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 PDF

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Publication number
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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chromosome
trisomy
amount
content
correction
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CA2866324A1 (en
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Zhang CHEN
Yuk Ming Dennis Lo
Kwan Chee Chan
Wenli Zheng
Hao Sun
Wai Kwun Rossa Chiu
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Chinese University of Hong Kong
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Chinese University of Hong Kong
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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
    • 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 [2D] or three-dimensional [3D] 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
    • 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)
  • Chemical & Material Sciences (AREA)
  • Biophysics (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA2866324A 2012-03-13 2013-03-13 Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis Active CA2866324C (en)

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

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Family Applications (1)

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CA2866324A Active CA2866324C (en) 2012-03-13 2013-03-13 Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis

Country Status (6)

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US (1) US9218449B2 (enExample)
EP (2) EP2825991B1 (enExample)
JP (1) JP6411995B2 (enExample)
AU (1) AU2013232123B2 (enExample)
CA (1) CA2866324C (enExample)
WO (1) WO2013138527A1 (enExample)

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US10424394B2 (en) 2011-10-06 2019-09-24 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US9984198B2 (en) 2011-10-06 2018-05-29 Sequenom, Inc. Reducing sequence read count error in assessment of complex genetic variations
US10196681B2 (en) 2011-10-06 2019-02-05 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
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US10504613B2 (en) 2012-12-20 2019-12-10 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US9920361B2 (en) 2012-05-21 2018-03-20 Sequenom, Inc. Methods and compositions for analyzing nucleic acid
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
EP4187543A1 (en) 2013-04-03 2023-05-31 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
AU2014268377B2 (en) 2013-05-24 2020-10-08 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
DK3011051T3 (en) 2013-06-21 2019-04-23 Sequenom Inc Method for non-invasive evaluation of genetic variations
US10964409B2 (en) 2013-10-04 2021-03-30 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
JP6680680B2 (ja) 2013-10-07 2020-04-15 セクエノム， インコーポレイテッド 染色体変化の非侵襲性評価のための方法およびプロセス
JP6534191B2 (ja) * 2013-10-21 2019-06-26 ベリナタ ヘルス インコーポレイテッド コピー数変動を決定することにおける検出の感度を向上させるための方法
KR102205950B1 (ko) 2013-11-07 2021-01-22 더 보드 어브 트러스티스 어브 더 리랜드 스탠포드 주니어 유니버시티 인간 마이크로바이옴 및 그의 성분의 분석을 위한 무세포 핵산
WO2015184404A1 (en) 2014-05-30 2015-12-03 Verinata Health, Inc. Detecting fetal sub-chromosomal aneuploidies and copy number variations
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
US11783911B2 (en) 2014-07-30 2023-10-10 Sequenom, Inc Methods and processes for non-invasive assessment of genetic variations
DK3230469T3 (da) 2014-12-12 2019-07-15 Verinata Health Inc Anvendelse af cellefri DNA-fragmentstørrelse til bestemmelse af kopiantalsvariationer
EP3298169B1 (en) 2015-05-18 2024-10-02 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
KR102326769B1 (ko) 2016-03-25 2021-11-17 카리우스, 인코포레이티드 합성 핵산 스파이크-인
ES2967443T3 (es) * 2016-07-06 2024-04-30 Guardant Health Inc Procedimientos de perfilado de fragmentoma de ácidos nucleicos sin células
US11200963B2 (en) 2016-07-27 2021-12-14 Sequenom, Inc. Genetic copy number alteration classifications
CA3207879C (en) 2017-01-24 2026-06-16 Sequenom, Inc. Methods and processes for assessment of genetic variations
EP3998350B1 (en) 2017-03-17 2025-05-07 Sequenom, Inc. Methods and processes for assessment of genetic mosaicism
CA3059370C (en) 2017-04-12 2022-05-10 Karius, Inc. Methods for concurrent analysis of dna and rna in mixed samples
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
US12590326B2 (en) 2018-01-10 2026-03-31 Guardant Health, Inc. Methods for fragmentome profiling of cell-free nucleic acids
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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)
EP1859051A4 (en) 2005-03-18 2009-08-05 Univ Hong Kong Chinese MARKERS FOR PRENATAL DIAGNOSIS AND SURVEILLANCE
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
WO2010033578A2 (en) 2008-09-20 2010-03-25 The Board Of Trustees Of The Leland Stanford Junior University Noninvasive diagnosis of fetal aneuploidy by sequencing
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Also Published As

Publication number Publication date
US9218449B2 (en) 2015-12-22
EP2825991A1 (en) 2015-01-21
EP3573066A1 (en) 2019-11-27
AU2013232123A1 (en) 2013-11-07
EP2825991A4 (en) 2015-09-02
US20130245961A1 (en) 2013-09-19
JP2015515266A (ja) 2015-05-28
CA2866324A1 (en) 2013-09-19
AU2013232123B2 (en) 2014-10-30
HK1204377A1 (en) 2015-11-13
EP3573066B1 (en) 2023-09-27
JP6411995B2 (ja) 2018-10-24
WO2013138527A1 (en) 2013-09-19
EP2825991B1 (en) 2019-05-15

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