CA3101527A1 - Methods for fingerprinting of biological samples - Google Patents

Methods for fingerprinting of biological samples Download PDF

Info

Publication number
CA3101527A1
CA3101527A1 CA3101527A CA3101527A CA3101527A1 CA 3101527 A1 CA3101527 A1 CA 3101527A1 CA 3101527 A CA3101527 A CA 3101527A CA 3101527 A CA3101527 A CA 3101527A CA 3101527 A1 CA3101527 A1 CA 3101527A1
Authority
CA
Canada
Prior art keywords
nucleic acid
acid molecules
sample
genetic loci
fingerprint
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.)
Pending
Application number
CA3101527A
Other languages
English (en)
French (fr)
Inventor
Alexander De Jong Robertson
Rohith Kannappan SRIVAS
Timothy Joseph WILSON
Neil PETERMAN
Nicole Jacinda LAMBERT
Haluk TEZCAN
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 CA3101527A1 publication Critical patent/CA3101527A1/en
Pending 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • 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
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/40—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Medical Informatics (AREA)
  • Analytical Chemistry (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Data Mining & Analysis (AREA)
  • General Engineering & Computer Science (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
  • Evolutionary Computation (AREA)
  • Software Systems (AREA)
  • Library & Information Science (AREA)
  • Primary Health Care (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA3101527A 2018-06-06 2019-06-06 Methods for fingerprinting of biological samples Pending CA3101527A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201862681642P 2018-06-06 2018-06-06
US62/681,642 2018-06-06
PCT/US2019/035871 WO2019236906A1 (en) 2018-06-06 2019-06-06 Methods for fingerprinting of biological samples

Publications (1)

Publication Number Publication Date
CA3101527A1 true CA3101527A1 (en) 2019-12-12

Family

ID=68770618

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3101527A Pending CA3101527A1 (en) 2018-06-06 2019-06-06 Methods for fingerprinting of biological samples

Country Status (11)

Country Link
US (1) US20210151126A1 (https=)
EP (1) EP3791012A4 (https=)
JP (2) JP2021526857A (https=)
KR (1) KR20210022622A (https=)
CN (1) CN112384982A (https=)
AU (1) AU2019280867A1 (https=)
BR (1) BR112020024646A2 (https=)
CA (1) CA3101527A1 (https=)
IL (1) IL279184A (https=)
SG (1) SG11202011652QA (https=)
WO (1) WO2019236906A1 (https=)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN112349348A (zh) * 2020-11-05 2021-02-09 北京市农林科学院 分子标记指纹数据的比对方法、非暂存态存储介质和装置

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20230135171A1 (en) * 2019-12-24 2023-05-04 Lexent Bio, Inc. Methods and systems for molecular disease assessment via analysis of circulating tumor dna
US12518859B2 (en) * 2023-07-26 2026-01-06 Helix, Inc. Systems and methods for providing test results of gene sequencing data on a recurring basis
WO2025090739A1 (en) * 2023-10-27 2025-05-01 Grail, Inc. Systems and methods for assessing similarity between samples using genotype signatures

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020086289A1 (en) * 1999-06-15 2002-07-04 Don Straus Genomic profiling: a rapid method for testing a complex biological sample for the presence of many types of organisms
CA2786564A1 (en) * 2010-01-19 2011-07-28 Verinata Health, Inc. Identification of polymorphic sequences in mixtures of genomic dna by whole genome sequencing
WO2012058316A1 (en) * 2010-10-26 2012-05-03 Stanford University Non-invasive fetal genetic screening by sequencing analysis
KR102768285B1 (ko) * 2013-02-14 2025-02-13 더 리전츠 오브 더 유니버시티 오브 콜로라도, 어 바디 코퍼레이트 간질 폐렴의 위험을 예측하는 방법
CN106460062A (zh) * 2014-05-05 2017-02-22 美敦力公司 用于scd、crt、crt‑d或sca治疗识别和/或选择的方法和组合物

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN112349348A (zh) * 2020-11-05 2021-02-09 北京市农林科学院 分子标记指纹数据的比对方法、非暂存态存储介质和装置
CN112349348B (zh) * 2020-11-05 2023-10-13 北京市农林科学院 分子标记指纹数据的比对方法、非暂存态存储介质和装置

Also Published As

Publication number Publication date
JP2024056939A (ja) 2024-04-23
US20210151126A1 (en) 2021-05-20
SG11202011652QA (en) 2020-12-30
CN112384982A (zh) 2021-02-19
KR20210022622A (ko) 2021-03-03
BR112020024646A2 (pt) 2021-03-02
EP3791012A4 (en) 2022-03-09
WO2019236906A1 (en) 2019-12-12
IL279184A (en) 2021-01-31
EP3791012A1 (en) 2021-03-17
AU2019280867A1 (en) 2021-01-07
JP2021526857A (ja) 2021-10-11

Similar Documents

Publication Publication Date Title
KR102381477B1 (ko) 심층 신경망에 기반한 변이체 분류자
US11972841B2 (en) Machine learning system and method for somatic mutation discovery
US12385097B2 (en) Normalizing tumor mutation burden
US20210151126A1 (en) Methods for fingerprinting of biological samples
US12509732B2 (en) Methods of detecting tumor progression via analysis of cell-free nucleic acids
US20210358569A1 (en) Methods and systems for assessing microsatellite instability
CN113748467A (zh) 基于等位基因频率的功能丧失计算模型
US20220389522A1 (en) Methods of assessing and monitoring tumor load
JP2025028203A (ja) 脱アミノ化に誘導される配列エラーの補正
US20220068433A1 (en) Computational detection of copy number variation at a locus in the absence of direct measurement of the locus
CA3187387A1 (en) Methods and systems for efficient sample pooling for diagnostic testing

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20220923

D15 Examination report completed

Free format text: ST27 STATUS EVENT CODE: A-2-2-D10-D15-D126 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: EXAMINER'S REPORT

Effective date: 20250505

B12 Application deemed to be withdrawn, abandoned or lapsed

Free format text: ST27 STATUS EVENT CODE: N-6-6-B10-B12-B303 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: DEEMED ABANDONED - FAILURE TO RESPOND TO AN EXAMINER'S REQUISITION

Effective date: 20250905

W00 Other event occurred

Free format text: ST27 STATUS EVENT CODE: A-2-2-W10-W00-W100 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: LETTER SENT

Effective date: 20251121

U13 Renewal or maintenance fee not paid

Free format text: ST27 STATUS EVENT CODE: N-2-6-U10-U13-U300 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: DEEMED ABANDONED - FAILURE TO RESPOND TO MAINTENANCE FEE NOTICE

Effective date: 20260121