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

Info

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
Authority
CA
Canada
Prior art keywords
chromosome
trisomy
amount
content
correction
Prior art date
Legal status (The legal status 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 status listed.)
Active
Application number
CA2866324A
Other languages
English (en)
French (fr)
Other versions
CA2866324A1 (en
Inventor
Zhang CHEN
Yuk Ming Dennis Lo
Kwan Chee Chan
Wenli Zheng
Hao Sun
Wai Kwun Rossa Chiu
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Chinese University of Hong Kong CUHK
Original Assignee
Chinese University of Hong Kong CUHK
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 Chinese University of Hong Kong CUHK filed Critical Chinese University of Hong Kong CUHK
Publication of CA2866324A1 publication Critical patent/CA2866324A1/en
Application granted granted Critical
Publication of CA2866324C publication Critical patent/CA2866324C/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

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
    • 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

Landscapes

  • 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

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 (enExample)
EP (2) EP3573066B1 (enExample)
JP (1) JP6411995B2 (enExample)
AU (1) AU2013232123B2 (enExample)
CA (1) CA2866324C (enExample)
WO (1) WO2013138527A1 (enExample)

Families Citing this family (42)

* Cited by examiner, † Cited by third party
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
US9367663B2 (en) * 2011-10-06 2016-06-14 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
US20140242588A1 (en) 2011-10-06 2014-08-28 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
EP2805280B1 (en) 2012-01-20 2022-10-05 Sequenom, Inc. Diagnostic processes that factor experimental conditions
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
EP4187543A1 (en) 2013-04-03 2023-05-31 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US10699800B2 (en) 2013-05-24 2020-06-30 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
KR102299305B1 (ko) 2013-06-21 2021-09-06 시쿼넘, 인코포레이티드 유전적 변이의 비침습 평가를 위한 방법 및 프로세스
DK3053071T3 (da) 2013-10-04 2024-01-22 Sequenom Inc Fremgangsmåder og processer til ikke-invasiv bedømmelse af genetiske variationer
EP3495496B1 (en) 2013-10-07 2020-11-25 Sequenom, Inc. Methods and processes for non-invasive assessment of chromosome alterations
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
CA2929557C (en) 2013-11-07 2023-09-26 The Board Of Trustees Of The Leland Stanford Junior University Cell-free nucleic acids for the analysis of the human microbiome and components thereof
JP6659672B2 (ja) 2014-05-30 2020-03-04 ベリナタ ヘルス インコーポレイテッド 胎児染色体部分異数性およびコピー数変動の検出
CA2956208C (en) 2014-07-25 2025-07-08 University Of Washington METHODS FOR DETERMINING TISSUES AND/OR CELL TYPES RENDERING CELL-FREE DNA AND RELATED METHODS FOR DETERMINING A DISEASE OR DISORDER
EP3175000B1 (en) 2014-07-30 2020-07-29 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
AU2015360298B2 (en) 2014-12-12 2018-06-07 Verinata Health, Inc. Using cell-free DNA fragment size to determine copy number variations
CA2986036C (en) 2015-05-18 2022-07-26 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
EP3433382B1 (en) 2016-03-25 2021-09-01 Karius, Inc. Synthetic nucleic acid spike-ins
CA3030038A1 (en) * 2016-07-06 2018-01-11 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
WO2018140521A1 (en) 2017-01-24 2018-08-02 Sequenom, Inc. Methods and processes for assessment of genetic variations
PT3596233T (pt) 2017-03-17 2022-08-22 Sequenom Inc Métodos e processos para avaliação de mosaicismo genético
CA3059370C (en) 2017-04-12 2022-05-10 Karius, Inc. Methods for concurrent analysis of dna and rna in mixed samples
JP2021500883A (ja) 2017-10-27 2021-01-14 ジュノ ダイアグノスティックス，インク． 超微量リキッドバイオプシーのためのデバイス、システム、および方法
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
WO2019178157A1 (en) 2018-03-16 2019-09-19 Karius, Inc. Sample series to differentiate target nucleic acids from contaminant nucleic acids
CA3095030A1 (en) 2018-03-30 2019-10-03 Juno Diagnostics, Inc. Deep learning-based methods, devices, and systems for prenatal testing
EP4428234B1 (en) 2018-11-21 2025-12-24 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
US11211147B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Estimation of circulating tumor fraction using off-target reads of targeted-panel sequencing
US11211144B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Methods and systems for refining copy number variation in a liquid biopsy assay
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)

* Cited by examiner, † Cited by third party
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)
CA2894337C (en) 2005-03-18 2018-08-28 The Chinese University Of Hong Kong Markers for prenatal diagnosis of trisomy 18
US7754428B2 (en) 2006-05-03 2010-07-13 The Chinese University Of Hong Kong Fetal methylation markers
US7901884B2 (en) 2006-05-03 2011-03-08 The Chinese University Of Hong Kong Markers for prenatal diagnosis and monitoring
US20100190777A1 (en) 2007-07-17 2010-07-29 Plexxikon Inc. Compounds and methods for kinase modulation, and indications therefor
US12180549B2 (en) 2007-07-23 2024-12-31 The Chinese University Of Hong Kong Diagnosing fetal chromosomal aneuploidy using genomic sequencing
ES2620012T3 (es) 2008-09-20 2017-06-27 The Board Of Trustees Of The Leland Stanford Junior University Diagnóstico no invasivo de la aneuploidia fetal por secuenciación
US8563242B2 (en) 2009-08-11 2013-10-22 The Chinese University Of Hong Kong Method for detecting chromosomal aneuploidy
SMT202300034T1 (it) 2009-11-05 2023-03-17 Sequenom Inc Analisi genomica fetale da un campione biologico materno
EA034241B1 (ru) * 2009-11-06 2020-01-21 Те Чайниз Юниверсити Ов Гонконг Способ пренатальной диагностики дисбаланса последовательности
US8725422B2 (en) 2010-10-13 2014-05-13 Complete Genomics, Inc. Methods for estimating genome-wide copy number variations

Also Published As

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

Similar Documents

Publication Publication Date Title
US9218449B2 (en) Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis
JP6068598B2 (ja) 多胎妊娠の分子検査
US10619214B2 (en) Detecting genetic aberrations associated with cancer using genomic sequencing
't Hoen et al. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
JP6001721B2 (ja) サイズに基づくゲノム分析
Chen et al. Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing
EP4112740B1 (en) Size-based analysis of fetal dna fraction in maternal plasma
US20140256559A1 (en) Diagnosing fetal chromosomal aneuploidy using massively parallel genomic sequencing
Brümmer et al. Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs
HK40017618B (en) Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis
HK40017618A (en) Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis
HK1204377B (en) Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis
Day-Williams et al. An evaluation of different target enrichment methods in pooled sequencing designs for complex disease association studies
AU2015200462B2 (en) Size-based genomic analysis
HK40084570B (en) Size-based analysis of fetal dna fraction in maternal plasma
HK1240282A1 (en) Size-based genomic analysis

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20140918

MPN Maintenance fee for patent paid

Free format text: FEE DESCRIPTION TEXT: MF (PATENT, 12TH ANNIV.) - STANDARD

Year of fee payment: 12

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20241212

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20241212

MPN Maintenance fee for patent paid

Free format text: FEE DESCRIPTION TEXT: MF (PATENT, 13TH ANNIV.) - STANDARD

Year of fee payment: 13

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20260105

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20260105