SG11201810924WA - System and method for secondary analysis of nucleotide sequencing data - Google Patents
System and method for secondary analysis of nucleotide sequencing dataInfo
- Publication number
- SG11201810924WA SG11201810924WA SG11201810924WA SG11201810924WA SG11201810924WA SG 11201810924W A SG11201810924W A SG 11201810924WA SG 11201810924W A SG11201810924W A SG 11201810924WA SG 11201810924W A SG11201810924W A SG 11201810924WA SG 11201810924W A SG11201810924W A SG 11201810924WA
- Authority
- SG
- Singapore
- Prior art keywords
- illumina
- international
- san diego
- way
- secondary analysis
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- 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
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- 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
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- 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
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- 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
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- 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
-
- 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
- G16B30/20—Sequence assembly
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- 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
-
- 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
- G16B40/30—Unsupervised data analysis
-
- 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
- G16B50/30—Data warehousing; Computing architectures
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- 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)
- Biophysics (AREA)
- General Health & Medical Sciences (AREA)
- Biotechnology (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)
- Molecular Biology (AREA)
- Genetics & Genomics (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Data Mining & Analysis (AREA)
- Immunology (AREA)
- Microbiology (AREA)
- General Engineering & Computer Science (AREA)
- Biochemistry (AREA)
- Software Systems (AREA)
- Databases & Information Systems (AREA)
- Epidemiology (AREA)
- Computer Vision & Pattern Recognition (AREA)
- Bioethics (AREA)
- Artificial Intelligence (AREA)
- Public Health (AREA)
- Evolutionary Computation (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
Abstract
ReceiveImaging Data of a Sequencing Cycle V Determine Bases and Quay Scores for Bases Determined 615 W O 20 18/0680 14 A9 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) CORRECTED VERSION (19) World Intellectual Property Organization International Bureau (43) International Publication Date 111111111111011010101111101111010 0111011011 101 IIMOEHRM110111 (10) International Publication Number WO 2018/068014 A9 12 April 2018 (12.04.2018) Wi P 0 I PCT START ) - 1 05 (51) International Patent Classification: GO6F 19/18 (2011.01) G06F 19/22 (2011.01) (21) International Application Number: PCT/US2017/055653 (22) International Filing Date: 06 October 2017 (06.10.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/405,824 07 October 2016 (07.10.2016) US (71) Applicant: ILLUMINA, INC. [US/US]; 5200 Illumina Way, San Diego, CA 92122 (US). (72) Inventors: GARCIA, Francisco, Jose; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). RACZY, Come; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). DAY, Aaron; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). CARNEY, Michael, J.; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). (74) Agent: FULLER, Michael, L.; Knobbe Martens Olson & Bear LLP, 2040 Main Street, Fourteenth Floor, Irvine, CA 92614 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (54) Title: SYSTEM AND METHOD FOR SECONDARY ANALYSIS OF NUCLEOTIDE SEQUENCING DATA (57) : Disclosed herein are systems and methods for performing sec- ondary analyses of nucleotide sequencing data in a time-efficient manner. Some embodiments include performing a secondary analysis iteratively while sequence reads are generated by a sequencing system. Secondary analyses can encompass both alignment of sequence reads to a reference sequence (e.g., the human ref- erence genome sequence) and utilization of this alignment to detect differences between a sample and the reference. Secondary analysis can enable detection of genetic differences, variant detection and genotyping, identification of sin- gle nucleotide polymorphisms (SNPs), small insertions and deletion (indels) and structural changes in the DNA, such as copy number variants (CNVs) and chro- Ye 620 mosomal rearrangements. Perform AI gnment 625 Perform Valiant Calling 630 Yes 635 No ( End )1 40 FIG. 6 [Continued on next page] WO 2018/068014 A9 11111111111111011101111111111101111101001110111111011111010111111111011111101111 TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: with international search report (Art. 21(3)) with information concerning authorization of rectification of an obvious mistake under Rule 91.3 (b) (Rule 48.2(0) (48) Date of publication of this corrected version: 30 August 2018 (30.08.2018) (15) Information about Correction: see Notice of 30 August 2018 (30.08.2018)
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201662405824P | 2016-10-07 | 2016-10-07 | |
| PCT/US2017/055653 WO2018068014A1 (en) | 2016-10-07 | 2017-10-06 | System and method for secondary analysis of nucleotide sequencing data |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| SG11201810924WA true SG11201810924WA (en) | 2019-01-30 |
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 Before (1)
| 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 |
Country Status (15)
| Country | Link |
|---|---|
| US (2) | US11646102B2 (en) |
| EP (2) | EP4586258A1 (en) |
| JP (3) | JP6898441B2 (en) |
| KR (3) | KR102515638B1 (en) |
| CN (2) | CN115810396A (en) |
| AU (3) | AU2017341069A1 (en) |
| BR (1) | BR122023004154A2 (en) |
| CA (1) | CA3027179C (en) |
| IL (2) | IL300135B2 (en) |
| MX (2) | MX2018015412A (en) |
| MY (2) | MY193917A (en) |
| RU (1) | RU2741807C2 (en) |
| SG (2) | SG10201911912XA (en) |
| WO (1) | WO2018068014A1 (en) |
| ZA (2) | ZA201808277B (en) |
Families Citing this family (18)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN103748236B (en) | 2011-04-15 | 2018-12-25 | 约翰·霍普金斯大学 | Safe sequencing system |
| AU2013338393C1 (en) | 2012-10-29 | 2024-07-25 | The Johns Hopkins University | Papanicolaou test for ovarian and endometrial cancers |
| WO2017027653A1 (en) | 2015-08-11 | 2017-02-16 | The Johns Hopkins University | Assaying ovarian cyst fluid |
| EP3555318A1 (en) * | 2016-12-15 | 2019-10-23 | Illumina, Inc. | Methods and systems for determining paralogs |
| CN111868260B (en) | 2017-08-07 | 2025-02-21 | 约翰斯霍普金斯大学 | Methods and materials for evaluating and treating cancer |
| WO2020092309A1 (en) | 2018-10-31 | 2020-05-07 | Illumina, Inc. | Systems and methods for grouping and collapsing sequencing reads |
| US11210554B2 (en) * | 2019-03-21 | 2021-12-28 | Illumina, Inc. | Artificial intelligence-based generation of sequencing metadata |
| MX2020014030A (en) | 2019-05-24 | 2021-03-09 | Illumina Inc | Flexible seed extension for hash table genomic mapping. |
| KR102292599B1 (en) * | 2019-11-06 | 2021-08-23 | 주식회사 뷰웍스 | Optical analysis device and optical analysis method |
| CA3170345A1 (en) | 2020-02-14 | 2021-08-19 | The Johns Hopkins University | Methods and materials for assessing nucleic acids |
| WO2021183833A1 (en) * | 2020-03-11 | 2021-09-16 | Illumina, Inc. | Incremental secondary analysis of nucleic acid sequences |
| US12006539B2 (en) * | 2020-03-17 | 2024-06-11 | Western Digital Technologies, Inc. | Reference-guided genome sequencing |
| CN113436683B (en) * | 2020-03-23 | 2024-08-16 | 北京合生基因科技有限公司 | Method and system for screening candidate inserts |
| AU2022202798A1 (en) * | 2021-05-26 | 2022-12-15 | Genieus Genomics Pty Ltd | Processing sequencing data relating to amyotrophic lateral sclerosis |
| CN113299344A (en) * | 2021-06-23 | 2021-08-24 | 深圳华大医学检验实验室 | Gene sequencing analysis method, gene sequencing analysis device, storage medium and computer equipment |
| KR20250109684A (en) * | 2022-10-13 | 2025-07-17 | 엘리먼트 바이오사이언스, 인크. | Separation of sequence analysis data while executing sequence analysis in next-generation sequencing data analysis |
| WO2025240241A1 (en) * | 2024-05-13 | 2025-11-20 | Illumina, Inc. | Modifying sequencing cycles during a sequencing run to meet customized coverage estimations for a target genomic region |
| CN119360966B (en) * | 2024-12-24 | 2025-04-04 | 苏州大学 | Genome assembly method and system based on iterative k-mer decomposition |
Family Cites Families (19)
| 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 |
| AU2005327056B2 (en) * | 2005-02-11 | 2010-09-16 | Smartgene Gmbh | Computer-implemented method and computer-based system for validating DNA sequencing data |
| 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 |
| 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 |
| US20140242588A1 (en) * | 2011-10-06 | 2014-08-28 | Sequenom, Inc | Methods and processes for non-invasive assessment of genetic variations |
| US10424394B2 (en) * | 2011-10-06 | 2019-09-24 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| KR101394339B1 (en) * | 2012-03-06 | 2014-05-13 | 삼성에스디에스 주식회사 | System and method for processing genome sequence in consideration of seed length |
| US20130345066A1 (en) * | 2012-05-09 | 2013-12-26 | Life Technologies Corporation | Systems and methods for identifying sequence variation |
| US10504613B2 (en) * | 2012-12-20 | 2019-12-10 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| KR101481457B1 (en) * | 2012-10-29 | 2015-01-12 | 삼성에스디에스 주식회사 | System and method for aligning genome sequence considering entire read |
| 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 |
| WO2014186604A1 (en) * | 2013-05-15 | 2014-11-20 | Edico Genome Corp. | Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform |
| US10191929B2 (en) | 2013-05-29 | 2019-01-29 | Noblis, Inc. | Systems and methods for SNP analysis and genome sequencing |
| RU2539038C1 (en) * | 2013-11-02 | 2015-01-10 | Общество с ограниченной ответственностью "Гамма" | Dna sequencing method and device therefor (versions) |
| WO2016062713A1 (en) * | 2014-10-21 | 2016-04-28 | Barcelona Supercomputing Center - Centro Nacional De Supercomputación | A computational method for the identification of variants in nucleic acid sequences |
| CN104462211B (en) * | 2014-11-04 | 2018-01-02 | 北京诺禾致源科技股份有限公司 | The processing method and processing unit of weight sequencing data |
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2017
- 2017-10-06 KR KR1020227011278A patent/KR102515638B1/en active Active
- 2017-10-06 MX MX2018015412A patent/MX2018015412A/en unknown
- 2017-10-06 KR KR1020237010257A patent/KR102694651B1/en active Active
- 2017-10-06 BR BR122023004154-2A patent/BR122023004154A2/en not_active Application Discontinuation
- 2017-10-06 IL IL300135A patent/IL300135B2/en unknown
- 2017-10-06 RU RU2018143972A patent/RU2741807C2/en active
- 2017-10-06 CA CA3027179A patent/CA3027179C/en active Active
- 2017-10-06 CN CN202211557451.6A patent/CN115810396A/en active Pending
- 2017-10-06 AU AU2017341069A patent/AU2017341069A1/en not_active Abandoned
- 2017-10-06 SG SG10201911912XA patent/SG10201911912XA/en unknown
- 2017-10-06 MY MYPI2018002632A patent/MY193917A/en unknown
- 2017-10-06 CN CN201780040788.0A patent/CN109416927B/en not_active Expired - Fee Related
- 2017-10-06 IL IL263512A patent/IL263512B2/en unknown
- 2017-10-06 EP EP25150789.3A patent/EP4586258A1/en active Pending
- 2017-10-06 US US16/311,141 patent/US11646102B2/en active Active
- 2017-10-06 JP JP2019519631A patent/JP6898441B2/en active Active
- 2017-10-06 SG SG11201810924WA patent/SG11201810924WA/en unknown
- 2017-10-06 EP EP17804976.3A patent/EP3458993A1/en not_active Withdrawn
- 2017-10-06 KR KR1020187038172A patent/KR102384832B1/en active Active
- 2017-10-06 WO PCT/US2017/055653 patent/WO2018068014A1/en not_active Ceased
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2018
- 2018-12-07 ZA ZA2018/08277A patent/ZA201808277B/en unknown
- 2018-12-11 MX MX2022011757A patent/MX2022011757A/en unknown
- 2018-12-17 MY MYPI2022003491A patent/MY209503A/en unknown
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2020
- 2020-05-27 JP JP2020091991A patent/JP7051937B2/en active Active
- 2020-07-22 AU AU2020207826A patent/AU2020207826B2/en not_active Ceased
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2021
- 2021-03-15 ZA ZA2021/01720A patent/ZA202101720B/en unknown
- 2021-12-01 AU AU2021277671A patent/AU2021277671B2/en active Active
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2022
- 2022-02-22 JP JP2022025557A patent/JP7387777B2/en active Active
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2023
- 2023-04-13 US US18/300,343 patent/US20230410945A1/en active Pending
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