SG11201602306SA - Methods and system for detecting sequence variants - Google Patents
Methods and system for detecting sequence variantsInfo
- Publication number
- SG11201602306SA SG11201602306SA SG11201602306SA SG11201602306SA SG11201602306SA SG 11201602306S A SG11201602306S A SG 11201602306SA SG 11201602306S A SG11201602306S A SG 11201602306SA SG 11201602306S A SG11201602306S A SG 11201602306SA SG 11201602306S A SG11201602306S A SG 11201602306SA
- Authority
- SG
- Singapore
- Prior art keywords
- methods
- sequence variants
- detecting sequence
- detecting
- variants
- Prior art date
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
- 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
- C12Q1/6869—Methods for sequencing
- C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
-
- 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
- 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
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B30/20—Sequence assembly
-
- 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
- C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
- C12Q2535/122—Massive parallel sequencing
-
- 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
- C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
- C12Q2565/60—Detection means characterised by use of a special device
- C12Q2565/601—Detection means characterised by use of a special device being a microscope, e.g. atomic force microscopy [AFM]
Landscapes
- Life Sciences & Earth Sciences (AREA)
- Physics & Mathematics (AREA)
- Chemical & Material Sciences (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Health & Medical Sciences (AREA)
- Analytical Chemistry (AREA)
- Biophysics (AREA)
- Biotechnology (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Medical Informatics (AREA)
- Bioinformatics & Computational Biology (AREA)
- Theoretical Computer Science (AREA)
- Evolutionary Biology (AREA)
- Organic Chemistry (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Genetics & Genomics (AREA)
- Molecular Biology (AREA)
- Microbiology (AREA)
- Biochemistry (AREA)
- General Engineering & Computer Science (AREA)
- Immunology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
- Debugging And Monitoring (AREA)
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201361884380P | 2013-09-30 | 2013-09-30 | |
| US14/041,850 US9116866B2 (en) | 2013-08-21 | 2013-09-30 | Methods and systems for detecting sequence variants |
| PCT/US2014/058328 WO2015048753A1 (en) | 2013-09-30 | 2014-09-30 | Methods and system for detecting sequence variants |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| SG11201602306SA true SG11201602306SA (en) | 2016-04-28 |
Family
ID=52744601
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| SG11201602306SA SG11201602306SA (en) | 2013-09-30 | 2014-09-30 | Methods and system for detecting sequence variants |
Country Status (9)
| Country | Link |
|---|---|
| EP (1) | EP3053073B1 (ko) |
| JP (1) | JP2016540275A (ko) |
| KR (2) | KR102446941B1 (ko) |
| CN (1) | CN105793859B (ko) |
| AU (2) | AU2014324438B2 (ko) |
| CA (1) | CA2925335C (ko) |
| HK (1) | HK1226158A1 (ko) |
| SG (1) | SG11201602306SA (ko) |
| WO (1) | WO2015048753A1 (ko) |
Families Citing this family (29)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US9898575B2 (en) | 2013-08-21 | 2018-02-20 | Seven Bridges Genomics Inc. | Methods and systems for aligning sequences |
| US9116866B2 (en) | 2013-08-21 | 2015-08-25 | Seven Bridges Genomics Inc. | Methods and systems for detecting sequence variants |
| CA2927102C (en) | 2013-10-18 | 2022-08-30 | Seven Bridges Genomics Inc. | Methods and systems for genotyping genetic samples |
| US11049587B2 (en) | 2013-10-18 | 2021-06-29 | Seven Bridges Genomics Inc. | Methods and systems for aligning sequences in the presence of repeating elements |
| WO2015058095A1 (en) | 2013-10-18 | 2015-04-23 | Seven Bridges Genomics Inc. | Methods and systems for quantifying sequence alignment |
| AU2014337093B2 (en) | 2013-10-18 | 2020-07-30 | Seven Bridges Genomics Inc. | Methods and systems for identifying disease-induced mutations |
| US9063914B2 (en) | 2013-10-21 | 2015-06-23 | Seven Bridges Genomics Inc. | Systems and methods for transcriptome analysis |
| US9817944B2 (en) | 2014-02-11 | 2017-11-14 | Seven Bridges Genomics Inc. | Systems and methods for analyzing sequence data |
| WO2016141294A1 (en) | 2015-03-05 | 2016-09-09 | Seven Bridges Genomics Inc. | Systems and methods for genomic pattern analysis |
| US10793895B2 (en) | 2015-08-24 | 2020-10-06 | Seven Bridges Genomics Inc. | Systems and methods for epigenetic analysis |
| US10584380B2 (en) | 2015-09-01 | 2020-03-10 | Seven Bridges Genomics Inc. | Systems and methods for mitochondrial analysis |
| US10724110B2 (en) | 2015-09-01 | 2020-07-28 | Seven Bridges Genomics Inc. | Systems and methods for analyzing viral nucleic acids |
| US11347704B2 (en) | 2015-10-16 | 2022-05-31 | Seven Bridges Genomics Inc. | Biological graph or sequence serialization |
| US20170199960A1 (en) | 2016-01-07 | 2017-07-13 | Seven Bridges Genomics Inc. | Systems and methods for adaptive local alignment for graph genomes |
| US10364468B2 (en) | 2016-01-13 | 2019-07-30 | Seven Bridges Genomics Inc. | Systems and methods for analyzing circulating tumor DNA |
| US10262102B2 (en) | 2016-02-24 | 2019-04-16 | Seven Bridges Genomics Inc. | Systems and methods for genotyping with graph reference |
| US10790044B2 (en) | 2016-05-19 | 2020-09-29 | Seven Bridges Genomics Inc. | Systems and methods for sequence encoding, storage, and compression |
| US11289177B2 (en) | 2016-08-08 | 2022-03-29 | Seven Bridges Genomics, Inc. | Computer method and system of identifying genomic mutations using graph-based local assembly |
| US11250931B2 (en) | 2016-09-01 | 2022-02-15 | Seven Bridges Genomics Inc. | Systems and methods for detecting recombination |
| US10319465B2 (en) | 2016-11-16 | 2019-06-11 | Seven Bridges Genomics Inc. | Systems and methods for aligning sequences to graph references |
| CN106709276A (zh) * | 2017-01-21 | 2017-05-24 | 深圳昆腾生物信息有限公司 | 一种基因变异成因分析方法及系统 |
| US10726110B2 (en) | 2017-03-01 | 2020-07-28 | Seven Bridges Genomics, Inc. | Watermarking for data security in bioinformatic sequence analysis |
| US11347844B2 (en) | 2017-03-01 | 2022-05-31 | Seven Bridges Genomics, Inc. | Data security in bioinformatic sequence analysis |
| JP7054133B2 (ja) * | 2017-11-09 | 2022-04-13 | 国立研究開発法人国立がん研究センター | 配列解析方法、配列解析装置、参照配列の生成方法、参照配列生成装置、プログラム、および記録媒体 |
| CN108154007B (zh) * | 2017-11-28 | 2021-06-29 | 西安电子科技大学 | 一种基于单肿瘤样本拷贝数变异及缺失类型检测方法 |
| IL283427B2 (en) * | 2018-01-15 | 2023-10-01 | Illumina Inc | Identifying variants using Empiric ranking of variants |
| SE541799C2 (en) | 2018-04-11 | 2019-12-17 | David Yudovich | Determination of frequency distribution of nucleotide sequence variants |
| CN111091870B (zh) * | 2019-12-18 | 2021-11-02 | 中国科学院大学 | 基因变异位点质量控制方法及系统 |
| CN113641628B (zh) * | 2021-08-13 | 2023-06-16 | 中国联合网络通信集团有限公司 | 数据质量检测方法、装置、设备及存储介质 |
Family Cites Families (25)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6818395B1 (en) | 1999-06-28 | 2004-11-16 | California Institute Of Technology | Methods and apparatus for analyzing polynucleotide sequences |
| CA2415775A1 (en) | 2000-07-18 | 2002-01-24 | Correlogic Systems, Inc. | A process for discriminating between biological states based on hidden patterns from biological data |
| NO20004869D0 (no) | 2000-09-28 | 2000-09-28 | Torbjoern Rognes | Metode for hurtig optimal lokal sekvensjustering ved bruk av parallell prosessering |
| JP2004523243A (ja) | 2001-03-12 | 2004-08-05 | カリフォルニア インスティチュート オブ テクノロジー | 非同期性塩基伸長によってポリヌクレオチド配列を分析するための方法および装置 |
| US6890763B2 (en) | 2001-04-30 | 2005-05-10 | Syn X Pharma, Inc. | Biopolymer marker indicative of disease state having a molecular weight of 1350 daltons |
| WO2003095978A2 (en) | 2002-05-09 | 2003-11-20 | Surromed, Inc. | Methods for time-alignment of liquid chromatography-mass spectrometry data |
| US7169560B2 (en) | 2003-11-12 | 2007-01-30 | Helicos Biosciences Corporation | Short cycle methods for sequencing polynucleotides |
| US20060195266A1 (en) | 2005-02-25 | 2006-08-31 | Yeatman Timothy J | Methods for predicting cancer outcome and gene signatures for use therein |
| US7282337B1 (en) | 2006-04-14 | 2007-10-16 | Helicos Biosciences Corporation | Methods for increasing accuracy of nucleic acid sequencing |
| US8349167B2 (en) | 2006-12-14 | 2013-01-08 | Life Technologies Corporation | Methods and apparatus for detecting molecular interactions using FET arrays |
| US8262900B2 (en) | 2006-12-14 | 2012-09-11 | Life Technologies Corporation | Methods and apparatus for measuring analytes using large scale FET arrays |
| GB2457851B (en) | 2006-12-14 | 2011-01-05 | Ion Torrent Systems Inc | Methods and apparatus for measuring analytes using large scale fet arrays |
| US20100035252A1 (en) | 2008-08-08 | 2010-02-11 | Ion Torrent Systems Incorporated | Methods for sequencing individual nucleic acids under tension |
| US20100301398A1 (en) | 2009-05-29 | 2010-12-02 | Ion Torrent Systems Incorporated | Methods and apparatus for measuring analytes |
| US20100137143A1 (en) | 2008-10-22 | 2010-06-03 | Ion Torrent Systems Incorporated | Methods and apparatus for measuring analytes |
| US8546128B2 (en) | 2008-10-22 | 2013-10-01 | Life Technologies Corporation | Fluidics system for sequential delivery of reagents |
| DK2511843T3 (en) * | 2009-04-29 | 2017-03-27 | Complete Genomics Inc | METHOD AND SYSTEM FOR DETERMINING VARIATIONS IN A SAMPLE POLYNUCLEOTIDE SEQUENCE IN TERMS OF A REFERENCE POLYNUCLEOTIDE SEQUENCE |
| US8574835B2 (en) | 2009-05-29 | 2013-11-05 | Life Technologies Corporation | Scaffolded nucleic acid polymer particles and methods of making and using |
| US8673627B2 (en) | 2009-05-29 | 2014-03-18 | Life Technologies Corporation | Apparatus and methods for performing electrochemical reactions |
| US20110098193A1 (en) * | 2009-10-22 | 2011-04-28 | Kingsmore Stephen F | Methods and Systems for Medical Sequencing Analysis |
| US9165109B2 (en) * | 2010-02-24 | 2015-10-20 | Pacific Biosciences Of California, Inc. | Sequence assembly and consensus sequence determination |
| US9342651B2 (en) * | 2010-05-13 | 2016-05-17 | Life Technologies Corporation | Computational methods for translating a sequence of multi-base color calls to a sequence of bases |
| WO2012098515A1 (en) * | 2011-01-19 | 2012-07-26 | Koninklijke Philips Electronics N.V. | Method for processing genomic data |
| US20120239706A1 (en) | 2011-03-18 | 2012-09-20 | Los Alamos National Security, Llc | Computer-facilitated parallel information alignment and analysis |
| US8209130B1 (en) * | 2012-04-04 | 2012-06-26 | Good Start Genetics, Inc. | Sequence assembly |
-
2014
- 2014-09-30 JP JP2016518122A patent/JP2016540275A/ja active Pending
- 2014-09-30 KR KR1020167011145A patent/KR102446941B1/ko active IP Right Grant
- 2014-09-30 SG SG11201602306SA patent/SG11201602306SA/en unknown
- 2014-09-30 WO PCT/US2014/058328 patent/WO2015048753A1/en active Application Filing
- 2014-09-30 CA CA2925335A patent/CA2925335C/en active Active
- 2014-09-30 AU AU2014324438A patent/AU2014324438B2/en active Active
- 2014-09-30 EP EP14847490.1A patent/EP3053073B1/en active Active
- 2014-09-30 KR KR1020227032673A patent/KR20220136449A/ko not_active Application Discontinuation
- 2014-09-30 CN CN201480065432.9A patent/CN105793859B/zh active Active
-
2016
- 2016-12-16 HK HK16114331A patent/HK1226158A1/zh unknown
-
2020
- 2020-03-04 AU AU2020201622A patent/AU2020201622B2/en active Active
Also Published As
| Publication number | Publication date |
|---|---|
| AU2014324438A1 (en) | 2016-04-14 |
| EP3053073B1 (en) | 2019-07-03 |
| AU2020201622A1 (en) | 2020-03-19 |
| EP3053073A1 (en) | 2016-08-10 |
| CA2925335A1 (en) | 2015-04-02 |
| KR102446941B1 (ko) | 2022-09-23 |
| CA2925335C (en) | 2023-03-28 |
| EP3053073A4 (en) | 2017-06-07 |
| CN105793859A (zh) | 2016-07-20 |
| CN105793859B (zh) | 2020-02-28 |
| HK1226158A1 (zh) | 2017-09-22 |
| WO2015048753A1 (en) | 2015-04-02 |
| KR20220136449A (ko) | 2022-10-07 |
| AU2020201622B2 (en) | 2022-03-17 |
| KR20160062127A (ko) | 2016-06-01 |
| JP2016540275A (ja) | 2016-12-22 |
| AU2014324438B2 (en) | 2019-12-05 |
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