CN107111693A - 用于确定高同源性区域中的基因型的方法 - Google Patents

用于确定高同源性区域中的基因型的方法 Download PDF

Info

Publication number
CN107111693A
CN107111693A CN201580070614.XA CN201580070614A CN107111693A CN 107111693 A CN107111693 A CN 107111693A CN 201580070614 A CN201580070614 A CN 201580070614A CN 107111693 A CN107111693 A CN 107111693A
Authority
CN
China
Prior art keywords
gene
homologue
pseudogene
copy number
sequence
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.)
Pending
Application number
CN201580070614.XA
Other languages
English (en)
Chinese (zh)
Inventor
D.E.马齐
A.D.J.罗伯逊
E.A.埃文斯
J.R.马圭尔
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.)
Kao Xier Limited-Liability Co
Original Assignee
Kao Xier Limited-Liability Co
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 Kao Xier Limited-Liability Co filed Critical Kao Xier Limited-Liability Co
Publication of CN107111693A publication Critical patent/CN107111693A/zh
Pending legal-status Critical Current

Links

Classifications

    • 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
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • 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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Molecular Biology (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CN201580070614.XA 2014-12-29 2015-12-28 用于确定高同源性区域中的基因型的方法 Pending CN107111693A (zh)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201462097139P 2014-12-29 2014-12-29
US62/097,139 2014-12-29
US201562234012P 2015-09-28 2015-09-28
US62/234,012 2015-09-28
PCT/US2015/067547 WO2016109364A1 (en) 2014-12-29 2015-12-28 Method for determining genotypes in regions of high homology

Publications (1)

Publication Number Publication Date
CN107111693A true CN107111693A (zh) 2017-08-29

Family

ID=56164482

Family Applications (1)

Application Number Title Priority Date Filing Date
CN201580070614.XA Pending CN107111693A (zh) 2014-12-29 2015-12-28 用于确定高同源性区域中的基因型的方法

Country Status (9)

Country Link
US (2) US20160188793A1 (https=)
EP (1) EP3289502A4 (https=)
JP (1) JP2018502602A (https=)
CN (1) CN107111693A (https=)
AU (1) AU2015374344A1 (https=)
CA (1) CA2970345A1 (https=)
HK (1) HK1243204A1 (https=)
IL (1) IL252793A0 (https=)
WO (1) WO2016109364A1 (https=)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN108251517A (zh) * 2017-12-29 2018-07-06 武汉艾德士生物科技有限公司 一种分析体系内相似序列相对数量的方法
CN113228192A (zh) * 2019-09-05 2021-08-06 因美纳有限公司 用于从全基因组测序数据进行诊断的方法和系统

Families Citing this family (24)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12129514B2 (en) 2009-04-30 2024-10-29 Molecular Loop Biosolutions, Llc Methods and compositions for evaluating genetic markers
US9163281B2 (en) 2010-12-23 2015-10-20 Good Start Genetics, Inc. Methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction
US10851414B2 (en) 2013-10-18 2020-12-01 Good Start Genetics, Inc. Methods for determining carrier status
US11408024B2 (en) * 2014-09-10 2022-08-09 Molecular Loop Biosciences, Inc. Methods for selectively suppressing non-target sequences
EP4095261B1 (en) 2015-01-06 2025-05-28 Molecular Loop Biosciences, Inc. Screening for structural variants
CN106407748A (zh) * 2016-11-04 2017-02-15 成都鑫云解码科技有限公司 内分泌与代谢系统对应的基因突变位点的获取方法及装置
CN106503490A (zh) * 2016-11-04 2017-03-15 成都鑫云解码科技有限公司 泌尿与生殖系统对应的基因的突变位点的获取方法及装置
CN106529209A (zh) * 2016-11-04 2017-03-22 成都鑫云解码科技有限公司 免疫系统对应的基因的突变位点的获取方法及装置
CN106407747A (zh) * 2016-11-04 2017-02-15 成都鑫云解码科技有限公司 肿瘤对应的基因的突变位点的获取方法及装置
CN106407745A (zh) * 2016-11-04 2017-02-15 成都鑫云解码科技有限公司 皮肤对应的基因的突变位点的获取方法及装置
CN106407746A (zh) * 2016-11-04 2017-02-15 成都鑫云解码科技有限公司 呼吸系统对应的基因的突变位点的获取方法及装置
CN106407744A (zh) * 2016-11-04 2017-02-15 成都鑫云解码科技有限公司 饮食与健康对应的基因的突变位点的获取方法及装置
CN106503489A (zh) * 2016-11-04 2017-03-15 成都鑫云解码科技有限公司 心血管系统对应的基因的突变位点的获取方法及装置
CN106503488A (zh) * 2016-11-04 2017-03-15 成都鑫云解码科技有限公司 消化系统对应的基因的突变位点的获取方法及装置
US11993811B2 (en) * 2017-01-31 2024-05-28 Myriad Women's Health, Inc. Systems and methods for identifying and quantifying gene copy number variations
US10894978B2 (en) 2017-12-19 2021-01-19 Bioo Scientific Corporation Genetic test for detecting congenital adrenal hyperplasia
WO2019182956A1 (en) * 2018-03-22 2019-09-26 Myriad Women's Health, Inc. Variant calling using machine learning
CN110699436B (zh) * 2018-07-10 2023-07-21 天津华大医学检验所有限公司 确定待测样本的smn1基因是否存在七号外显子缺失的方法和系统
EP3830828A4 (en) * 2018-07-27 2022-05-04 Myriad Women's Health, Inc. METHODS FOR DETECTING GENETIC VARIATIONS IN HIGHLY HOMOLOGOUS SEQUENCES BY INDEPENDENT ALIGNMENT AND PAIRING OF SEQUENCE READS
US20220223228A1 (en) * 2019-05-22 2022-07-14 Seoul National University R&Db Foundation Method and device for predicting genotype using ngs data
CN113724791B (zh) * 2021-09-09 2024-03-12 天津华大医学检验所有限公司 Cyp21a2基因ngs数据分析的方法、装置及应用
CN113564247B (zh) * 2021-09-24 2022-01-28 北京贝瑞和康生物技术有限公司 同时检测先天性肾上腺皮质增生症相关9个基因多种突变的引物组和试剂盒
US12431218B2 (en) 2022-03-08 2025-09-30 Illumina, Inc. Multi-pass software-accelerated genomic read mapping engine
KR20250034300A (ko) * 2022-07-07 2025-03-11 일루미나, 인코포레이티드 재조합 이벤트를 검출하기 위한 방법 및 시스템

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN101067156A (zh) * 2007-05-18 2007-11-07 中国人民解放军第三军医大学第一附属医院 一种基于选择性探针的多重pcr方法及其应用
US20140371078A1 (en) * 2013-06-17 2014-12-18 Verinata Health, Inc. Method for determining copy number variations in sex chromosomes

Family Cites Families (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20060210967A1 (en) * 2004-07-02 2006-09-21 Agan Brian K Re-sequencing pathogen microarray
US8407013B2 (en) * 2005-06-07 2013-03-26 Peter K. Rogan AB initio generation of single copy genomic probes
WO2010104608A2 (en) * 2009-03-13 2010-09-16 Life Technologies Corporation Computer implemented method for indexing reference genome
US9361426B2 (en) * 2009-11-12 2016-06-07 Esoterix Genetic Laboratories, Llc Copy number analysis of genetic locus
US20120215463A1 (en) * 2011-02-23 2012-08-23 The Mitre Corporation Rapid Genomic Sequence Homology Assessment Scheme Based on Combinatorial-Analytic Concepts
WO2012125848A2 (en) * 2011-03-16 2012-09-20 Baylor College Of Medicine A method for comprehensive sequence analysis using deep sequencing technology
US20130184999A1 (en) * 2012-01-05 2013-07-18 Yan Ding Systems and methods for cancer-specific drug targets and biomarkers discovery
CN102952877B (zh) * 2012-08-06 2014-09-24 深圳华大基因研究院 检测α珠蛋白基因拷贝数的方法和系统
GB2533006B (en) * 2012-09-04 2017-06-07 Guardant Health Inc Systems and methods to detect copy number variation
US10851414B2 (en) * 2013-10-18 2020-12-01 Good Start Genetics, Inc. Methods for determining carrier status
WO2015058086A1 (en) * 2013-10-18 2015-04-23 Good Start Genetics, Inc. Methods for copy number determination
US11408024B2 (en) * 2014-09-10 2022-08-09 Molecular Loop Biosciences, Inc. Methods for selectively suppressing non-target sequences

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN101067156A (zh) * 2007-05-18 2007-11-07 中国人民解放军第三军医大学第一附属医院 一种基于选择性探针的多重pcr方法及其应用
US20140371078A1 (en) * 2013-06-17 2014-12-18 Verinata Health, Inc. Method for determining copy number variations in sex chromosomes

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
VALENTINA BOEVA等: "Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data", 《BIOINFORMATICS》 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN108251517A (zh) * 2017-12-29 2018-07-06 武汉艾德士生物科技有限公司 一种分析体系内相似序列相对数量的方法
CN113228192A (zh) * 2019-09-05 2021-08-06 因美纳有限公司 用于从全基因组测序数据进行诊断的方法和系统

Also Published As

Publication number Publication date
HK1243204A1 (zh) 2018-07-06
US20210012859A1 (en) 2021-01-14
CA2970345A1 (en) 2016-07-07
EP3289502A1 (en) 2018-03-07
JP2018502602A (ja) 2018-02-01
EP3289502A4 (en) 2018-09-12
US20160188793A1 (en) 2016-06-30
IL252793A0 (en) 2017-08-31
WO2016109364A1 (en) 2016-07-07
AU2015374344A1 (en) 2017-07-06

Similar Documents

Publication Publication Date Title
CN107111693A (zh) 用于确定高同源性区域中的基因型的方法
Edge et al. Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing
Sedlazeck et al. Accurate detection of complex structural variations using single-molecule sequencing
Takayama et al. Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference
Li et al. A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data
Shigemizu et al. A practical method to detect SNVs and indels from whole genome and exome sequencing data
Liu et al. Interrogating the “unsequenceable” genomic trinucleotide repeat disorders by long-read sequencing
Rimmer et al. Integrating mapping-, assembly-and haplotype-based approaches for calling variants in clinical sequencing applications
Hasan et al. Performance evaluation of indel calling tools using real short-read data
Reumers et al. Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing
KR102447079B1 (ko) 유전적 변이의 비침습 평가를 위한 방법 및 프로세스
KR102665592B1 (ko) 유전적 변이의 비침습 평가를 위한 방법 및 프로세스
CN107408163B (zh) 用于分析基因的方法及装置
GB2444410A (en) Genetic profiling method
JP7361774B2 (ja) シーケンスリードの独立したアラインメントおよびペアリングによって高度に相同なシーケンスにおける遺伝的変異を検出するための方法
Rajaby et al. INSurVeyor: improving insertion calling from short read sequencing data
Wong et al. DNA sequencing technologies: sequencing data protocols and bioinformatics tools
Heinrich et al. Estimating exome genotyping accuracy by comparing to data from large scale sequencing projects
US20250014680A1 (en) System and Method for Correlated Error Event Mitigation for Variant Calling
Ruark et al. The ICR1000 UK exome series: a resource of gene variation in an outbred population
Fu et al. MethPhaser: methylation-based long-read haplotype phasing of human genomes
Shukla et al. hg19KIndel: ethnicity normalized human reference genome
Sitarčík et al. WarpSTR: determining tandem repeat lengths using raw nanopore signals
Lu et al. Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data
Garimella et al. Population-scale long-read sequencing in the All of Us research program

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination
REG Reference to a national code

Ref country code: HK

Ref legal event code: DE

Ref document number: 1243204

Country of ref document: HK

WD01 Invention patent application deemed withdrawn after publication

Application publication date: 20170829

WD01 Invention patent application deemed withdrawn after publication
REG Reference to a national code

Ref country code: HK

Ref legal event code: WD

Ref document number: 1243204

Country of ref document: HK