CN103843001B - 复杂核酸序列数据的处理和分析 - Google Patents

复杂核酸序列数据的处理和分析 Download PDF

Info

Publication number
CN103843001B
CN103843001B CN201280029331.7A CN201280029331A CN103843001B CN 103843001 B CN103843001 B CN 103843001B CN 201280029331 A CN201280029331 A CN 201280029331A CN 103843001 B CN103843001 B CN 103843001B
Authority
CN
China
Prior art keywords
haplotype
sequence
allele
heterozygous
genome
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
CN201280029331.7A
Other languages
English (en)
Chinese (zh)
Other versions
CN103843001A (zh
Inventor
R.卓马纳克
B.A.彼得斯
B.G.科尔马尼
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.)
Complete Genomics Inc
Original Assignee
Complete Genomics 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 Complete Genomics Inc filed Critical Complete Genomics Inc
Priority to CN201710362635.XA priority Critical patent/CN107368705B/zh
Publication of CN103843001A publication Critical patent/CN103843001A/zh
Application granted granted Critical
Publication of CN103843001B publication Critical patent/CN103843001B/zh
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
    • 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

Landscapes

  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CN201280029331.7A 2011-04-14 2012-04-13 复杂核酸序列数据的处理和分析 Active CN103843001B (zh)

Priority Applications (1)

Application Number Priority Date Filing Date Title
CN201710362635.XA CN107368705B (zh) 2011-04-14 2012-04-13 分析生物体的基因组dna的方法和计算机系统

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US201161517196P 2011-04-14 2011-04-14
US61/517,196 2011-04-14
US201161527428P 2011-08-25 2011-08-25
US61/527,428 2011-08-25
US201161546516P 2011-10-12 2011-10-12
US61/546,516 2011-10-12
PCT/US2012/033686 WO2012142531A2 (en) 2011-04-14 2012-04-13 Processing and analysis of complex nucleic acid sequence data

Related Child Applications (1)

Application Number Title Priority Date Filing Date
CN201710362635.XA Division CN107368705B (zh) 2011-04-14 2012-04-13 分析生物体的基因组dna的方法和计算机系统

Publications (2)

Publication Number Publication Date
CN103843001A CN103843001A (zh) 2014-06-04
CN103843001B true CN103843001B (zh) 2017-06-09

Family

ID=47010019

Family Applications (2)

Application Number Title Priority Date Filing Date
CN201280029331.7A Active CN103843001B (zh) 2011-04-14 2012-04-13 复杂核酸序列数据的处理和分析
CN201710362635.XA Active CN107368705B (zh) 2011-04-14 2012-04-13 分析生物体的基因组dna的方法和计算机系统

Family Applications After (1)

Application Number Title Priority Date Filing Date
CN201710362635.XA Active CN107368705B (zh) 2011-04-14 2012-04-13 分析生物体的基因组dna的方法和计算机系统

Country Status (7)

Country Link
US (1) US20140051588A9 (enExample)
EP (1) EP2754078A4 (enExample)
JP (2) JP2014516514A (enExample)
CN (2) CN103843001B (enExample)
AU (1) AU2012242525B2 (enExample)
CA (1) CA2833165A1 (enExample)
WO (1) WO2012142531A2 (enExample)

Families Citing this family (203)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2611671C (en) 2005-06-15 2013-10-08 Callida Genomics, Inc. Single molecule arrays for genetic and chemical analysis
US9424392B2 (en) 2005-11-26 2016-08-23 Natera, Inc. System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals
US10083273B2 (en) 2005-07-29 2018-09-25 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US10081839B2 (en) 2005-07-29 2018-09-25 Natera, Inc System and method for cleaning noisy genetic data and determining chromosome copy number
US11111544B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US11111543B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US8592150B2 (en) 2007-12-05 2013-11-26 Complete Genomics, Inc. Methods and compositions for long fragment read sequencing
US9524369B2 (en) 2009-06-15 2016-12-20 Complete Genomics, Inc. Processing and analysis of complex nucleic acid sequence data
EP2473638B1 (en) 2009-09-30 2017-08-09 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US20190010543A1 (en) 2010-05-18 2019-01-10 Natera, Inc. Methods for simultaneous amplification of target loci
US11332785B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US12152275B2 (en) 2010-05-18 2024-11-26 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
US10316362B2 (en) 2010-05-18 2019-06-11 Natera, Inc. Methods for simultaneous amplification of target loci
US11332793B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for simultaneous amplification of target loci
US11408031B2 (en) 2010-05-18 2022-08-09 Natera, Inc. Methods for non-invasive prenatal paternity testing
US12221653B2 (en) 2010-05-18 2025-02-11 Natera, Inc. Methods for simultaneous amplification of target loci
US8825412B2 (en) 2010-05-18 2014-09-02 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11326208B2 (en) 2010-05-18 2022-05-10 Natera, Inc. Methods for nested PCR amplification of cell-free DNA
US11339429B2 (en) 2010-05-18 2022-05-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
CA2821906C (en) 2010-12-22 2020-08-25 Natera, Inc. Methods for non-invasive prenatal paternity testing
CA2824387C (en) 2011-02-09 2019-09-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11591637B2 (en) 2012-08-14 2023-02-28 10X Genomics, Inc. Compositions and methods for sample processing
US10323279B2 (en) 2012-08-14 2019-06-18 10X Genomics, Inc. Methods and systems for processing polynucleotides
EP4397767A3 (en) 2012-08-14 2024-07-31 10X Genomics, Inc. Microcapsule compositions and methods
US10752949B2 (en) 2012-08-14 2020-08-25 10X Genomics, Inc. Methods and systems for processing polynucleotides
US9951386B2 (en) 2014-06-26 2018-04-24 10X Genomics, Inc. Methods and systems for processing polynucleotides
US9701998B2 (en) 2012-12-14 2017-07-11 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10584381B2 (en) 2012-08-14 2020-03-10 10X Genomics, Inc. Methods and systems for processing polynucleotides
US20140100126A1 (en) 2012-08-17 2014-04-10 Natera, Inc. Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
US10829816B2 (en) 2012-11-19 2020-11-10 Apton Biosystems, Inc. Methods of analyte detection
CA2891939C (en) 2012-11-19 2020-10-27 Apton Biosystems, Inc. Digital analysis of molecular analytes using single molecule detection
US10533221B2 (en) 2012-12-14 2020-01-14 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10068054B2 (en) 2013-01-17 2018-09-04 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
WO2014113736A1 (en) 2013-01-17 2014-07-24 Edico Genome Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US10691775B2 (en) 2013-01-17 2020-06-23 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US9679104B2 (en) 2013-01-17 2017-06-13 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US9792405B2 (en) 2013-01-17 2017-10-17 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US10847251B2 (en) 2013-01-17 2020-11-24 Illumina, Inc. Genomic infrastructure for on-site or cloud-based DNA and RNA processing and analysis
US20140242581A1 (en) * 2013-01-23 2014-08-28 Reproductive Genetics And Technology Solutions, Llc Compositions and methods for genetic analysis of embryos
US9411930B2 (en) 2013-02-01 2016-08-09 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
CA3209385A1 (en) * 2013-02-01 2014-08-07 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
CN108753766A (zh) 2013-02-08 2018-11-06 10X基因组学有限公司 多核苷酸条形码生成
EP2959011A1 (en) * 2013-02-19 2015-12-30 Cergentis B.V. Sequencing strategies for genomic regions of interest
WO2014151554A1 (en) * 2013-03-15 2014-09-25 The Trustees Of The University Of Pennsylvania Phi29 method for library preparation
US9328382B2 (en) 2013-03-15 2016-05-03 Complete Genomics, Inc. Multiple tagging of individual long DNA fragments
WO2015010051A1 (en) * 2013-07-19 2015-01-22 Ludwig Institute For Cancer Research Whole-genome and targeted haplotype reconstruction
US9116866B2 (en) 2013-08-21 2015-08-25 Seven Bridges Genomics Inc. Methods and systems for detecting sequence variants
US9898575B2 (en) 2013-08-21 2018-02-20 Seven Bridges Genomics Inc. Methods and systems for aligning sequences
WO2015027245A1 (en) * 2013-08-23 2015-02-26 Complete Genomics, Inc. Long fragment de novo assembly using short reads
US10395758B2 (en) 2013-08-30 2019-08-27 10X Genomics, Inc. Sequencing methods
US10262755B2 (en) 2014-04-21 2019-04-16 Natera, Inc. Detecting cancer mutations and aneuploidy in chromosomal segments
US10577655B2 (en) 2013-09-27 2020-03-03 Natera, Inc. Cell free DNA diagnostic testing standards
CN105593683B (zh) 2013-10-01 2018-11-30 考利达基因组股份有限公司 鉴定基因组中的变异的定相和连接方法
SG11201603039PA (en) 2013-10-18 2016-05-30 Seven Bridges Genomics Inc Methods and systems for identifying disease-induced mutations
US11049587B2 (en) 2013-10-18 2021-06-29 Seven Bridges Genomics Inc. Methods and systems for aligning sequences in the presence of repeating elements
AU2014337089B2 (en) 2013-10-18 2019-08-08 Seven Bridges Genomics Inc. Methods and systems for genotyping genetic samples
US10832797B2 (en) 2013-10-18 2020-11-10 Seven Bridges Genomics Inc. Method and system for quantifying sequence alignment
US9092402B2 (en) 2013-10-21 2015-07-28 Seven Bridges Genomics Inc. Systems and methods for using paired-end data in directed acyclic structure
US9824068B2 (en) 2013-12-16 2017-11-21 10X Genomics, Inc. Methods and apparatus for sorting data
CN105980578B (zh) * 2013-12-16 2020-02-14 深圳华大智造科技有限公司 用于使用机器学习进行dna测序的碱基判定器
JP2017510871A (ja) 2014-01-10 2017-04-13 セブン ブリッジズ ジェノミクス インコーポレイテッド リードマッピングにおける公知の対立遺伝子の使用のためのシステム及び方法
US9817944B2 (en) * 2014-02-11 2017-11-14 Seven Bridges Genomics Inc. Systems and methods for analyzing sequence data
CA2943624A1 (en) 2014-04-10 2015-10-15 10X Genomics, Inc. Fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same
US12492429B2 (en) 2014-04-21 2025-12-09 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
EP3957749A1 (en) 2014-04-21 2022-02-23 Natera, Inc. Detecting tumour specific mutations in biopsies with whole exome sequencing and in cell-free samples
US20180173846A1 (en) 2014-06-05 2018-06-21 Natera, Inc. Systems and Methods for Detection of Aneuploidy
EP3161160B1 (en) 2014-06-26 2021-10-13 10X Genomics, Inc. Methods of analyzing nucleic acids from individual cells or cell populations
EP3161700B1 (en) 2014-06-26 2023-03-29 10X Genomics, Inc. Processes and systems for nucleic acid sequence assembly
AU2015279617A1 (en) 2014-06-26 2017-01-12 10X Genomics, Inc. Analysis of nucleic acid sequences
US12312640B2 (en) 2014-06-26 2025-05-27 10X Genomics, Inc. Analysis of nucleic acid sequences
WO2016019360A1 (en) 2014-08-01 2016-02-04 Dovetail Genomics Llc Tagging nucleic acids for sequence assembly
CA2964349C (en) 2014-10-14 2023-03-21 Seven Bridges Genomics Inc. Systems and methods for smart tools in sequence pipelines
US9859394B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US9618474B2 (en) 2014-12-18 2017-04-11 Edico Genome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US10006910B2 (en) 2014-12-18 2018-06-26 Agilome, Inc. Chemically-sensitive field effect transistors, systems, and methods for manufacturing and using the same
US10429342B2 (en) 2014-12-18 2019-10-01 Edico Genome Corporation Chemically-sensitive field effect transistor
US9857328B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Chemically-sensitive field effect transistors, systems and methods for manufacturing and using the same
US10020300B2 (en) 2014-12-18 2018-07-10 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
CN107427808B (zh) 2015-01-12 2020-10-23 10X基因组学有限公司 用于制备核酸测序文库的方法和系统以及用其制备的文库
KR20170106979A (ko) * 2015-01-13 2017-09-22 10엑스 제노믹스, 인크. 구조 변이 및 위상 조정 정보를 시각화하기 위한 시스템 및 방법
CN105986011B (zh) * 2015-01-30 2019-10-15 深圳华大基因研究院 一种杂合性缺失的检测方法
EP3256606B1 (en) 2015-02-09 2019-05-22 10X Genomics, Inc. Systems and methods for determining structural variation
WO2016134034A1 (en) 2015-02-17 2016-08-25 Dovetail Genomics Llc Nucleic acid sequence assembly
WO2016141294A1 (en) 2015-03-05 2016-09-09 Seven Bridges Genomics Inc. Systems and methods for genomic pattern analysis
EP3329491A2 (en) 2015-03-23 2018-06-06 Edico Genome Corporation Method and system for genomic visualization
WO2016154540A1 (en) 2015-03-26 2016-09-29 Dovetail Genomics Llc Physical linkage preservation in dna storage
US11479812B2 (en) 2015-05-11 2022-10-25 Natera, Inc. Methods and compositions for determining ploidy
US10275567B2 (en) 2015-05-22 2019-04-30 Seven Bridges Genomics Inc. Systems and methods for haplotyping
US10793895B2 (en) 2015-08-24 2020-10-06 Seven Bridges Genomics Inc. Systems and methods for epigenetic analysis
US10724110B2 (en) 2015-09-01 2020-07-28 Seven Bridges Genomics Inc. Systems and methods for analyzing viral nucleic acids
US10584380B2 (en) 2015-09-01 2020-03-10 Seven Bridges Genomics Inc. Systems and methods for mitochondrial analysis
US11347704B2 (en) 2015-10-16 2022-05-31 Seven Bridges Genomics Inc. Biological graph or sequence serialization
CN108368542B (zh) 2015-10-19 2022-04-08 多弗泰尔基因组学有限责任公司 用于基因组组装、单元型定相以及独立于靶标的核酸检测的方法
US20170141793A1 (en) * 2015-11-13 2017-05-18 Microsoft Technology Licensing, Llc Error correction for nucleotide data stores
US11371094B2 (en) 2015-11-19 2022-06-28 10X Genomics, Inc. Systems and methods for nucleic acid processing using degenerate nucleotides
US20170199960A1 (en) 2016-01-07 2017-07-13 Seven Bridges Genomics Inc. Systems and methods for adaptive local alignment for graph genomes
US10068183B1 (en) 2017-02-23 2018-09-04 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on a quantum processing platform
US20170270245A1 (en) 2016-01-11 2017-09-21 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing
US10364468B2 (en) 2016-01-13 2019-07-30 Seven Bridges Genomics Inc. Systems and methods for analyzing circulating tumor DNA
US10460829B2 (en) 2016-01-26 2019-10-29 Seven Bridges Genomics Inc. Systems and methods for encoding genetic variation for a population
CN108779491B (zh) 2016-02-11 2021-03-09 10X基因组学有限公司 用于全基因组序列数据的从头组装的系统、方法和介质
EP3420108A4 (en) 2016-02-23 2019-11-06 Dovetail Genomics LLC GENERATION OF LIVE PHASES FOR THE GENERATION ARRANGEMENT AND HAPLOTYPE PHASE RULES
US10262102B2 (en) 2016-02-24 2019-04-16 Seven Bridges Genomics Inc. Systems and methods for genotyping with graph reference
JP7280044B2 (ja) 2016-04-15 2023-05-23 ナテラ， インコーポレイテッド 肺癌の検出方法
KR102412442B1 (ko) 2016-05-13 2022-06-22 더브테일 제노믹스 엘엘씨 보존된 샘플로부터의 장범위 링키지 정보의 회수
WO2017201081A1 (en) 2016-05-16 2017-11-23 Agilome, Inc. Graphene fet devices, systems, and methods of using the same for sequencing nucleic acids
US10790044B2 (en) 2016-05-19 2020-09-29 Seven Bridges Genomics Inc. Systems and methods for sequence encoding, storage, and compression
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
US11289177B2 (en) 2016-08-08 2022-03-29 Seven Bridges Genomics, Inc. Computer method and system of identifying genomic mutations using graph-based local assembly
US11250931B2 (en) 2016-09-01 2022-02-15 Seven Bridges Genomics Inc. Systems and methods for detecting recombination
WO2018067517A1 (en) 2016-10-04 2018-04-12 Natera, Inc. Methods for characterizing copy number variation using proximity-litigation sequencing
GB201618485D0 (en) 2016-11-02 2016-12-14 Ucl Business Plc Method of detecting tumour recurrence
US10319465B2 (en) 2016-11-16 2019-06-11 Seven Bridges Genomics Inc. Systems and methods for aligning sequences to graph references
US10011870B2 (en) 2016-12-07 2018-07-03 Natera, Inc. Compositions and methods for identifying nucleic acid molecules
CN108234551B (zh) * 2016-12-15 2021-06-25 腾讯科技（深圳）有限公司 一种数据处理方法及装置
US10011872B1 (en) 2016-12-22 2018-07-03 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10550429B2 (en) 2016-12-22 2020-02-04 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10815525B2 (en) 2016-12-22 2020-10-27 10X Genomics, Inc. Methods and systems for processing polynucleotides
US12264411B2 (en) 2017-01-30 2025-04-01 10X Genomics, Inc. Methods and systems for analysis
EP4029939B1 (en) 2017-01-30 2023-06-28 10X Genomics, Inc. Methods and systems for droplet-based single cell barcoding
US10995333B2 (en) 2017-02-06 2021-05-04 10X Genomics, Inc. Systems and methods for nucleic acid preparation
US10894976B2 (en) 2017-02-21 2021-01-19 Natera, Inc. Compositions, methods, and kits for isolating nucleic acids
US10726110B2 (en) 2017-03-01 2020-07-28 Seven Bridges Genomics, Inc. Watermarking for data security in bioinformatic sequence analysis
US11347844B2 (en) 2017-03-01 2022-05-31 Seven Bridges Genomics, Inc. Data security in bioinformatic sequence analysis
WO2018170518A1 (en) 2017-03-17 2018-09-20 Apton Biosystems, Inc. Sequencing and high resolution imaging
WO2018213774A1 (en) 2017-05-19 2018-11-22 10X Genomics, Inc. Systems and methods for analyzing datasets
US10837047B2 (en) 2017-10-04 2020-11-17 10X Genomics, Inc. Compositions, methods, and systems for bead formation using improved polymers
WO2019084043A1 (en) 2017-10-26 2019-05-02 10X Genomics, Inc. METHODS AND SYSTEMS FOR NUCLEIC ACID PREPARATION AND CHROMATIN ANALYSIS
WO2019084165A1 (en) 2017-10-27 2019-05-02 10X Genomics, Inc. METHODS AND SYSTEMS FOR SAMPLE PREPARATION AND ANALYSIS
SG11201913654QA (en) 2017-11-15 2020-01-30 10X Genomics Inc Functionalized gel beads
US10829815B2 (en) 2017-11-17 2020-11-10 10X Genomics, Inc. Methods and systems for associating physical and genetic properties of biological particles
WO2019108851A1 (en) 2017-11-30 2019-06-06 10X Genomics, Inc. Systems and methods for nucleic acid preparation and analysis
WO2019118355A1 (en) 2017-12-12 2019-06-20 10X Genomics, Inc. Systems and methods for single cell processing
WO2019118926A1 (en) 2017-12-14 2019-06-20 Tai Diagnostics, Inc. Assessing graft suitability for transplantation
CN111712579B (zh) 2017-12-22 2024-10-15 10X基因组学有限公司 用于处理来自一个或多个细胞的核酸分子的系统和方法
AU2019214956B2 (en) 2018-01-31 2025-06-26 Dovetail Genomics, Llc Sample prep for DNA linkage recovery
EP3752832A1 (en) 2018-02-12 2020-12-23 10X Genomics, Inc. Methods characterizing multiple analytes from individual cells or cell populations
US12046325B2 (en) 2018-02-14 2024-07-23 Seven Bridges Genomics Inc. System and method for sequence identification in reassembly variant calling
US12398389B2 (en) 2018-02-15 2025-08-26 Natera, Inc. Methods for isolating nucleic acids with size selection
US11639928B2 (en) 2018-02-22 2023-05-02 10X Genomics, Inc. Methods and systems for characterizing analytes from individual cells or cell populations
WO2019169028A1 (en) 2018-02-28 2019-09-06 10X Genomics, Inc. Transcriptome sequencing through random ligation
SG11202009889VA (en) 2018-04-06 2020-11-27 10X Genomics Inc Systems and methods for quality control in single cell processing
US12024738B2 (en) 2018-04-14 2024-07-02 Natera, Inc. Methods for cancer detection and monitoring
EP3790967B1 (en) 2018-05-08 2023-04-19 MGI Tech Co., Ltd. Single tube bead-based dna co-barcoding for accurate and cost-effective sequencing, haplotyping, and assembly
WO2019217758A1 (en) 2018-05-10 2019-11-14 10X Genomics, Inc. Methods and systems for molecular library generation
US11932899B2 (en) 2018-06-07 2024-03-19 10X Genomics, Inc. Methods and systems for characterizing nucleic acid molecules
US11703427B2 (en) 2018-06-25 2023-07-18 10X Genomics, Inc. Methods and systems for cell and bead processing
US12234509B2 (en) 2018-07-03 2025-02-25 Natera, Inc. Methods for detection of donor-derived cell-free DNA
US12188014B1 (en) 2018-07-25 2025-01-07 10X Genomics, Inc. Compositions and methods for nucleic acid processing using blocking agents
US20200032335A1 (en) 2018-07-27 2020-01-30 10X Genomics, Inc. Systems and methods for metabolome analysis
EP3830289A1 (en) 2018-08-03 2021-06-09 10X Genomics, Inc. Methods and systems to minimize barcode exchange
WO2020041148A1 (en) 2018-08-20 2020-02-27 10X Genomics, Inc. Methods and systems for detection of protein-dna interactions using proximity ligation
US12065688B2 (en) 2018-08-20 2024-08-20 10X Genomics, Inc. Compositions and methods for cellular processing
CN109273052B (zh) * 2018-09-13 2022-03-18 北京百迈客生物科技有限公司 一种基因组单倍体组装方法及装置
JP2022501026A (ja) 2018-09-19 2022-01-06 アプトン バイオシステムズ インコーポレイテッド 高密度に詰め込まれた分析物の層および検出方法
KR20210091126A (ko) 2018-10-23 2021-07-21 엠쥐아이 테크 컴퍼니 엘티디. Fpga 기반 리시퀀싱 분석 방법 및 장치
US11459607B1 (en) 2018-12-10 2022-10-04 10X Genomics, Inc. Systems and methods for processing-nucleic acid molecules from a single cell using sequential co-partitioning and composite barcodes
WO2020123647A1 (en) * 2018-12-12 2020-06-18 University Of Washington Current-to-current nanopore data blast alignment
US12169198B2 (en) 2019-01-08 2024-12-17 10X Genomics, Inc. Systems and methods for sample analysis
US11845983B1 (en) 2019-01-09 2023-12-19 10X Genomics, Inc. Methods and systems for multiplexing of droplet based assays
US20220195624A1 (en) 2019-01-29 2022-06-23 Mgi Tech Co., Ltd. High coverage stlfr
US11713455B2 (en) 2019-02-05 2023-08-01 Cardea Bio, Inc. Enhanced selection of efficient targeted genome manipulating agents
US11467153B2 (en) 2019-02-12 2022-10-11 10X Genomics, Inc. Methods for processing nucleic acid molecules
WO2020167862A1 (en) 2019-02-12 2020-08-20 10X Genomics, Inc. Systems and methods for transfer of reagents between droplets
WO2020167866A1 (en) 2019-02-12 2020-08-20 10X Genomics, Inc. Systems and methods for transposon loading
US11851683B1 (en) 2019-02-12 2023-12-26 10X Genomics, Inc. Methods and systems for selective analysis of cellular samples
US12305239B2 (en) 2019-02-12 2025-05-20 10X Genomics, Inc. Analysis of nucleic acid sequences
SG11202108788TA (en) 2019-02-12 2021-09-29 10X Genomics Inc Methods for processing nucleic acid molecules
US12275993B2 (en) 2019-02-12 2025-04-15 10X Genomics, Inc. Analysis of nucleic acid sequences
US11655499B1 (en) 2019-02-25 2023-05-23 10X Genomics, Inc. Detection of sequence elements in nucleic acid molecules
WO2020185791A1 (en) 2019-03-11 2020-09-17 10X Genomics, Inc. Systems and methods for processing optically tagged beads
US11210554B2 (en) 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata
US11783917B2 (en) * 2019-03-21 2023-10-10 Illumina, Inc. Artificial intelligence-based base calling
US11593649B2 (en) 2019-05-16 2023-02-28 Illumina, Inc. Base calling using convolutions
US11423306B2 (en) 2019-05-16 2022-08-23 Illumina, Inc. Systems and devices for characterization and performance analysis of pixel-based sequencing
WO2020247263A1 (en) 2019-06-06 2020-12-10 Natera, Inc. Methods for detecting immune cell dna and monitoring immune system
US12235262B1 (en) 2019-09-09 2025-02-25 10X Genomics, Inc. Methods and systems for single cell protein analysis
CN120473129A (zh) * 2019-09-30 2025-08-12 迈欧米公司 用于体外受精的多基因风险得分
US12449419B1 (en) 2020-02-12 2025-10-21 10X Genomics, Inc. Methods for detecting binding of peptide-MHC monomers to T cells
EP4104179A1 (en) 2020-02-13 2022-12-21 10X Genomics, Inc. Systems and methods for joint interactive visualization of gene expression and dna chromatin accessibility
US12354008B2 (en) 2020-02-20 2025-07-08 Illumina, Inc. Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller
EP4107735B1 (en) 2020-02-20 2025-11-26 Illumina, Inc. Artificial intelligence-based many-to-many base calling
US20210265016A1 (en) 2020-02-20 2021-08-26 Illumina, Inc. Data Compression for Artificial Intelligence-Based Base Calling
CN111445953B (zh) * 2020-03-27 2022-04-26 武汉古奥基因科技有限公司 一种利用全基因组比对拆分四倍体鱼类亚基因组的方法
US11851700B1 (en) 2020-05-13 2023-12-26 10X Genomics, Inc. Methods, kits, and compositions for processing extracellular molecules
CN111755074B (zh) * 2020-07-03 2022-05-17 桂林电子科技大学 一种酿酒酵母菌中dna复制起点的预测方法
CA3189557A1 (en) * 2020-08-05 2022-02-10 Inivata Ltd. Highly sensitive method for detecting cancer dna in a sample
US12084715B1 (en) 2020-11-05 2024-09-10 10X Genomics, Inc. Methods and systems for reducing artifactual antisense products
US12480158B1 (en) 2020-11-05 2025-11-25 10X Genomics, Inc. Methods and systems for processing polynucleotides
CN112712853B (zh) * 2020-12-31 2023-11-21 北京优迅医学检验实验室有限公司 一种无创产前检测装置
US12398262B1 (en) 2021-01-22 2025-08-26 10X Genomics, Inc. Triblock copolymer-based cell stabilization and fixation system and methods of use thereof
EP4298244A1 (en) 2021-02-23 2024-01-03 10X Genomics, Inc. Probe-based analysis of nucleic acids and proteins
US20220336057A1 (en) 2021-04-15 2022-10-20 Illumina, Inc. Efficient voxelization for deep learning
US12217829B2 (en) 2021-04-15 2025-02-04 Illumina, Inc. Artificial intelligence-based analysis of protein three-dimensional (3D) structures
US12176070B2 (en) * 2021-04-19 2024-12-24 University Of Utah Research Foundation Systems and methods for facilitating rapid genome sequence analysis
GB2621782B (en) * 2021-05-05 2024-08-14 Univ Leland Stanford Junior Methods and systems for analyzing nucleic acid molecules
CN118715566A (zh) 2022-03-08 2024-09-27 因美纳有限公司 多通道软件加速基因组读段映射引擎
CN115035948B (zh) * 2022-07-20 2023-01-24 北京阅微基因技术股份有限公司 一种str引物的设计方法和系统
CN115985400B (zh) * 2022-12-02 2024-03-15 江苏先声医疗器械有限公司 一种宏基因组多重比对序列重分配的方法及应用
US20240404627A1 (en) * 2023-01-26 2024-12-05 Regeneron Pharmaceuticals, Inc. Systems and Methods for Correcting for Noise and Systemic Variations in Sequencing Data

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN101432439A (zh) * 2006-02-24 2009-05-13 考利达基因组股份有限公司 Dna阵列上的高通量基因组测序
CN101466847A (zh) * 2005-06-15 2009-06-24 考利达基因组股份有限公司 用于遗传和化学分析的单分子阵列
US7565346B2 (en) * 2004-05-31 2009-07-21 International Business Machines Corporation System and method for sequence-based subspace pattern clustering

Family Cites Families (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7534568B2 (en) * 1999-10-29 2009-05-19 Hologic Inc. Methods for detection of a target nucleic acid by forming a cleavage structure with a cleavage resistant probe
CA2468601A1 (en) * 2001-12-03 2003-06-12 Dnaprint Genomics, Inc. Methods and apparatus for complex genetics classification based on correspondence analysis and linear/quadratic analysis
US20040072217A1 (en) * 2002-06-17 2004-04-15 Affymetrix, Inc. Methods of analysis of linkage disequilibrium
JP2004234580A (ja) * 2003-01-31 2004-08-19 Fujitsu Ltd ゲノム情報解析支援方法、ゲノム情報解析支援プログラムおよびゲノム情報解析支援装置
US20050026173A1 (en) * 2003-02-27 2005-02-03 Methexis Genomics, N.V. Genetic diagnosis using multiple sequence variant analysis combined with mass spectrometry
US20060073501A1 (en) * 2004-09-10 2006-04-06 Van Den Boom Dirk J Methods for long-range sequence analysis of nucleic acids
CN1807580B (zh) * 2006-01-23 2010-05-12 重庆大学 一种从感病昆虫血淋巴中分离纯化昆虫病原真菌菌体的方法
DK2152885T3 (da) * 2007-05-23 2014-08-18 Syngenta Participations Ag Polynukleotidmarkører
EP2179062A2 (en) * 2007-06-13 2010-04-28 Decode Genetics EHF Genetic variants on chr 15q24 as markers for use in diagnosis, prognosis and treatment of exfoliation syndrome and glaucoma
US8592150B2 (en) * 2007-12-05 2013-11-26 Complete Genomics, Inc. Methods and compositions for long fragment read sequencing
US8407554B2 (en) * 2009-02-03 2013-03-26 Complete Genomics, Inc. Method and apparatus for quantification of DNA sequencing quality and construction of a characterizable model system using Reed-Solomon codes
EP2282031B1 (en) * 2009-07-02 2012-06-06 Eurocopter Deutschland GmbH Filtering device with integrated bypass for an air inlet

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7565346B2 (en) * 2004-05-31 2009-07-21 International Business Machines Corporation System and method for sequence-based subspace pattern clustering
CN101466847A (zh) * 2005-06-15 2009-06-24 考利达基因组股份有限公司 用于遗传和化学分析的单分子阵列
CN101432439A (zh) * 2006-02-24 2009-05-13 考利达基因组股份有限公司 Dna阵列上的高通量基因组测序

Also Published As

Publication number Publication date
CN107368705A (zh) 2017-11-21
CN107368705B (zh) 2021-07-13
EP2754078A2 (en) 2014-07-16
HK1246901A1 (zh) 2018-09-14
CA2833165A1 (en) 2012-10-18
JP2014516514A (ja) 2014-07-17
US20140051588A9 (en) 2014-02-20
AU2012242525B2 (en) 2015-09-17
CN103843001A (zh) 2014-06-04
US20130059740A1 (en) 2013-03-07
EP2754078A4 (en) 2015-12-02
WO2012142531A2 (en) 2012-10-18
AU2012242525A1 (en) 2013-05-02
WO2012142531A3 (en) 2014-05-08
JP2017184742A (ja) 2017-10-12

Similar Documents

Publication Publication Date Title
CN103843001B (zh) 复杂核酸序列数据的处理和分析
CN103987857B (zh) 对少量复杂核酸测序
US20240287598A1 (en) Multiple tagging of individual long dna fragments
AU2015264833B2 (en) Processing and analysis of complex nucleic acid sequence data
HK1246901B (zh) 分析生物体的基因组dna的方法和计算机系统
HK1197565B (en) Processing and analysis of complex nucleic acid sequence data
HK1197565A (en) Processing and analysis of complex nucleic acid sequence data
HK1201077B (en) Sequencing small amounts of complex nucleic acids
HK40041078B (en) Multiple tagging of long dna fragments
HK1218412B (zh) 长dna片段的多重标记
HK1219709B (en) Multiple tagging of long dna fragments

Legal Events

Date Code Title Description
C06 Publication
PB01 Publication
C10 Entry into 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: 1197565

Country of ref document: HK

GR01 Patent grant
GR01 Patent grant
REG Reference to a national code

Ref country code: HK

Ref legal event code: GR

Ref document number: 1197565

Country of ref document: HK

CP01 Change in the name or title of a patent holder
CP01 Change in the name or title of a patent holder

Address after: California, USA

Patentee after: COMPLETE GENOMICS Inc.

Address before: California, USA

Patentee before: Complete Genomics, Inc.