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SG10201911912XA - System and method for secondary analysis of nucleotide sequencing data - Google Patents

System and method for secondary analysis of nucleotide sequencing data

Info

Publication number
SG10201911912XA
SG10201911912XA SG10201911912XA SG10201911912XA SG10201911912XA SG 10201911912X A SG10201911912X A SG 10201911912XA SG 10201911912X A SG10201911912X A SG 10201911912XA SG 10201911912X A SG10201911912X A SG 10201911912XA SG 10201911912X A SG10201911912X A SG 10201911912XA
Authority
SG
Singapore
Prior art keywords
sequencing data
nucleotide sequencing
secondary analysis
analysis
nucleotide
Prior art date
Application number
SG10201911912XA
Other languages
English (en)
Inventor
Francisco Jose Garcia
Come Raczy
Aaron Day
Michael J Carney
Original Assignee
Illumina 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 Illumina Inc filed Critical Illumina Inc
Publication of SG10201911912XA publication Critical patent/SG10201911912XA/en

Links

Classifications

    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10Sequence alignment; Homology search
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20Sequence assembly
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/30Unsupervised data analysis

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Medical Informatics (AREA)
  • Analytical Chemistry (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Data Mining & Analysis (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
SG10201911912XA 2016-10-07 2017-10-06 System and method for secondary analysis of nucleotide sequencing data SG10201911912XA (en)

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
US201662405824P 2016-10-07 2016-10-07

Publications (1)

Publication Number Publication Date
SG10201911912XA true SG10201911912XA (en) 2020-02-27

Family

ID=60480359

Family Applications (2)

Application Number Title Priority Date Filing Date
SG10201911912XA SG10201911912XA (en) 2016-10-07 2017-10-06 System and method for secondary analysis of nucleotide sequencing data
SG11201810924WA SG11201810924WA (en) 2016-10-07 2017-10-06 System and method for secondary analysis of nucleotide sequencing data

Family Applications After (1)

Application Number Title Priority Date Filing Date
SG11201810924WA SG11201810924WA (en) 2016-10-07 2017-10-06 System and method for secondary analysis of nucleotide sequencing data

Country Status (15)

Country Link
US (2) US11646102B2 (ja)
EP (1) EP3458993A1 (ja)
JP (3) JP6898441B2 (ja)
KR (3) KR102515638B1 (ja)
CN (2) CN115810396A (ja)
AU (3) AU2017341069A1 (ja)
BR (1) BR122023004154A2 (ja)
CA (1) CA3027179C (ja)
IL (2) IL263512B2 (ja)
MX (2) MX2018015412A (ja)
MY (1) MY193917A (ja)
RU (1) RU2741807C2 (ja)
SG (2) SG10201911912XA (ja)
WO (1) WO2018068014A1 (ja)
ZA (2) ZA201808277B (ja)

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* Cited by examiner, † Cited by third party
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EP2697397B1 (en) 2011-04-15 2017-04-05 The Johns Hopkins University Safe sequencing system
AU2013338393C1 (en) 2012-10-29 2024-07-25 The Johns Hopkins University Papanicolaou test for ovarian and endometrial cancers
US11286531B2 (en) 2015-08-11 2022-03-29 The Johns Hopkins University Assaying ovarian cyst fluid
EP3555318A1 (en) * 2016-12-15 2019-10-23 Illumina, Inc. Methods and systems for determining paralogs
CA3072195A1 (en) 2017-08-07 2019-04-04 The Johns Hopkins University Methods and materials for assessing and treating cancer
US11210554B2 (en) 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata
JP2022533492A (ja) 2019-05-24 2022-07-25 イルミナ インコーポレイテッド ハッシュテーブルゲノムマッピングのための柔軟性のあるシード伸長
KR102292599B1 (ko) * 2019-11-06 2021-08-23 주식회사 뷰웍스 광학 분석 장치 및 광학 분석 방법
JP2023519496A (ja) * 2020-03-11 2023-05-11 イルミナ インコーポレイテッド 核酸シーケンスのインクリメンタル二次解析
CN113436683B (zh) * 2020-03-23 2024-08-16 北京合生基因科技有限公司 筛选候选插入片段的方法和系统
AU2022202798A1 (en) * 2021-05-26 2022-12-15 Genieus Genomics Pty Ltd Processing sequencing data relating to amyotrophic lateral sclerosis
CN113299344A (zh) * 2021-06-23 2021-08-24 深圳华大医学检验实验室 基因测序分析方法、装置、存储介质和计算机设备
WO2024081805A1 (en) * 2022-10-13 2024-04-18 Element Biosciences, Inc. Separating sequencing data in parallel with a sequencing run in next generation sequencing data analysis

Family Cites Families (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2357263A1 (en) 2001-09-07 2003-03-07 Bioinformatics Solutions Inc. New methods for faster and more sensitive homology search in dna sequences
US7575865B2 (en) * 2003-01-29 2009-08-18 454 Life Sciences Corporation Methods of amplifying and sequencing nucleic acids
DE602005009406D1 (de) * 2005-02-11 2008-10-09 Smartgene Gmbh Computerimplementiertes verfahren und computergestütztes system zur validierung von dna-sequenzierungsdaten
WO2011137368A2 (en) * 2010-04-30 2011-11-03 Life Technologies Corporation Systems and methods for analyzing nucleic acid sequences
US20120203792A1 (en) 2011-02-01 2012-08-09 Life Technologies Corporation Systems and methods for mapping sequence reads
US10424394B2 (en) * 2011-10-06 2019-09-24 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
WO2013052907A2 (en) * 2011-10-06 2013-04-11 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
KR101394339B1 (ko) * 2012-03-06 2014-05-13 삼성에스디에스 주식회사 시드의 길이를 고려한 염기 서열 처리 시스템 및 방법
US10504613B2 (en) * 2012-12-20 2019-12-10 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
KR101481457B1 (ko) 2012-10-29 2015-01-12 삼성에스디에스 주식회사 리드 전체를 고려한 염기 서열 정렬 시스템 및 방법
US20140238250A1 (en) 2013-02-28 2014-08-28 Wki Holding Company, Inc. Microwavable Heating Element and Composition
WO2014152990A1 (en) * 2013-03-14 2014-09-25 University Of Rochester System and method for detecting population variation from nucleic acid sequencing data
US10191929B2 (en) 2013-05-29 2019-01-29 Noblis, Inc. Systems and methods for SNP analysis and genome sequencing
RU2539038C1 (ru) 2013-11-02 2015-01-10 Общество с ограниченной ответственностью "Гамма" Способ секвенирования днк и устройство для его осуществления (варианты)
CN104462211B (zh) * 2014-11-04 2018-01-02 北京诺禾致源科技股份有限公司 重测序数据的处理方法和处理装置

Also Published As

Publication number Publication date
JP2019522861A (ja) 2019-08-15
CA3027179C (en) 2023-06-27
JP6898441B2 (ja) 2021-07-07
IL263512A (en) 2019-03-31
BR122023004154A2 (pt) 2023-10-10
AU2021277671B2 (en) 2023-10-12
AU2020207826B2 (en) 2021-09-09
SG11201810924WA (en) 2019-01-30
RU2018143972A3 (ja) 2020-06-15
JP2022060425A (ja) 2022-04-14
CN109416927B (zh) 2023-05-02
IL300135B2 (en) 2024-06-01
MY193917A (en) 2022-11-01
CN115810396A (zh) 2023-03-17
ZA202101720B (en) 2023-05-31
RU2018143972A (ru) 2020-06-15
MX2022011757A (es) 2022-10-18
KR102515638B1 (ko) 2023-03-29
KR20220047887A (ko) 2022-04-19
IL300135A (en) 2023-03-01
US20190385699A1 (en) 2019-12-19
EP3458993A1 (en) 2019-03-27
AU2017341069A1 (en) 2019-01-24
AU2020207826A1 (en) 2020-08-13
US11646102B2 (en) 2023-05-09
WO2018068014A9 (en) 2018-08-30
BR112018076983A2 (pt) 2019-04-16
WO2018068014A1 (en) 2018-04-12
JP7387777B2 (ja) 2023-11-28
KR20230044335A (ko) 2023-04-03
ZA201808277B (en) 2022-06-29
MX2018015412A (es) 2019-05-27
JP7051937B2 (ja) 2022-04-11
IL263512B2 (en) 2023-09-01
IL300135B1 (en) 2024-02-01
RU2741807C2 (ru) 2021-01-28
BR112018076983A8 (pt) 2023-10-10
US20230410945A1 (en) 2023-12-21
KR102694651B1 (ko) 2024-08-12
CN109416927A (zh) 2019-03-01
KR20190017825A (ko) 2019-02-20
KR102384832B1 (ko) 2022-04-08
AU2021277671A1 (en) 2021-12-23
IL263512B1 (en) 2023-05-01
JP2020144936A (ja) 2020-09-10
CA3027179A1 (en) 2018-04-12

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