
AU2019339511A1 AU2019339511A AU2019339511A AU2019339511A1 AU 2019339511 A1 AU2019339511 A1 AU 2019339511A1 AU 2019339511 A AU2019339511 A AU 2019339511A AU 2019339511 A AU2019339511 A AU 2019339511A AU 2019339511 A1 AU2019339511 A1 AU 2019339511A1
Authority
AU
Australia
Prior art keywords
subject
microsatellite
repeat elements
readable medium
transitory computer
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.)
Abandoned
Application number
AU2019339511A
Other languages
English (en)
Inventor
Nicole Jacinda LAMBERT
Neil PETERMAN
Alexander De Jong Robertson
Rohith Kannappan SRIVAS
Haluk TEZCAN
Ram YALAMANCHILI
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.)
Lexent Bio Inc
Original Assignee
Lexent Bio Inc
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 Lexent Bio Inc filed Critical Lexent Bio Inc
Publication of AU2019339511A1 publication Critical patent/AU2019339511A1/en
Abandoned 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
    • 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
    • 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
    • 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
    • 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
    • G16H20/40—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance relating to mechanical, radiation or invasive therapies, e.g. surgery, laser therapy, dialysis or acupuncture
    • 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
    • C12Q2600/156—Polymorphic or mutational markers
    • 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
    • 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

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Medical Informatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Zoology (AREA)
  • Pathology (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Bioethics (AREA)
  • Evolutionary Computation (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Data Mining & Analysis (AREA)
  • Artificial Intelligence (AREA)
  • Software Systems (AREA)
  • Databases & Information Systems (AREA)
  • Microbiology (AREA)
  • Oncology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Surgery (AREA)
  • Urology & Nephrology (AREA)
AU2019339511A 2018-09-14 2019-09-13 Methods and systems for assessing microsatellite instability Abandoned AU2019339511A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201862731718P 2018-09-14 2018-09-14
US62/731,718 2018-09-14
PCT/US2019/051138 WO2020056347A1 (en) 2018-09-14 2019-09-13 Methods and systems for assessing microsatellite instability

Publications (1)

Publication Number Publication Date
AU2019339511A1 true AU2019339511A1 (en) 2021-05-13

Family

ID=69777893

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2019339511A Abandoned AU2019339511A1 (en) 2018-09-14 2019-09-13 Methods and systems for assessing microsatellite instability

Country Status (11)

Country Link
US (1) US20210358569A1 (https=)
EP (1) EP3850111A4 (https=)
JP (1) JP7514224B2 (https=)
KR (1) KR20210092196A (https=)
CN (1) CN112955570B (https=)
AU (1) AU2019339511A1 (https=)
BR (1) BR112021004763A2 (https=)
CA (1) CA3112562A1 (https=)
IL (1) IL281417A (https=)
SG (1) SG11202102528UA (https=)
WO (1) WO2020056347A1 (https=)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP7539367B2 (ja) 2018-08-31 2024-08-23 ガーダント ヘルス， インコーポレイテッド 無細胞ｄｎａにおけるマイクロサテライト不安定性の検出
KR102781271B1 (ko) * 2021-08-10 2025-03-17 (주)디엑솜 현미부수체 지역의 서열 길이의 최대값과 최소값의 차이를 이용한 현미부수체 불안정성 진단방법
KR102688594B1 (ko) * 2021-08-10 2024-07-24 (주)디엑솜 현미부수체 지역의 서열 길이의 변화율을 이용한 현미부수체 불안정성 진단방법
CN114464257B (zh) * 2022-03-15 2025-02-25 郑州安图生物工程股份有限公司 一种基于二代测序的微卫星不稳定性检测方法及装置
CN118942537B (zh) * 2023-09-21 2026-01-23 杭州链康医学检验实验室有限公司 一种构建标记微卫星位点稳定性预测模型的方法

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2836606B1 (en) 2012-04-10 2021-12-29 Vib Vzw Novel markers for detecting microsatellite instability in cancer and determining synthetic lethality with inhibition of the dna base excision repair pathway
WO2014099979A2 (en) * 2012-12-17 2014-06-26 Virginia Tech Intellectual Properties, Inc. Methods and compositions for identifying global microsatellite instability and for characterizing informative microsatellite loci
WO2017008165A1 (en) * 2015-07-14 2017-01-19 British Columbia Cancer Agency Branch Classification method and treatment for endometrial cancers
EP3405574A4 (en) * 2016-01-22 2019-10-02 Grail, Inc. VARIANTS-BASED SICKNESS DIAGNOSTICS AND PURSUIT
GB201614474D0 (en) 2016-08-24 2016-10-05 Univ Of Newcastle Upon Tyne The Methods of identifying microsatellite instability
CN106755501B (zh) 2017-01-25 2020-11-17 广州燃石医学检验所有限公司 一种基于二代测序的同时检测微卫星位点稳定性和基因组变化的方法
CA3083787A1 (en) * 2017-12-01 2019-06-06 Personal Genome Diagnositics Inc. Process for microsatellite instability detection

Also Published As

Publication number Publication date
BR112021004763A2 (pt) 2021-08-03
KR20210092196A (ko) 2021-07-23
CA3112562A1 (en) 2020-03-19
SG11202102528UA (en) 2021-04-29
CN112955570B (zh) 2025-01-21
WO2020056347A1 (en) 2020-03-19
EP3850111A4 (en) 2022-06-29
JP2022500764A (ja) 2022-01-04
CN112955570A (zh) 2021-06-11
IL281417A (en) 2021-04-29
US20210358569A1 (en) 2021-11-18
EP3850111A1 (en) 2021-07-21
JP7514224B2 (ja) 2024-07-10

Similar Documents

Publication Publication Date Title
JP7022188B2 (ja) 無細胞核酸の多重解像度分析のための方法
JP7514224B2 (ja) マイクロサテライト不安定性を評価するための方法およびシステム
US12509732B2 (en) Methods of detecting tumor progression via analysis of cell-free nucleic acids
JP2020536509A (ja) 体細胞および生殖細胞系統バリアントを鑑別するための方法およびシステム
TW202010845A (zh) 組織特異性甲基化標記
US20220389522A1 (en) Methods of assessing and monitoring tumor load
US20240132965A1 (en) Highly sensitive method for detecting cancer dna in a sample
KR20210132139A (ko) 대립유전자 빈도에 기초한 기능 손실의 컴퓨터 모델링
JP2024056939A (ja) 生体試料のフィンガープリンティングのための方法
JP7763764B2 (ja) 標的バリアントがクローンレベルで存在しないことの有意性モデリング
CN111542616A (zh) 脱氨引起的序列错误的纠正
CN116134546A (zh) 用于诊断检验的有效样本混合的方法和系统

Legal Events

Date Code Title Description
MK5 Application lapsed section 142(2)(e) - patent request and compl. specification not accepted