JP6411995B2 - 非侵襲的出生前診断のために大量並列シークエンシング・データを分析する方法 - Google Patents

非侵襲的出生前診断のために大量並列シークエンシング・データを分析する方法 Download PDF

Info

Publication number
JP6411995B2
JP6411995B2 JP2015500578A JP2015500578A JP6411995B2 JP 6411995 B2 JP6411995 B2 JP 6411995B2 JP 2015500578 A JP2015500578 A JP 2015500578A JP 2015500578 A JP2015500578 A JP 2015500578A JP 6411995 B2 JP6411995 B2 JP 6411995B2
Authority
JP
Japan
Prior art keywords
chromosome
trisomy
chromosomal region
content
region
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
JP2015500578A
Other languages
English (en)
Japanese (ja)
Other versions
JP2015515266A (ja
JP2015515266A5 (cg-RX-API-DMAC7.html
Inventor
ジャーン チェン
ジャーン チェン
ユク ミン デニス ロー
ユク ミン デニス ロー
クワン チー チャン
クワン チー チャン
ウェンリ ジュヨン
ウェンリ ジュヨン
ハオ スン
ハオ スン
ワイ クン ロッサ チウ
ワイ クン ロッサ チウ
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 JP2015515266A publication Critical patent/JP2015515266A/ja
Publication of JP2015515266A5 publication Critical patent/JP2015515266A5/ja
Application granted granted Critical
Publication of JP6411995B2 publication Critical patent/JP6411995B2/ja
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Images

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 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
    • 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)
JP2015500578A 2012-03-13 2013-03-13 非侵襲的出生前診断のために大量並列シークエンシング・データを分析する方法 Active JP6411995B2 (ja)

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 (3)

Publication Number Publication Date
JP2015515266A JP2015515266A (ja) 2015-05-28
JP2015515266A5 JP2015515266A5 (cg-RX-API-DMAC7.html) 2015-12-10
JP6411995B2 true JP6411995B2 (ja) 2018-10-24

Family

ID=49158429

Family Applications (1)

Application Number Title Priority Date Filing Date
JP2015500578A Active JP6411995B2 (ja) 2012-03-13 2013-03-13 非侵襲的出生前診断のために大量並列シークエンシング・データを分析する方法

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)

* 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
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)

* 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)
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

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
CA2866324C (en) 2019-01-15
EP3573066B1 (en) 2023-09-27
AU2013232123B2 (en) 2014-10-30
HK1204377A1 (en) 2015-11-13
WO2013138527A1 (en) 2013-09-19
US9218449B2 (en) 2015-12-22
EP2825991B1 (en) 2019-05-15

Similar Documents

Publication Publication Date Title
JP6411995B2 (ja) 非侵襲的出生前診断のために大量並列シークエンシング・データを分析する方法
JP6001721B2 (ja) サイズに基づくゲノム分析
JP6068598B2 (ja) 多胎妊娠の分子検査
JP2023017006A (ja) Ｄｎａのサイズに基づく解析
CA2823618C (en) Noninvasive prenatal genotyping of fetal sex chromosomes
CN115035949A (zh) 通过母亲血浆dna的浅深度测序准确定量胎儿dna分数
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
AU2015200462B2 (en) Size-based genomic analysis
HK1204377B (en) Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis
HK40080394A (en) Accurate quantification of fetal dna fraction by shallow-depth sequencing of maternal plasma dna
HK1240282A1 (en) Size-based genomic analysis
AU2015227510A1 (en) Noninvasive prenatal genotyping of fetal sex chromosomes

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20151022

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20151022

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20160809

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20161109

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20161125

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20170404

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20170704

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20170801

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20180109

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20180404

TRDD Decision of grant or rejection written
A01 Written decision to grant a patent or to grant a registration (utility model)

Free format text: JAPANESE INTERMEDIATE CODE: A01

Effective date: 20180828

A61 First payment of annual fees (during grant procedure)

Free format text: JAPANESE INTERMEDIATE CODE: A61

Effective date: 20180927

R150 Certificate of patent or registration of utility model

Ref document number: 6411995

Country of ref document: JP

Free format text: JAPANESE INTERMEDIATE CODE: R150

R250 Receipt of annual fees

Free format text: JAPANESE INTERMEDIATE CODE: R250

R250 Receipt of annual fees

Free format text: JAPANESE INTERMEDIATE CODE: R250

R250 Receipt of annual fees

Free format text: JAPANESE INTERMEDIATE CODE: R250

R250 Receipt of annual fees

Free format text: JAPANESE INTERMEDIATE CODE: R250

R250 Receipt of annual fees

Free format text: JAPANESE INTERMEDIATE CODE: R250