CA3112562A1 - Methods and systems for assessing microsatellite instability - Google Patents

Methods and systems for assessing microsatellite instability Download PDF

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Publication number
CA3112562A1
CA3112562A1 CA3112562A CA3112562A CA3112562A1 CA 3112562 A1 CA3112562 A1 CA 3112562A1 CA 3112562 A CA3112562 A CA 3112562A CA 3112562 A CA3112562 A CA 3112562A CA 3112562 A1 CA3112562 A1 CA 3112562A1
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Prior art keywords
subject
microsatellite
repeat elements
readable medium
transitory computer
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Pending
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CA3112562A
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English (en)
French (fr)
Inventor
Alexander De Jong Robertson
Nicole Jacinda LAMBERT
Haluk TEZCAN
Ram YALAMANCHILI
Neil PETERMAN
Rohith Kannappan SRIVAS
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Lexent Bio Inc
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Lexent Bio Inc
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Publication of CA3112562A1 publication Critical patent/CA3112562A1/en
Pending legal-status Critical Current

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    • 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

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  • 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)
CA3112562A 2018-09-14 2019-09-13 Methods and systems for assessing microsatellite instability Pending CA3112562A1 (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
CA3112562A1 true CA3112562A1 (en) 2020-03-19

Family

ID=69777893

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3112562A Pending CA3112562A1 (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
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
AU2019339511A1 (en) 2021-05-13
EP3850111A1 (en) 2021-07-21
JP7514224B2 (ja) 2024-07-10

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