CN112218956A - 用于解析核酸混合物和混合细胞群体的方法和试剂及相关应用 - Google Patents

用于解析核酸混合物和混合细胞群体的方法和试剂及相关应用 Download PDF

Info

Publication number
CN112218956A
CN112218956A CN201980037564.3A CN201980037564A CN112218956A CN 112218956 A CN112218956 A CN 112218956A CN 201980037564 A CN201980037564 A CN 201980037564A CN 112218956 A CN112218956 A CN 112218956A
Authority
CN
China
Prior art keywords
nucleic acid
mixture
sequence
genotype
double
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
CN201980037564.3A
Other languages
English (en)
Chinese (zh)
Inventor
J·J·索尔克
C·C·瓦伦丁三世
P·达那赫
罗方吟
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.)
Twinstrand Biosciences Inc
Original Assignee
Twinstrand Biosciences 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 Twinstrand Biosciences Inc filed Critical Twinstrand Biosciences Inc
Publication of CN112218956A publication Critical patent/CN112218956A/zh
Pending legal-status Critical Current

Links

Images

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
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification
    • 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
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/143—Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
    • 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
    • C12Q2600/16—Primer sets for multiplex assays
    • 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
    • C12Q2600/172—Haplotypes

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Physics & Mathematics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CN201980037564.3A 2018-05-16 2019-05-16 用于解析核酸混合物和混合细胞群体的方法和试剂及相关应用 Pending CN112218956A (zh)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201862672573P 2018-05-16 2018-05-16
US62/672,573 2018-05-16
US201962811517P 2019-02-27 2019-02-27
US62/811,517 2019-02-27
PCT/US2019/032755 WO2019222560A1 (en) 2018-05-16 2019-05-16 Methods and reagents for resolving nucleic acid mixtures and mixed cell populations and associated applications

Publications (1)

Publication Number Publication Date
CN112218956A true CN112218956A (zh) 2021-01-12

Family

ID=68540783

Family Applications (1)

Application Number Title Priority Date Filing Date
CN201980037564.3A Pending CN112218956A (zh) 2018-05-16 2019-05-16 用于解析核酸混合物和混合细胞群体的方法和试剂及相关应用

Country Status (10)

Country Link
US (2) US20210292836A1 (https=)
EP (1) EP3794120A4 (https=)
JP (2) JP7497879B2 (https=)
KR (1) KR102873073B1 (https=)
CN (1) CN112218956A (https=)
AU (1) AU2019269635A1 (https=)
BR (1) BR112020023296A2 (https=)
CA (1) CA3099819A1 (https=)
SG (1) SG11202011050TA (https=)
WO (1) WO2019222560A1 (https=)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN120877853A (zh) * 2025-07-03 2025-10-31 武汉海希生物科技有限公司 一种基于二代测序数据检测嵌合率的方法和系统

Families Citing this family (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10844428B2 (en) 2015-04-28 2020-11-24 Illumina, Inc. Error suppression in sequenced DNA fragments using redundant reads with unique molecular indices (UMIS)
CA3006792A1 (en) 2015-12-08 2017-06-15 Twinstrand Biosciences, Inc. Improved adapters, methods, and compositions for duplex sequencing
SG11201906428SA (en) 2017-01-18 2019-08-27 Illumina Inc Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths
AU2018261332B2 (en) 2017-05-01 2024-12-05 Illumina, Inc. Optimal index sequences for multiplex massively parallel sequencing
EP3622089B1 (en) 2017-05-08 2024-07-17 Illumina, Inc. Method for sequencing using universal short adapters for indexing of polynucleotide samples
US11447818B2 (en) 2017-09-15 2022-09-20 Illumina, Inc. Universal short adapters with variable length non-random unique molecular identifiers
AU2018366213B2 (en) 2017-11-08 2025-05-15 Twinstrand Biosciences, Inc. Reagents and adapters for nucleic acid sequencing and methods for making such reagents and adapters
WO2019222560A1 (en) * 2018-05-16 2019-11-21 Twinstrand Biosciences, Inc. Methods and reagents for resolving nucleic acid mixtures and mixed cell populations and associated applications
BR112021000409A2 (pt) 2018-07-12 2021-04-06 Twinstrand Biosciences, Inc. Métodos e reagentes para caracterizar edição genômica, expansão clonal e aplicações associadas

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2013142389A1 (en) * 2012-03-20 2013-09-26 University Of Washington Through Its Center For Commercialization Methods of lowering the error rate of massively parallel dna sequencing using duplex consensus sequencing
US20170029900A1 (en) * 2015-07-20 2017-02-02 The Chinese University Of Hong Kong Methylation pattern analysis of haplotypes in tissues in a dna mixture
US20170121769A1 (en) * 2010-08-06 2017-05-04 Ariosa Diagnostics, Inc. Assay systems for genetic analysis
WO2017100441A1 (en) * 2015-12-08 2017-06-15 Twinstrand Biosciences, Inc. Improved adapters, methods, and compositions for duplex sequencing
WO2017139492A1 (en) * 2016-02-09 2017-08-17 Toma Biosciences, Inc. Systems and methods for analyzing nucelic acids

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20120034603A1 (en) * 2010-08-06 2012-02-09 Tandem Diagnostics, Inc. Ligation-based detection of genetic variants
IL269431B2 (en) * 2017-03-23 2025-05-01 Univ Washington Methods for targeted nucleic acid sequence enrichment with applications to error corrected nucleic acid sequencing
CA3093846A1 (en) * 2018-03-15 2019-09-19 Twinstrand Biosciences, Inc. Methods and reagents for enrichment of nucleic acid material for sequencing applications and other nucleic acid material interrogations
WO2019222560A1 (en) * 2018-05-16 2019-11-21 Twinstrand Biosciences, Inc. Methods and reagents for resolving nucleic acid mixtures and mixed cell populations and associated applications
BR112021000409A2 (pt) * 2018-07-12 2021-04-06 Twinstrand Biosciences, Inc. Métodos e reagentes para caracterizar edição genômica, expansão clonal e aplicações associadas

Patent Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20170121769A1 (en) * 2010-08-06 2017-05-04 Ariosa Diagnostics, Inc. Assay systems for genetic analysis
WO2013142389A1 (en) * 2012-03-20 2013-09-26 University Of Washington Through Its Center For Commercialization Methods of lowering the error rate of massively parallel dna sequencing using duplex consensus sequencing
US20150044687A1 (en) * 2012-03-20 2015-02-12 University Of Washington Through Its Center For Commercialization Methods of lowering the error rate of massively parallel dna sequencing using duplex consensus sequencing
US20170029900A1 (en) * 2015-07-20 2017-02-02 The Chinese University Of Hong Kong Methylation pattern analysis of haplotypes in tissues in a dna mixture
WO2017100441A1 (en) * 2015-12-08 2017-06-15 Twinstrand Biosciences, Inc. Improved adapters, methods, and compositions for duplex sequencing
US20170211140A1 (en) * 2015-12-08 2017-07-27 Twinstrand Biosciences, Inc. Adapters, methods, and compositions for duplex sequencing
WO2017139492A1 (en) * 2016-02-09 2017-08-17 Toma Biosciences, Inc. Systems and methods for analyzing nucelic acids

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
KIDD, KENNETH K等: "Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics", FORENSIC SCIENCE INTERNATIONAL: GENETICS, vol. 12, pages 215 - 224, XP029006955, DOI: 10.1016/j.fsigen.2014.06.014 *
SALK, JESSE J等: "Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations", NATURE REVIEWS GENETICS, vol. 19, no. 5, pages 4 - 6 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN120877853A (zh) * 2025-07-03 2025-10-31 武汉海希生物科技有限公司 一种基于二代测序数据检测嵌合率的方法和系统

Also Published As

Publication number Publication date
AU2019269635A1 (en) 2020-11-26
JP2024116167A (ja) 2024-08-27
JP7497879B2 (ja) 2024-06-11
JP2021524736A (ja) 2021-09-16
CA3099819A1 (en) 2019-11-21
BR112020023296A2 (pt) 2021-05-04
US20250232837A1 (en) 2025-07-17
EP3794120A4 (en) 2022-03-23
SG11202011050TA (en) 2020-12-30
EP3794120A1 (en) 2021-03-24
WO2019222560A1 (en) 2019-11-21
KR20210013061A (ko) 2021-02-03
KR102873073B1 (ko) 2025-10-17
US20210292836A1 (en) 2021-09-23

Similar Documents

Publication Publication Date Title
US20250232837A1 (en) Methods and reagents for resolving nucleic acid mixtures and mixed cell populations and associated applications
US12087401B2 (en) Using cell-free DNA fragment size to detect tumor-associated variant
JP7541363B2 (ja) プーリングを介した多数の試料の効率的な遺伝子型決定のための方法および試薬
KR102487135B1 (ko) 기지 또는 미지의 유전자형의 다수의 기여자로부터 dna 혼합물을 분해 및 정량하기 위한 방법 및 시스템
KR102543270B1 (ko) 미지의 유전자형의 기여자로부터의 dna 혼합물의 정확한 컴퓨팅 분해를 위한 방법
CN112673099A (zh) 用于表征基因组编辑、克隆扩增的方法和试剂及相关应用
Kehl et al. Review of molecular technologies for investigating canine cancer
HK40039254A (en) Methods and reagents for resolving nucleic acid mixtures and mixed cell populations and associated applications
HK40059649A (en) Methods and reagents for efficient genotyping of large numbers of samples via pooling
Pala Sequence Variation Of Copy Number Variable Regions In The Human Genome
HK40050975A (en) Methods and reagents for characterizing genomic editing, clonal expansion, and associated applications
HK40019713B (en) Methods for accurate computational decomposition of dna mixtures from contributors of unknown genotypes
HK40019713A (en) Methods for accurate computational decomposition of dna mixtures from contributors of unknown genotypes
HK40019712B (en) Methods and systems for decomposition and quantification of dna mixtures from multiple contributors of known or unknown genotypes
HK40019712A (en) Methods and systems for decomposition and quantification of dna mixtures from multiple contributors of known or unknown genotypes

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination
REG Reference to a national code

Ref country code: HK

Ref legal event code: DE

Ref document number: 40039254

Country of ref document: HK