CA2866324C - Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis - Google Patents
Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis Download PDFInfo
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- CA2866324C CA2866324C CA2866324A CA2866324A CA2866324C CA 2866324 C CA2866324 C CA 2866324C CA 2866324 A CA2866324 A CA 2866324A CA 2866324 A CA2866324 A CA 2866324A CA 2866324 C CA2866324 C CA 2866324C
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Classifications
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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
- G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
-
- 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
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/10—Ploidy or copy number detection
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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
-
- 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
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
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- Physics & Mathematics (AREA)
- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Engineering & Computer Science (AREA)
- Spectroscopy & Molecular Physics (AREA)
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- Medical Informatics (AREA)
- Bioinformatics & Computational Biology (AREA)
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Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201261610422P | 2012-03-13 | 2012-03-13 | |
| US61/610,422 | 2012-03-13 | ||
| PCT/US2013/031082 WO2013138527A1 (en) | 2012-03-13 | 2013-03-13 | Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CA2866324A1 CA2866324A1 (en) | 2013-09-19 |
| CA2866324C true CA2866324C (en) | 2019-01-15 |
Family
ID=49158429
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2866324A Active CA2866324C (en) | 2012-03-13 | 2013-03-13 | Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis |
Country Status (6)
| Country | Link |
|---|---|
| US (1) | US9218449B2 (cg-RX-API-DMAC7.html) |
| EP (2) | EP3573066B1 (cg-RX-API-DMAC7.html) |
| JP (1) | JP6411995B2 (cg-RX-API-DMAC7.html) |
| AU (1) | AU2013232123B2 (cg-RX-API-DMAC7.html) |
| CA (1) | CA2866324C (cg-RX-API-DMAC7.html) |
| WO (1) | WO2013138527A1 (cg-RX-API-DMAC7.html) |
Families Citing this family (41)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20140235474A1 (en) | 2011-06-24 | 2014-08-21 | Sequenom, Inc. | Methods and processes for non invasive assessment of a genetic variation |
| US9984198B2 (en) | 2011-10-06 | 2018-05-29 | Sequenom, Inc. | Reducing sequence read count error in assessment of complex genetic variations |
| CA2850785C (en) | 2011-10-06 | 2022-12-13 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| US9367663B2 (en) | 2011-10-06 | 2016-06-14 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| US10196681B2 (en) | 2011-10-06 | 2019-02-05 | 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 |
| JP6431769B2 (ja) | 2012-01-20 | 2018-11-28 | セクエノム， インコーポレイテッド | 実験条件を要因として含める診断プロセス |
| US9920361B2 (en) | 2012-05-21 | 2018-03-20 | Sequenom, Inc. | Methods and compositions for analyzing nucleic acid |
| US10504613B2 (en) | 2012-12-20 | 2019-12-10 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| US10497461B2 (en) | 2012-06-22 | 2019-12-03 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| US10482994B2 (en) | 2012-10-04 | 2019-11-19 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| US20130309666A1 (en) | 2013-01-25 | 2013-11-21 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| PL2981921T3 (pl) | 2013-04-03 | 2023-05-08 | Sequenom, Inc. | Metody i procesy nieinwazyjnej oceny zmienności genetycznych |
| AU2014268377B2 (en) | 2013-05-24 | 2020-10-08 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| US10622094B2 (en) | 2013-06-21 | 2020-04-14 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| IL320112A (en) | 2013-10-04 | 2025-06-01 | Sequenom Inc | Methods and processes for non-invasive assessment of genetic variations |
| WO2015054080A1 (en) | 2013-10-07 | 2015-04-16 | Sequenom, Inc. | Methods and processes for non-invasive assessment of chromosome alterations |
| WO2015061359A1 (en) | 2013-10-21 | 2015-04-30 | Verinata Health, Inc. | Method for improving the sensitivity of detection in determining copy number variations |
| CN105829589B (zh) | 2013-11-07 | 2021-02-02 | 小利兰·斯坦福大学理事会 | 用于分析人体微生物组及其组分的无细胞核酸 |
| IL249095B2 (en) | 2014-05-30 | 2023-10-01 | Verinata Health Inc | Detection of subchromosomal aneuploidy in the fetus and variations in the number of copies |
| CN107002122B (zh) | 2014-07-25 | 2023-09-19 | 华盛顿大学 | 确定导致无细胞dna的产生的组织和/或细胞类型的方法以及使用其鉴定疾病或紊乱的方法 |
| EP3760739B1 (en) | 2014-07-30 | 2025-09-03 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| WO2016094853A1 (en) | 2014-12-12 | 2016-06-16 | Verinata Health, Inc. | Using cell-free dna fragment size to determine copy number variations |
| WO2016187234A1 (en) | 2015-05-18 | 2016-11-24 | Karius, Inc. | Compositions and methods for enriching populations of nucleic acids |
| KR101678962B1 (ko) * | 2015-08-21 | 2016-12-06 | 이승재 | 대규모 병렬형 게놈서열분석 방법을 이용한 비침습적 산전검사 장치 및 방법 |
| US10095831B2 (en) | 2016-02-03 | 2018-10-09 | Verinata Health, Inc. | Using cell-free DNA fragment size to determine copy number variations |
| KR102531487B1 (ko) | 2016-03-25 | 2023-05-10 | 카리우스, 인코포레이티드 | 합성 핵산 스파이크-인 |
| EP4322168A3 (en) * | 2016-07-06 | 2024-05-15 | Guardant Health, Inc. | Methods for fragmentome profiling of cell-free nucleic acids |
| US11200963B2 (en) | 2016-07-27 | 2021-12-14 | Sequenom, Inc. | Genetic copy number alteration classifications |
| EP3574424A1 (en) | 2017-01-24 | 2019-12-04 | Sequenom, Inc. | Methods and processes for assessment of genetic variations |
| WO2018170511A1 (en) | 2017-03-17 | 2018-09-20 | Sequenom, Inc. | Methods and processes for assessment of genetic mosaicism |
| WO2018191563A1 (en) | 2017-04-12 | 2018-10-18 | Karius, Inc. | Sample preparation methods, systems and compositions |
| AU2018355575A1 (en) | 2017-10-27 | 2020-05-21 | Juno Diagnostics, Inc. | Devices, systems and methods for ultra-low volume liquid biopsy |
| CN108733979A (zh) * | 2017-10-30 | 2018-11-02 | 成都凡迪医疗器械有限公司 | Nipt的gc含量校准方法、装置及计算机可读存储介质 |
| WO2019178157A1 (en) | 2018-03-16 | 2019-09-19 | Karius, Inc. | Sample series to differentiate target nucleic acids from contaminant nucleic acids |
| AU2019244115A1 (en) | 2018-03-30 | 2020-11-19 | Juno Diagnostics, Inc. | Deep learning-based methods, devices, and systems for prenatal testing |
| CA3118990A1 (en) | 2018-11-21 | 2020-05-28 | Karius, Inc. | Direct-to-library methods, systems, and compositions |
| US11475981B2 (en) | 2020-02-18 | 2022-10-18 | Tempus Labs, Inc. | Methods and systems for dynamic variant thresholding in a liquid biopsy assay |
| US11211144B2 (en) | 2020-02-18 | 2021-12-28 | Tempus Labs, Inc. | Methods and systems for refining copy number variation in a liquid biopsy assay |
| US11211147B2 (en) | 2020-02-18 | 2021-12-28 | Tempus Labs, Inc. | Estimation of circulating tumor fraction using off-target reads of targeted-panel sequencing |
| CN115938473A (zh) * | 2022-01-20 | 2023-04-07 | 重庆师范大学 | 一种化学计量基因组基础分析的计算方法 |
Family Cites Families (13)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6927028B2 (en) | 2001-08-31 | 2005-08-09 | Chinese University Of Hong Kong | Non-invasive methods for detecting non-host DNA in a host using epigenetic differences between the host and non-host DNA |
| AT412476B (de) | 2002-09-24 | 2005-03-25 | Forsch Krebskranke Kinder | Verfahren zur herstellung eines virtuellen chromosoms |
| US7371525B2 (en) | 2003-07-29 | 2008-05-13 | The Chinese University Of Hong Kong | Compositions and methods for diagnosing and treating severe acute respiratory syndrome (SARS) |
| TWI367260B (en) | 2005-03-18 | 2012-07-01 | Univ Hong Kong Chinese | Method for detecting the presence of a fetus with trisomy 21 in a pregnant woman and kit thereof |
| US7901884B2 (en) | 2006-05-03 | 2011-03-08 | The Chinese University Of Hong Kong | Markers for prenatal diagnosis and monitoring |
| US7754428B2 (en) | 2006-05-03 | 2010-07-13 | The Chinese University Of Hong Kong | Fetal methylation markers |
| JP2010533729A (ja) | 2007-07-17 | 2010-10-28 | プレキシコン，インコーポレーテッド | キナーゼ調節のための化合物と方法、及びそのための適応 |
| US12180549B2 (en) | 2007-07-23 | 2024-12-31 | The Chinese University Of Hong Kong | Diagnosing fetal chromosomal aneuploidy using genomic sequencing |
| EP2952589B1 (en) | 2008-09-20 | 2018-02-14 | The Board of Trustees of The Leland Stanford Junior University | Noninvasive diagnosis of fetal aneuploidy by sequencing |
| US8563242B2 (en) | 2009-08-11 | 2013-10-22 | The Chinese University Of Hong Kong | Method for detecting chromosomal aneuploidy |
| CN102770558B (zh) | 2009-11-05 | 2016-04-06 | 香港中文大学 | 由母本生物样品进行胎儿基因组的分析 |
| CA2780016C (en) | 2009-11-06 | 2017-09-19 | The Chinese University Of Hong Kong | Size-based genomic analysis |
| US8725422B2 (en) | 2010-10-13 | 2014-05-13 | Complete Genomics, Inc. | Methods for estimating genome-wide copy number variations |
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2013
- 2013-03-13 CA CA2866324A patent/CA2866324C/en active Active
- 2013-03-13 EP EP19174472.1A patent/EP3573066B1/en active Active
- 2013-03-13 WO PCT/US2013/031082 patent/WO2013138527A1/en not_active Ceased
- 2013-03-13 AU AU2013232123A patent/AU2013232123B2/en active Active
- 2013-03-13 US US13/802,268 patent/US9218449B2/en active Active
- 2013-03-13 EP EP13760635.6A patent/EP2825991B1/en active Active
- 2013-03-13 JP JP2015500578A patent/JP6411995B2/ja active Active
Also Published As
| Publication number | Publication date |
|---|---|
| EP2825991A4 (en) | 2015-09-02 |
| CA2866324A1 (en) | 2013-09-19 |
| US20130245961A1 (en) | 2013-09-19 |
| EP3573066A1 (en) | 2019-11-27 |
| JP2015515266A (ja) | 2015-05-28 |
| AU2013232123A1 (en) | 2013-11-07 |
| EP2825991A1 (en) | 2015-01-21 |
| EP3573066B1 (en) | 2023-09-27 |
| AU2013232123B2 (en) | 2014-10-30 |
| HK1204377A1 (en) | 2015-11-13 |
| WO2013138527A1 (en) | 2013-09-19 |
| JP6411995B2 (ja) | 2018-10-24 |
| US9218449B2 (en) | 2015-12-22 |
| EP2825991B1 (en) | 2019-05-15 |
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Effective date: 20140918 |