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MX2017012367A - Producto en desarrollo de analisis de secuenciacion de alineacion y variante. - Google Patents

Producto en desarrollo de analisis de secuenciacion de alineacion y variante.

Info

Publication number
MX2017012367A
MX2017012367A MX2017012367A MX2017012367A MX2017012367A MX 2017012367 A MX2017012367 A MX 2017012367A MX 2017012367 A MX2017012367 A MX 2017012367A MX 2017012367 A MX2017012367 A MX 2017012367A MX 2017012367 A MX2017012367 A MX 2017012367A
Authority
MX
Mexico
Prior art keywords
amplification
sequence
ngs
solid phase
methods
Prior art date
Application number
MX2017012367A
Other languages
English (en)
Other versions
MX394296B (es
Inventor
Elzinga Christopher
Original Assignee
Quest Diagnostics Invest Inc
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 Quest Diagnostics Invest Inc filed Critical Quest Diagnostics Invest Inc
Publication of MX2017012367A publication Critical patent/MX2017012367A/es
Publication of MX394296B publication Critical patent/MX394296B/es

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
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/12—Computing arrangements based on biological models using genetic models
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00—Computing arrangements using knowledge-based models
    • G06N5/04—Inference or reasoning models
    • 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
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • 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
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Physics & Mathematics (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Theoretical Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Pathology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Oncology (AREA)
  • Hospice & Palliative Care (AREA)
  • Artificial Intelligence (AREA)
  • Computational Linguistics (AREA)
  • Data Mining & Analysis (AREA)
  • Evolutionary Computation (AREA)
  • Computing Systems (AREA)
  • General Physics & Mathematics (AREA)
  • Mathematical Physics (AREA)
  • Software Systems (AREA)
  • Biomedical Technology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Se proporcionan sistemas y métodos para analizar datos de secuencia genéticos a partir de plataformas de secuencia de siguiente generación (NGS). También se proporcionan métodos para la preparación de muestras para análisis de secuencia de ácido nucleico mediante NGS. La llamada de variante se realiza con un llamador de variante GATK modificado. El mapeo de las lecturas para una secuencia de referencia genómica se realiza con un Alineador Burrows Wheeler (BWA) y no comprende recorte suave. La secuencia de referencia genómica es referencia de genoma humano GRCh37.1. El método de secuenciación comprende PCR en emulsión (emPCR), amplificación de círculo rodante, o amplificación en fase sólida. En algunas modalidades, la amplificación en fase sólida es amplificación de puente clonal.
MX2017012367A 2015-03-26 2016-03-25 Producto en desarrollo de análisis de secuenciación de alineación y variante. MX394296B (es)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562138620P 2015-03-26 2015-03-26
US201562253908P 2015-11-11 2015-11-11
PCT/US2016/024319 WO2016154584A1 (en) 2015-03-26 2016-03-25 Alignment and variant sequencing analysis pipeline

Publications (2)

Publication Number Publication Date
MX2017012367A true MX2017012367A (es) 2017-12-14
MX394296B MX394296B (es) 2025-03-24

Family

ID=56978583

Family Applications (2)

Application Number Title Priority Date Filing Date
MX2017012367A MX394296B (es) 2015-03-26 2016-03-25 Producto en desarrollo de análisis de secuenciación de alineación y variante.
MX2022009242A MX2022009242A (es) 2015-03-26 2017-09-26 Producto en desarrollo de analisis de secuenciacion de alineacion y variante.

Family Applications After (1)

Application Number Title Priority Date Filing Date
MX2022009242A MX2022009242A (es) 2015-03-26 2017-09-26 Producto en desarrollo de analisis de secuenciacion de alineacion y variante.

Country Status (6)

Country Link
US (1) US20180051329A1 (es)
EP (2) EP4425500A3 (es)
CN (2) CN107849612B (es)
CA (1) CA2980327A1 (es)
MX (2) MX394296B (es)
WO (1) WO2016154584A1 (es)

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CN103748236B (zh) 2011-04-15 2018-12-25 约翰·霍普金斯大学 安全测序系统
AU2013338393C1 (en) 2012-10-29 2024-07-25 The Johns Hopkins University Papanicolaou test for ovarian and endometrial cancers
US10395759B2 (en) 2015-05-18 2019-08-27 Regeneron Pharmaceuticals, Inc. Methods and systems for copy number variant detection
WO2017027653A1 (en) 2015-08-11 2017-02-16 The Johns Hopkins University Assaying ovarian cyst fluid
CN115273970A (zh) 2016-02-12 2022-11-01 瑞泽恩制药公司 用于检测异常核型的方法和系统
US10600499B2 (en) 2016-07-13 2020-03-24 Seven Bridges Genomics Inc. Systems and methods for reconciling variants in sequence data relative to reference sequence data
US10296842B2 (en) 2017-07-21 2019-05-21 Helix OpCo, LLC Genomic services system with dual-phase genotype imputation
US10622095B2 (en) * 2017-07-21 2020-04-14 Helix OpCo, LLC Genomic services platform supporting multiple application providers
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CN109321646A (zh) * 2018-09-12 2019-02-12 山东省农作物种质资源中心 基于ngs读段与参考序列比对的虚拟pcr方法
EP3867400A4 (en) * 2018-10-17 2022-07-27 Quest Diagnostics Investments LLC GENOME SEQUENCE SELECTION SYSTEM
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CN111243666B (zh) * 2020-01-08 2023-04-07 华南理工大学 一种基于Nextflow的环状核糖核酸自动化分析方法及系统
KR102345994B1 (ko) * 2020-01-22 2022-01-03 가톨릭대학교 산학협력단 Ngs 분석에서의 질병 관련 유전자 선별 방법 및 장치
CA3170345A1 (en) 2020-02-14 2021-08-19 The Johns Hopkins University Methods and materials for assessing nucleic acids
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EP4332975A1 (en) * 2022-08-29 2024-03-06 Siemens Healthcare Diagnostics Products GmbH Method for eliminating non-natural sequence portions from fastq sequence data
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CN116612808B (zh) * 2023-05-05 2025-11-25 成都爱诺言医学检验实验室有限公司 基于ngs技术的hiv-1耐药基因检测方法
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Also Published As

Publication number Publication date
EP3274475A4 (en) 2018-12-05
CN107849612B (zh) 2023-04-14
BR112017020363A2 (pt) 2018-06-05
EP3274475B1 (en) 2024-07-31
MX2022009242A (es) 2022-08-18
CN107849612A (zh) 2018-03-27
US20180051329A1 (en) 2018-02-22
HK1250520A1 (en) 2018-12-21
CA2980327A1 (en) 2016-09-29
WO2016154584A1 (en) 2016-09-29
EP4425500A3 (en) 2025-04-02
CN116042833A (zh) 2023-05-02
EP4425500A2 (en) 2024-09-04
MX394296B (es) 2025-03-24
EP3274475A1 (en) 2018-01-31

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