JP2014516514A - 複合核酸配列データの処理および解析 - Google Patents

複合核酸配列データの処理および解析 Download PDF

Info

Publication number
JP2014516514A
JP2014516514A JP2014505385A JP2014505385A JP2014516514A JP 2014516514 A JP2014516514 A JP 2014516514A JP 2014505385 A JP2014505385 A JP 2014505385A JP 2014505385 A JP2014505385 A JP 2014505385A JP 2014516514 A JP2014516514 A JP 2014516514A
Authority
JP
Japan
Prior art keywords
sequence
genome
fading
nucleic acid
dna
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
JP2014505385A
Other languages
English (en)
Japanese (ja)
Other versions
JP2014516514A5 (enExample
Inventor
ラドジェ・ドルマナック
ブロック・エイ・ピータース
バーラム・ガファルザデー・ケルマニ
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
Publication of JP2014516514A publication Critical patent/JP2014516514A/ja
Publication of JP2014516514A5 publication Critical patent/JP2014516514A5/ja
Pending legal-status Critical Current

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
    • G16B30/20—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
    • 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

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)
JP2014505385A 2011-04-14 2012-04-13 複合核酸配列データの処理および解析 Pending JP2014516514A (ja)

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
JP2017083584A Division JP2017184742A (ja) 2011-04-14 2017-04-20 複合核酸配列データの処理および解析

Publications (2)

Publication Number Publication Date
JP2014516514A true JP2014516514A (ja) 2014-07-17
JP2014516514A5 JP2014516514A5 (enExample) 2015-05-28

Family

ID=47010019

Family Applications (2)

Application Number Title Priority Date Filing Date
JP2014505385A Pending JP2014516514A (ja) 2011-04-14 2012-04-13 複合核酸配列データの処理および解析
JP2017083584A Pending JP2017184742A (ja) 2011-04-14 2017-04-20 複合核酸配列データの処理および解析

Family Applications After (1)

Application Number Title Priority Date Filing Date
JP2017083584A Pending JP2017184742A (ja) 2011-04-14 2017-04-20 複合核酸配列データの処理および解析

Country Status (7)

Country Link
US (1) US20140051588A9 (enExample)
EP (1) EP2754078A4 (enExample)
JP (2) JP2014516514A (enExample)
CN (2) CN107368705B (enExample)
AU (1) AU2012242525B2 (enExample)
CA (1) CA2833165A1 (enExample)
WO (1) WO2012142531A2 (enExample)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2023536325A (ja) * 2020-08-05 2023-08-24 イニヴァータ リミテッド 試料中のがんｄｎａを検出するための高感度の方法

Families Citing this family (214)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DK1907571T3 (en) 2005-06-15 2017-08-21 Complete Genomics Inc NUCLEIC ACID ANALYSIS USING INCIDENTAL MIXTURES OF NON-OVERLAPPING FRAGMENTS
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
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
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
ES2640776T3 (es) 2009-09-30 2017-11-06 Natera, Inc. Métodos para denominar de forma no invasiva ploidía prenatal
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
EP2854058A3 (en) 2010-05-18 2015-10-28 Natera, Inc. Methods for non-invasive pre-natal ploidy calling
US11332793B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for simultaneous amplification of target loci
US20240158855A1 (en) 2010-05-18 2024-05-16 Natera, Inc. Methods for simultaneous amplification of target loci
US12655483B2 (en) 2010-05-18 2026-06-16 Natera, Inc. Methods for simultaneous amplification of target loci
US11339429B2 (en) 2010-05-18 2022-05-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11408031B2 (en) 2010-05-18 2022-08-09 Natera, Inc. Methods for non-invasive prenatal paternity testing
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
US11326208B2 (en) 2010-05-18 2022-05-10 Natera, Inc. Methods for nested PCR amplification of cell-free DNA
US11332785B2 (en) 2010-05-18 2022-05-17 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
US10316362B2 (en) 2010-05-18 2019-06-11 Natera, Inc. Methods for simultaneous amplification of target loci
US12545960B2 (en) 2010-05-18 2026-02-10 Natera, Inc. Methods for simultaneous amplification of target loci
US12221653B2 (en) 2010-05-18 2025-02-11 Natera, Inc. Methods for simultaneous amplification of target loci
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US12152275B2 (en) 2010-05-18 2024-11-26 Natera, Inc. Methods for non-invasive prenatal ploidy calling
AU2011348100B2 (en) 2010-12-22 2016-08-25 Natera, Inc. Methods for non-invasive prenatal paternity testing
JP6153874B2 (ja) 2011-02-09 2017-06-28 ナテラ， インコーポレイテッド 非侵襲的出生前倍数性呼び出しのための方法
US9701998B2 (en) 2012-12-14 2017-07-11 10X Genomics, Inc. Methods and systems for processing polynucleotides
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
US10323279B2 (en) 2012-08-14 2019-06-18 10X Genomics, Inc. Methods and systems for processing polynucleotides
CN114891871A (zh) 2012-08-14 2022-08-12 10X基因组学有限公司 微胶囊组合物及方法
US10584381B2 (en) 2012-08-14 2020-03-10 10X Genomics, Inc. Methods and systems for processing polynucleotides
US11591637B2 (en) 2012-08-14 2023-02-28 10X Genomics, Inc. Compositions and methods for sample processing
US20140100126A1 (en) 2012-08-17 2014-04-10 Natera, Inc. Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
JP6395718B2 (ja) 2012-11-19 2018-09-26 アプトン バイオシステムズ インコーポレイテッド 単一分子検出を用いた分子分析物のデジタル分析の方法
US10829816B2 (en) 2012-11-19 2020-11-10 Apton Biosystems, Inc. Methods of analyte detection
US10533221B2 (en) 2012-12-14 2020-01-14 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10847251B2 (en) 2013-01-17 2020-11-24 Illumina, Inc. Genomic infrastructure for on-site or cloud-based DNA and RNA processing and analysis
GB202020510D0 (en) 2013-01-17 2021-02-03 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
US9679104B2 (en) 2013-01-17 2017-06-13 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US10068054B2 (en) 2013-01-17 2018-09-04 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
EP2958574A4 (en) * 2013-01-23 2016-11-02 Reproductive Genetics And Technology Solutions Llc COMPOSITIONS AND METHODS FOR GENETIC ANALYSIS OF EMBRYOS
CN108624668B (zh) * 2013-02-01 2022-12-02 加利福尼亚大学董事会 用于基因组组装及单体型定相的方法
US9411930B2 (en) 2013-02-01 2016-08-09 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
KR20230003659A (ko) 2013-02-08 2023-01-06 10엑스 제노믹스, 인크. 폴리뉴클레오티드 바코드 생성
EP2959011A1 (en) * 2013-02-19 2015-12-30 Cergentis B.V. Sequencing strategies for genomic regions of interest
US9328382B2 (en) 2013-03-15 2016-05-03 Complete Genomics, Inc. Multiple tagging of individual long DNA fragments
WO2014151554A1 (en) * 2013-03-15 2014-09-25 The Trustees Of The University Of Pennsylvania Phi29 method for library preparation
EP3022320B2 (en) * 2013-07-19 2024-09-25 Ludwig Institute for Cancer Research Ltd 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
CN105637099B (zh) * 2013-08-23 2020-05-19 深圳华大智造科技有限公司 使用短读段的长片段从头组装
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
WO2015051006A2 (en) 2013-10-01 2015-04-09 Complete Genomics, Inc. Phasing and linking processes to identify variations in a genome
WO2015058120A1 (en) 2013-10-18 2015-04-23 Seven Bridges Genomics Inc. Methods and systems for aligning sequences in the presence of repeating elements
JP2017500004A (ja) 2013-10-18 2017-01-05 セブン ブリッジズ ジェノミクス インコーポレイテッド 遺伝子試料について遺伝子型解析するための方法およびシステム
US10832797B2 (en) 2013-10-18 2020-11-10 Seven Bridges Genomics Inc. Method and system for quantifying sequence alignment
US10053736B2 (en) 2013-10-18 2018-08-21 Seven Bridges Genomics Inc. Methods and systems for identifying disease-induced mutations
US9092402B2 (en) 2013-10-21 2015-07-28 Seven Bridges Genomics Inc. Systems and methods for using paired-end data in directed acyclic structure
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
US9824068B2 (en) 2013-12-16 2017-11-21 10X Genomics, Inc. Methods and apparatus for sorting data
US10867693B2 (en) 2014-01-10 2020-12-15 Seven Bridges Genomics Inc. Systems and methods for use of known alleles in read mapping
US9817944B2 (en) * 2014-02-11 2017-11-14 Seven Bridges Genomics Inc. Systems and methods for analyzing sequence data
US9694361B2 (en) 2014-04-10 2017-07-04 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
RU2717641C2 (ru) 2014-04-21 2020-03-24 Натера, Инк. Обнаружение мутаций и плоидности в хромосомных сегментах
US20180173845A1 (en) 2014-06-05 2018-06-21 Natera, Inc. Systems and Methods for Detection of Aneuploidy
EP4235677A3 (en) 2014-06-26 2023-11-22 10X Genomics, Inc. Processes and systems for nucleic acid sequence assembly
US12312640B2 (en) 2014-06-26 2025-05-27 10X Genomics, Inc. Analysis of nucleic acid sequences
KR20170026383A (ko) 2014-06-26 2017-03-08 10엑스 제노믹스, 인크. 핵산 서열의 분석
EP4574974A3 (en) 2014-06-26 2025-10-08 10x Genomics, Inc. Methods of analyzing nucleic acids from individual cells or cell populations
AU2015296029B2 (en) 2014-08-01 2022-01-27 Dovetail Genomics, Llc Tagging nucleic acids for sequence assembly
US9558321B2 (en) 2014-10-14 2017-01-31 Seven Bridges Genomics Inc. Systems and methods for smart tools in sequence pipelines
US10429342B2 (en) 2014-12-18 2019-10-01 Edico Genome Corporation Chemically-sensitive field effect transistor
US10020300B2 (en) 2014-12-18 2018-07-10 Agilome, 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
US9857328B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Chemically-sensitive field effect transistors, systems and methods for manufacturing and using the same
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
AU2016207023B2 (en) 2015-01-12 2019-12-05 10X Genomics, Inc. Processes and systems for preparing nucleic acid sequencing libraries and libraries prepared using same
CA2968417A1 (en) * 2015-01-13 2016-07-21 10X Genomics, Inc. Systems and methods for visualizing structural variation and phasing information
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
SG11201705996PA (en) 2015-02-09 2017-09-28 10X Genomics Inc Systems and methods for determining structural variation and phasing using variant call data
JP6777966B2 (ja) 2015-02-17 2020-10-28 ダブテイル ゲノミクス エルエルシー 核酸配列アセンブリ
US10192026B2 (en) 2015-03-05 2019-01-29 Seven Bridges Genomics Inc. Systems and methods for genomic pattern analysis
HK1255431A1 (zh) 2015-03-23 2019-08-16 Edico Genome Corporation 用於基因组可视化的方法和系统
WO2016154540A1 (en) 2015-03-26 2016-09-29 Dovetail Genomics Llc Physical linkage preservation in dna storage
EP4428863A3 (en) * 2015-05-11 2024-12-11 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
SG11201803289VA (en) 2015-10-19 2018-05-30 Dovetail Genomics Llc Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection
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
JP6735348B2 (ja) 2016-02-11 2020-08-05 １０エックス ジェノミクス， インコーポレイテッド 全ゲノム配列データのデノボアセンブリのためのシステム、方法及び媒体
US10975417B2 (en) 2016-02-23 2021-04-13 Dovetail Genomics, Llc Generation of phased read-sets for genome assembly and haplotype phasing
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
WO2017197300A1 (en) 2016-05-13 2017-11-16 Dovetail Genomics Llc Recovering long-range linkage information from preserved samples
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
EP4682891A3 (en) 2016-10-28 2026-04-01 Illumina, Inc. Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing
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
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
US10011872B1 (en) 2016-12-22 2018-07-03 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
EP4310183B1 (en) 2017-01-30 2025-07-09 10X Genomics, Inc. Methods and systems for droplet-based single cell barcoding
WO2018145041A1 (en) 2017-02-06 2018-08-09 10X Genomics, Inc. Systems and methods for nucleic acid preparation
CA3049139A1 (en) 2017-02-21 2018-08-30 Natera, Inc. Compositions, methods, and kits for isolating nucleic acids
US11347844B2 (en) 2017-03-01 2022-05-31 Seven Bridges Genomics, Inc. Data security in bioinformatic sequence analysis
US10726110B2 (en) 2017-03-01 2020-07-28 Seven Bridges Genomics, Inc. Watermarking for data security in bioinformatic sequence analysis
EP3595806A4 (en) 2017-03-17 2021-06-16 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
CN111479631B (zh) 2017-10-27 2022-02-22 10X基因组学有限公司 用于样品制备和分析的方法和系统
EP3625361A1 (en) 2017-11-15 2020-03-25 10X Genomics, Inc. Functionalized gel beads
WO2019099908A1 (en) 2017-11-17 2019-05-23 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
CN118818037A (zh) 2017-12-12 2024-10-22 10X基因组学有限公司 用于单细胞处理的系统和方法
WO2019118926A1 (en) 2017-12-14 2019-06-20 Tai Diagnostics, Inc. Assessing graft suitability for transplantation
WO2019126789A1 (en) 2017-12-22 2019-06-27 10X Genomics, Inc. Systems and methods for processing nucleic acid molecules from one or more cells
EP3737773B1 (en) 2018-01-12 2023-04-12 Natera, Inc. Novel primers and uses thereof
WO2019152543A1 (en) 2018-01-31 2019-08-08 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
WO2019161244A1 (en) 2018-02-15 2019-08-22 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
EP3775271B1 (en) 2018-04-06 2025-03-12 10X Genomics, Inc. Systems and methods for quality control in single cell processing
DK3781714T3 (da) 2018-04-14 2026-03-30 Natera Inc Fremgangsmåder til cancerpåvisning og -overvågning ved personlig påvisning af cirkulerende tumor-dna
ES2947437T3 (es) 2018-05-08 2023-08-09 Mgi Tech Co Ltd Creación de Códigos de barra compartidos en el ADN, en un solo tubo con perlas, para la secuenciación, haplotipado y ensamblaje preciso y rentable
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
US12163179B2 (en) 2018-08-03 2024-12-10 10X Gemomics, 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
WO2020061237A1 (en) 2018-09-19 2020-03-26 Apton Biosystems, Inc. Densely-packed analyte layers and detection methods
WO2020082224A1 (zh) * 2018-10-23 2020-04-30 深圳华大智造科技有限公司 基于fpga的重测序分析方法和装置
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
EP3918088B1 (en) 2019-01-29 2024-03-13 MGI Tech Co., Ltd. High coverage stlfr
CN113661392B (zh) * 2019-02-05 2025-05-27 卡蒂亚生物公司 有效靶向基因组操纵剂的增强选择
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
WO2020167862A1 (en) 2019-02-12 2020-08-20 10X Genomics, Inc. Systems and methods for transfer of reagents between droplets
US11467153B2 (en) 2019-02-12 2022-10-11 10X Genomics, Inc. Methods for processing nucleic acid molecules
WO2020168013A1 (en) 2019-02-12 2020-08-20 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
SG11202111242PA (en) 2019-03-11 2021-11-29 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
US11347965B2 (en) * 2019-03-21 2022-05-31 Illumina, Inc. Training data generation for artificial intelligence-based sequencing
EP3947722A1 (en) 2019-03-27 2022-02-09 10X Genomics, Inc. Systems and methods for processing rna from cells
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
US12305235B2 (en) 2019-06-06 2025-05-20 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
US20210074381A1 (en) 2019-09-11 2021-03-11 Enancio Method for the compression of genome sequence data
US20220367063A1 (en) * 2019-09-30 2022-11-17 Myome, Inc. Polygenic risk score for in vitro fertilization
US12449419B1 (en) 2020-02-12 2025-10-21 10X Genomics, Inc. Methods for detecting binding of peptide-MHC monomers to T cells
EP4104179B1 (en) 2020-02-13 2026-01-28 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
US12592298B2 (en) 2020-02-20 2026-03-31 Illumina, Inc. Hardware execution and acceleration of artificial intelligence-based base caller
US12591780B2 (en) 2020-02-20 2026-03-31 Illumina, Inc. Data compression for artificial intelligence-based base calling
JP7747643B2 (ja) 2020-02-20 2025-10-01 イルミナ インコーポレイテッド 人工知能ベースの多対多ベースコール
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
US12655450B1 (en) 2020-10-27 2026-06-16 10X Genomics, Inc. Methods, systems, and kits for detection of nucleic acid molecules
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
AU2022227563A1 (en) 2021-02-23 2023-08-24 10X Genomics, Inc. Probe-based analysis of nucleic acids and proteins
US20220301657A1 (en) 2021-03-16 2022-09-22 Illumina, Inc. Tile location and/or cycle based weight set selection for base calling
US12217829B2 (en) 2021-04-15 2025-02-04 Illumina, Inc. Artificial intelligence-based analysis of protein three-dimensional (3D) structures
US12444482B2 (en) 2021-04-15 2025-10-14 Illumina, Inc. Multi-channel protein voxelization to predict variant pathogenicity using deep convolutional neural networks
US12176070B2 (en) * 2021-04-19 2024-12-24 University Of Utah Research Foundation Systems and methods for facilitating rapid genome sequence analysis
CA3216428A1 (en) * 2021-05-05 2022-11-10 The Board Of Trustees Of The Leland Stanford Junior University Methods and systems for analyzing nucleic acid molecules
US12530882B2 (en) 2021-07-01 2026-01-20 Illumina, Inc. Efficient artificial intelligence-based base calling of index sequences
JP7846205B2 (ja) 2021-07-22 2026-04-14 深▲セン▼華大智造科技股▲ふん▼有限公司 ニック－連結ｓｔｌｆｒ
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
WO2024159011A1 (en) * 2023-01-26 2024-08-02 Regeneron Pharmaceuticals, Inc. Systems and methods for correcting for noise and systemic variations in sequencing data

Citations (2)

* 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
US20110033854A1 (en) * 2007-12-05 2011-02-10 Complete Genomics, Inc. Methods and compositions for long fragment read sequencing

Family Cites Families (13)

* 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
US7640113B2 (en) * 2001-12-03 2009-12-29 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
US7584058B2 (en) * 2003-02-27 2009-09-01 Methexis Genomics N.V. Genetic diagnosis using multiple sequence variant analysis
US20060073501A1 (en) * 2004-09-10 2006-04-06 Van Den Boom Dirk J Methods for long-range sequence analysis of nucleic acids
DK1907571T3 (en) * 2005-06-15 2017-08-21 Complete Genomics Inc NUCLEIC ACID ANALYSIS USING INCIDENTAL MIXTURES OF NON-OVERLAPPING FRAGMENTS
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
CN101432439B (zh) * 2006-02-24 2013-07-24 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
EP2152885B1 (en) * 2007-05-23 2014-06-18 Syngenta Participations AG Polynucleotide markers
KR20100037592A (ko) * 2007-06-13 2010-04-09 디코드 제네틱스 이에이치에프 낙설 증후군 및 녹내장의 진단, 예후 및 치료용 마커인 염색체 １５ｑ２４ 상의 유전적 변이
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 (2)

* 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
US20110033854A1 (en) * 2007-12-05 2011-02-10 Complete Genomics, Inc. Methods and compositions for long fragment read sequencing

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2023536325A (ja) * 2020-08-05 2023-08-24 イニヴァータ リミテッド 試料中のがんｄｎａを検出するための高感度の方法

Also Published As

Publication number Publication date
WO2012142531A3 (en) 2014-05-08
AU2012242525B2 (en) 2015-09-17
CN103843001A (zh) 2014-06-04
CN107368705B (zh) 2021-07-13
HK1246901A1 (zh) 2018-09-14
AU2012242525A1 (en) 2013-05-02
WO2012142531A2 (en) 2012-10-18
CN107368705A (zh) 2017-11-21
EP2754078A2 (en) 2014-07-16
CN103843001B (zh) 2017-06-09
EP2754078A4 (en) 2015-12-02
CA2833165A1 (en) 2012-10-18
US20140051588A9 (en) 2014-02-20
US20130059740A1 (en) 2013-03-07
JP2017184742A (ja) 2017-10-12

Similar Documents

Publication Publication Date Title
JP6297972B2 (ja) 少量の複合核酸の配列決定
US20240287598A1 (en) Multiple tagging of individual long dna fragments
JP2017184742A (ja) 複合核酸配列データの処理および解析
US20160186262A1 (en) Compositions and methods for genetic analysis of embryos
AU2015264833B2 (en) Processing and analysis of complex nucleic acid sequence data
HK1246901B (en) Method and computer system for analyzing genomic dna of organisms
HK1197565B (en) Processing and analysis of complex nucleic acid sequence data
HK1201077B (en) Sequencing small amounts of complex nucleic acids
HK1197565A (en) Processing and analysis of complex nucleic acid sequence data
HK40041078B (en) Multiple tagging of long dna fragments
HK1261728A1 (en) Multiple tagging of long dna fragments
HK1218412B (en) Multiple tagging of long dna fragments

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20150406

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20150406

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20160223

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20160520

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20160708

A02 Decision of refusal

Free format text: JAPANESE INTERMEDIATE CODE: A02

Effective date: 20161220