JP7636400B2 - ２つの変異シーケンスリードが、同一の変異を含むシーケンスに由来する確率と相関する尺度を決定するための方法 - Google Patents

２つの変異シーケンスリードが、同一の変異を含むシーケンスに由来する確率と相関する尺度を決定するための方法 Download PDF

Info

Publication number
JP7636400B2
JP7636400B2 JP2022517384A JP2022517384A JP7636400B2 JP 7636400 B2 JP7636400 B2 JP 7636400B2 JP 2022517384 A JP2022517384 A JP 2022517384A JP 2022517384 A JP2022517384 A JP 2022517384A JP 7636400 B2 JP7636400 B2 JP 7636400B2
Authority
JP
Japan
Prior art keywords
sequence
mutation
mers
mutant
sequence reads
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.)
Active
Application number
JP2022517384A
Other languages
English (en)
Japanese (ja)
Other versions
JP2022550013A (ja
JP2022550013A5 (https=
Inventor
アーロン アール ダーリング，
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.)
Illumina Singapore Pte Ltd
Original Assignee
Illumina Singapore Pte Ltd
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 Illumina Singapore Pte Ltd filed Critical Illumina Singapore Pte Ltd
Publication of JP2022550013A publication Critical patent/JP2022550013A/ja
Publication of JP2022550013A5 publication Critical patent/JP2022550013A5/ja
Application granted granted Critical
Publication of JP7636400B2 publication Critical patent/JP7636400B2/ja
Active legal-status Critical Current
Anticipated expiration legal-status Critical

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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • G16B30/20—Sequence assembly
    • 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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Software Systems (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Complex Calculations (AREA)
JP2022517384A 2019-09-30 2020-09-29 ２つの変異シーケンスリードが、同一の変異を含むシーケンスに由来する確率と相関する尺度を決定するための方法 Active JP7636400B2 (ja)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
GB201914064A GB201914064D0 (en) 2019-09-30 2019-09-30 Method for determining a measure correlated to the probability that two mutated sequence reads derive from the same sequence comprising mutations
GB1914064.9 2019-09-30
PCT/GB2020/052358 WO2021064365A1 (en) 2019-09-30 2020-09-29 Method for determining a measure correlated to the probability that two mutated sequence reads derive from the same sequence comprising mutations

Publications (3)

Publication Number Publication Date
JP2022550013A JP2022550013A (ja) 2022-11-30
JP2022550013A5 JP2022550013A5 (https=) 2023-09-01
JP7636400B2 true JP7636400B2 (ja) 2025-02-26

Family

ID=68538862

Family Applications (1)

Application Number Title Priority Date Filing Date
JP2022517384A Active JP7636400B2 (ja) 2019-09-30 2020-09-29 ２つの変異シーケンスリードが、同一の変異を含むシーケンスに由来する確率と相関する尺度を決定するための方法

Country Status (13)

Country Link
US (1) US20230044570A1 (https=)
EP (1) EP4042430A1 (https=)
JP (1) JP7636400B2 (https=)
KR (1) KR102903933B1 (https=)
CN (1) CN114424288A (https=)
AU (1) AU2020358797A1 (https=)
BR (1) BR112022005730A2 (https=)
CA (1) CA3155101A1 (https=)
GB (1) GB201914064D0 (https=)
IL (1) IL291709B1 (https=)
MX (1) MX2022003605A (https=)
NZ (1) NZ786015A (https=)
WO (1) WO2021064365A1 (https=)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN115662523B (zh) * 2022-10-21 2023-06-20 哈尔滨工业大学 面向群体基因组索引表示与构建的方法及设备
JP2026509693A (ja) 2023-03-10 2026-03-25 イルミナ インコーポレイテッド ポリヌクレオチド配列をアセンブルするためのｋ－ｍｅｒベースの方法
WO2025254714A1 (en) 2024-06-03 2025-12-11 Illumina, Inc. System and method for assembling a polynucleotide sequence
WO2025255494A1 (en) 2024-06-07 2025-12-11 Illumina, Inc. Identifying the origin of amplified rna molecules
WO2026072259A1 (en) 2024-09-30 2026-04-02 Illumina, Inc. Methods, systems, and kits for sequencing nucleic acids with deamination and mutagenesis

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002079502A1 (en) 2001-03-28 2002-10-10 The University Of Queensland A method for nucleic acid sequence analysis
US20130110407A1 (en) 2011-09-16 2013-05-02 Complete Genomics, Inc. Determining variants in genome of a heterogeneous sample
US20180365375A1 (en) 2015-04-24 2018-12-20 University Of Utah Research Foundation Methods and systems for multiple taxonomic classification
WO2019022018A1 (ja) 2017-07-24 2019-01-31 国立研究開発法人農業・食品産業技術総合研究機構 多型検出法
US20190164627A1 (en) 2017-11-28 2019-05-30 Grail, Inc. Models for Targeted Sequencing

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2016130578A1 (en) * 2015-02-09 2016-08-18 10X Genomics, Inc. Systems and methods for determining structural variation and phasing using variant call data

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002079502A1 (en) 2001-03-28 2002-10-10 The University Of Queensland A method for nucleic acid sequence analysis
US20040152108A1 (en) 2001-03-28 2004-08-05 Keith Jonathan Macgregor Method for sequence analysis
US20130110407A1 (en) 2011-09-16 2013-05-02 Complete Genomics, Inc. Determining variants in genome of a heterogeneous sample
US20180365375A1 (en) 2015-04-24 2018-12-20 University Of Utah Research Foundation Methods and systems for multiple taxonomic classification
WO2019022018A1 (ja) 2017-07-24 2019-01-31 国立研究開発法人農業・食品産業技術総合研究機構 多型検出法
US20190164627A1 (en) 2017-11-28 2019-05-30 Grail, Inc. Models for Targeted Sequencing

Also Published As

Publication number Publication date
JP2022550013A (ja) 2022-11-30
CN114424288A (zh) 2022-04-29
AU2020358797A1 (en) 2022-04-14
BR112022005730A2 (pt) 2022-06-21
CA3155101A1 (en) 2021-04-08
US20230044570A1 (en) 2023-02-09
IL291709A (en) 2022-05-01
WO2021064365A1 (en) 2021-04-08
IL291709B1 (en) 2026-03-01
MX2022003605A (es) 2022-05-30
EP4042430A1 (en) 2022-08-17
KR102903933B1 (ko) 2025-12-23
KR20220070452A (ko) 2022-05-31
GB201914064D0 (en) 2019-11-13
NZ786015A (en) 2024-11-29

Similar Documents

Publication Publication Date Title
JP7636400B2 (ja) ２つの変異シーケンスリードが、同一の変異を含むシーケンスに由来する確率と相関する尺度を決定するための方法
US11149308B2 (en) Sequence assembly
Zhbannikov et al. SeqyClean: a pipeline for high-throughput sequence data preprocessing
EP3049557B1 (en) Methods and systems for large scale scaffolding of genome assemblies
Dvorkina et al. The string decomposition problem and its applications to centromere analysis and assembly
CN102460155A (zh) 用于关于参考多核苷酸序列标注样本多核苷酸序列中的变异的方法和系统
JP7795566B2 (ja) 配列決定アルゴリズム
Alic et al. Objective review of de novo stand‐alone error correction methods for NGS data
Seifert et al. Estimating fitness of viral quasispecies from next-generation sequencing data
RU2799778C9 (ru) Способ определения показателя, коррелированного с вероятностью того, что два мутированных прочтения последовательности происходят от одной и той же содержащей мутации последовательности
RU2799778C1 (ru) Способ определения показателя, коррелированного с вероятностью того, что два мутированных прочтения последовательности происходят от одной и той же содержащей мутации последовательности
CN109935274A (zh) 一种基于k-mer分布特征的长读数重叠区检测方法
Jackson Parallel methods for short read assembly
He et al. Hap-seq: an optimal algorithm for haplotype phasing with imputation using sequencing data
Wade Homology unleashed: nonparametric and alignment-free methods for understanding genome evolution
Chrisman Unmapped or Untapped? Leveraging the Unmapped Read Space of Whole Genome Sequences to Understand the Human Genome, Virome, and Contaminome
Kale et al. 11 Navigating Bacterial Taxonomy in World of Unchartered Microbial Organisms
Hong Computational Methods for Biological Sequential Pattern Analysis
Hartmann Discovering nucleotide-level and structural variants in cancer genome data from second-and third-generation sequencing technologies
Chen Inference of Viral Strains Using Metagenomics Data
Lim Copy number estimation for high-throughput short read shotgun sequencing de novo whole-genome assembly contigs
Bristow De novo sequence assembly of viral quasispecies
Brudno et al. ISMB 2008 Special Interest Group on Algorithms for Short Read Sequencing
Lenzini The structure of bacterial intergenic sequences: relation with regulation and denaturation
Patuzzi 16S rRNA gene sequencing sparse count matrices: a count data simulator and optimal pre-processing pipelines

Legal Events

Date Code Title Description
A711 Notification of change in applicant

Free format text: JAPANESE INTERMEDIATE CODE: A711

Effective date: 20221028

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A821

Effective date: 20221028

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20230824

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20230824

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20240912

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20241212

TRDD Decision of grant or rejection written
A01 Written decision to grant a patent or to grant a registration (utility model)

Free format text: JAPANESE INTERMEDIATE CODE: A01

Effective date: 20250204

A61 First payment of annual fees (during grant procedure)

Free format text: JAPANESE INTERMEDIATE CODE: A61

Effective date: 20250213

R150 Certificate of patent or registration of utility model

Ref document number: 7636400

Country of ref document: JP

Free format text: JAPANESE INTERMEDIATE CODE: R150