CA2832643C - Sequencing small amounts of complex nucleic acids - Google Patents

Sequencing small amounts of complex nucleic acids Download PDF

Info

Publication number
CA2832643C
CA2832643C CA2832643A CA2832643A CA2832643C CA 2832643 C CA2832643 C CA 2832643C CA 2832643 A CA2832643 A CA 2832643A CA 2832643 A CA2832643 A CA 2832643A CA 2832643 C CA2832643 C CA 2832643C
Authority
CA
Canada
Prior art keywords
sequence
genome
aliquot
dna
sequencing
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
CA2832643A
Other languages
English (en)
French (fr)
Other versions
CA2832643A1 (en
Inventor
Radoje Drmanac
Brock A. Peters
Bahram Ghaffarzadeh Kermani
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 CA2832643A1 publication Critical patent/CA2832643A1/en
Application granted granted Critical
Publication of CA2832643C publication Critical patent/CA2832643C/en
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
    • 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
    • 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

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Organic Chemistry (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CA2832643A 2011-04-14 2012-04-16 Sequencing small amounts of complex nucleic acids Active CA2832643C (en)

Applications Claiming Priority (9)

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
US13/447,087 2012-04-13
US13/447,087 US9524369B2 (en) 2009-06-15 2012-04-13 Processing and analysis of complex nucleic acid sequence data
PCT/US2012/033832 WO2012142611A2 (en) 2011-04-14 2012-04-16 Sequencing small amounts of complex nucleic acids

Publications (2)

Publication Number Publication Date
CA2832643A1 CA2832643A1 (en) 2012-10-18
CA2832643C true CA2832643C (en) 2022-07-19

Family

ID=47010039

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2832643A Active CA2832643C (en) 2011-04-14 2012-04-16 Sequencing small amounts of complex nucleic acids

Country Status (7)

Country Link
US (2) US9524369B2 (enExample)
EP (1) EP2997157A4 (enExample)
JP (1) JP6297972B2 (enExample)
CN (1) CN103987857B (enExample)
AU (2) AU2012242508B2 (enExample)
CA (1) CA2832643C (enExample)
WO (1) WO2012142611A2 (enExample)

Families Citing this family (211)

* 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
US8592150B2 (en) 2007-12-05 2013-11-26 Complete Genomics, Inc. Methods and compositions for long fragment read sequencing
WO2013004005A1 (zh) * 2011-07-05 2013-01-10 深圳华大基因科技有限公司 组装测序片段的方法
WO2013028739A1 (en) * 2011-08-25 2013-02-28 Complete Genomics Phasing of heterozygous loci to determine genomic haplotypes
HK1199745A1 (en) * 2011-09-09 2015-07-17 The Board Of Trustees Of The Leland Stanford Junior University Methods for obtaining a sequence
US10221442B2 (en) 2012-08-14 2019-03-05 10X Genomics, Inc. Compositions and methods for sample processing
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
US10273541B2 (en) 2012-08-14 2019-04-30 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
US10323279B2 (en) 2012-08-14 2019-06-18 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
US11591637B2 (en) 2012-08-14 2023-02-28 10X Genomics, Inc. Compositions and methods for sample processing
US9701998B2 (en) 2012-12-14 2017-07-11 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
PL2893040T3 (pl) 2012-09-04 2019-05-31 Guardant Health Inc Sposoby wykrywania rzadkich mutacji i wariantu liczby kopii
US20160040229A1 (en) * 2013-08-16 2016-02-11 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
US10876152B2 (en) 2012-09-04 2020-12-29 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
US11913065B2 (en) 2012-09-04 2024-02-27 Guardent Health, Inc. Systems and methods to detect rare mutations and copy number variation
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
EP3567116A1 (en) 2012-12-14 2019-11-13 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10533221B2 (en) 2012-12-14 2020-01-14 10X Genomics, Inc. Methods and systems for processing polynucleotides
US9792405B2 (en) 2013-01-17 2017-10-17 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
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
US9679104B2 (en) 2013-01-17 2017-06-13 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
CN105190656B (zh) 2013-01-17 2018-01-16 佩索纳里斯公司 用于遗传分析的方法和系统
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
US9328382B2 (en) 2013-03-15 2016-05-03 Complete Genomics, Inc. Multiple tagging of individual long DNA fragments
SG10201708498VA (en) 2013-04-17 2017-11-29 Agency Science Tech & Res Method for generating extended sequence reads
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
GB2534067B (en) 2013-08-30 2021-07-21 Personalis Inc Methods and systems for genomic analysis
US10395758B2 (en) 2013-08-30 2019-08-27 10X Genomics, Inc. Sequencing methods
WO2015051006A2 (en) * 2013-10-01 2015-04-09 Complete Genomics, Inc. Phasing and linking processes to identify variations in a genome
GB2535066A (en) 2013-10-03 2016-08-10 Personalis Inc Methods for analyzing genotypes
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
US10053736B2 (en) 2013-10-18 2018-08-21 Seven Bridges Genomics Inc. Methods and systems for identifying disease-induced mutations
WO2015058120A1 (en) 2013-10-18 2015-04-23 Seven Bridges Genomics Inc. Methods and systems for aligning sequences in the presence of repeating elements
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
CN111534580B (zh) 2013-12-28 2024-06-04 夸登特健康公司 用于检测遗传变异的方法和系统
US10867693B2 (en) 2014-01-10 2020-12-15 Seven Bridges Genomics Inc. Systems and methods for use of known alleles in read mapping
US20150199476A1 (en) * 2014-01-16 2015-07-16 Electronics And Telecommunications Research Institute Method of analyzing genome by genome analyzing device
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
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
EP4574974A3 (en) 2014-06-26 2025-10-08 10x Genomics, Inc. Methods of analyzing nucleic acids from individual cells or cell populations
KR20170026383A (ko) 2014-06-26 2017-03-08 10엑스 제노믹스, 인크. 핵산 서열의 분석
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
JP2017532042A (ja) * 2014-10-29 2017-11-02 １０エックス ゲノミクス，インコーポレイテッド 標的化核酸配列決定のための方法及び組成物
US10125399B2 (en) 2014-10-30 2018-11-13 Personalis, Inc. Methods for using mosaicism in nucleic acids sampled distal to their origin
US9975122B2 (en) 2014-11-05 2018-05-22 10X Genomics, Inc. Instrument systems for integrated sample processing
US10900065B2 (en) 2014-11-14 2021-01-26 University Of Washington Methods and kits for labeling cellular molecules
US10233490B2 (en) 2014-11-21 2019-03-19 Metabiotech Corporation Methods for assembling and reading nucleic acid sequences from mixed populations
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
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
US10429342B2 (en) 2014-12-18 2019-10-01 Edico Genome Corporation Chemically-sensitive field effect transistor
US9859394B2 (en) 2014-12-18 2018-01-02 Agilome, 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
WO2016124069A1 (zh) * 2015-02-04 2016-08-11 深圳华大基因研究院 一种构建长片段测序文库的方法
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
AU2016222719B2 (en) 2015-02-24 2022-03-31 10X Genomics, Inc. Methods for targeted nucleic acid sequence coverage
EP4286516A3 (en) 2015-02-24 2024-03-06 10X Genomics, Inc. Partition processing methods and systems
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
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
US10584380B2 (en) 2015-09-01 2020-03-10 Seven Bridges Genomics Inc. Systems and methods for mitochondrial analysis
US10724110B2 (en) 2015-09-01 2020-07-28 Seven Bridges Genomics Inc. Systems and methods for analyzing viral nucleic acids
AU2016321204B2 (en) 2015-09-08 2022-12-01 Cold Spring Harbor Laboratory Genetic copy number determination using high throughput multiplex sequencing of smashed nucleotides
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
US10853130B1 (en) * 2015-12-02 2020-12-01 Color Genomics, Inc. Load balancing and conflict processing in workflow with task dependencies
KR102723865B1 (ko) 2015-12-04 2024-10-29 10엑스 제노믹스, 인크. 핵산 분석을 위한 방법 및 조성물
SG11201805119QA (en) 2015-12-17 2018-07-30 Guardant Health Inc Methods to determine tumor gene copy number by analysis of cell-free dna
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
WO2017197343A2 (en) 2016-05-12 2017-11-16 10X Genomics, Inc. Microfluidic on-chip filters
WO2017197300A1 (en) 2016-05-13 2017-11-16 Dovetail Genomics Llc Recovering long-range linkage information from preserved samples
WO2017197338A1 (en) 2016-05-13 2017-11-16 10X Genomics, Inc. Microfluidic systems and methods of use
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
US11299783B2 (en) 2016-05-27 2022-04-12 Personalis, Inc. Methods and systems for genetic analysis
US20190177719A1 (en) * 2016-06-01 2019-06-13 Institute For Systems Biology Method and System for Generating and Comparing Reduced Genome Data Sets
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
EP4682891A3 (en) 2016-10-28 2026-04-01 Illumina, Inc. Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing
US10319465B2 (en) 2016-11-16 2019-06-11 Seven Bridges Genomics Inc. Systems and methods for aligning sequences to graph references
CN108103052B (zh) * 2016-11-24 2021-05-07 浙江安诺优达生物科技有限公司 提高基因组覆盖度的单细胞全基因组扩增及文库构建方法
CN108121897B (zh) * 2016-11-29 2020-05-08 华为技术有限公司 一种基因组变异检测方法及检测装置
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
EP4310183B1 (en) 2017-01-30 2025-07-09 10X Genomics, Inc. Methods and systems for droplet-based single cell barcoding
US12264411B2 (en) 2017-01-30 2025-04-01 10X Genomics, Inc. Methods and systems for analysis
WO2018145041A1 (en) 2017-02-06 2018-08-09 10X Genomics, Inc. Systems and methods for nucleic acid preparation
US10689684B2 (en) 2017-02-14 2020-06-23 Microsoft Technology Licensing, Llc Modifications to polynucleotides for sequencing
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
US10930370B2 (en) 2017-03-03 2021-02-23 Microsoft Technology Licensing, Llc Polynucleotide sequencer tuned to artificial polynucleotides
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
US10844372B2 (en) 2017-05-26 2020-11-24 10X Genomics, Inc. Single cell analysis of transposase accessible chromatin
CN116064732A (zh) 2017-05-26 2023-05-05 10X基因组学有限公司 转座酶可接近性染色质的单细胞分析
DK3684949T3 (en) 2017-09-22 2024-07-08 Univ Washington In situ combinatorial labeling of cellular molecules
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
WO2019126789A1 (en) 2017-12-22 2019-06-27 10X Genomics, Inc. Systems and methods for processing nucleic acid molecules from one or more cells
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
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
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
US11814750B2 (en) 2018-05-31 2023-11-14 Personalis, Inc. Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples
US10801064B2 (en) 2018-05-31 2020-10-13 Personalis, Inc. Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples
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
EP3619712B1 (en) * 2018-07-11 2024-02-14 Illumina, Inc. Deep learning-based framework for identifying sequence patterns that cause sequence-specific errors
CN110021351B (zh) * 2018-07-19 2023-04-28 深圳华大生命科学研究院 分析碱基连锁强度以及基因分型方法和系统
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
JP7407193B2 (ja) 2018-08-08 2023-12-28 イニヴァータ リミテッド 可変の複製多重ｐｃｒを使用した配列決定方法
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
WO2020061237A1 (en) 2018-09-19 2020-03-26 Apton Biosystems, Inc. Densely-packed analyte layers and detection methods
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
TWI725686B (zh) 2018-12-26 2021-04-21 財團法人工業技術研究院 用於產生液珠的管狀結構及液珠產生方法
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
US11821031B2 (en) * 2019-01-25 2023-11-21 Pacific Biosciences Of California, Inc. Systems and methods for graph based mapping of nucleic acid fragments
EP3918088B1 (en) 2019-01-29 2024-03-13 MGI Tech Co., Ltd. High coverage stlfr
US11851683B1 (en) 2019-02-12 2023-12-26 10X Genomics, Inc. Methods and systems for selective analysis of cellular samples
WO2020167866A1 (en) 2019-02-12 2020-08-20 10X Genomics, Inc. Systems and methods for transposon loading
US12305239B2 (en) 2019-02-12 2025-05-20 10X Genomics, Inc. Analysis of nucleic acid sequences
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
WO2020167862A1 (en) 2019-02-12 2020-08-20 10X Genomics, Inc. Systems and methods for transfer of reagents between droplets
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
GB2597202B (en) * 2019-05-22 2023-12-13 Hitachi High Tech Corp Analysis system and analysis method
AU2020319063B2 (en) * 2019-07-23 2025-10-09 Memorial Sloan Kettering Cancer Center Managing and accessing experiment data using referential identifiers
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
JP7470787B2 (ja) 2019-11-05 2024-04-18 パーソナリス，インコーポレイティド 単一試料からの腫瘍純度の推定
US12163189B2 (en) 2019-11-27 2024-12-10 University Of Washington Method for preparation and high-throughput microbial single-cell RNA sequencing of bacteria
US20230028058A1 (en) * 2019-12-16 2023-01-26 Ohio State Innovation Foundation Next-generation sequencing diagnostic platform and related methods
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
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
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
US11851700B1 (en) 2020-05-13 2023-12-26 10X Genomics, Inc. Methods, kits, and compositions for processing extracellular molecules
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
WO2023012521A1 (en) * 2021-08-05 2023-02-09 Inivata Limited Highly sensitive method for detecting cancer dna in a sample
CN112233741B (zh) * 2020-09-30 2024-03-01 吾征智能技术(北京)有限公司 一种基于聚类的文本分类系统、设备、存储介质
US12655450B1 (en) 2020-10-27 2026-06-16 10X Genomics, Inc. Methods, systems, and kits for detection of nucleic acid molecules
US12480158B1 (en) 2020-11-05 2025-11-25 10X Genomics, Inc. Methods and systems for processing polynucleotides
US12084715B1 (en) 2020-11-05 2024-09-10 10X Genomics, Inc. Methods and systems for reducing artifactual antisense products
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
US12444482B2 (en) 2021-04-15 2025-10-14 Illumina, Inc. Multi-channel protein voxelization to predict variant pathogenicity using deep convolutional neural networks
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
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
WO2023044229A1 (en) * 2021-09-17 2023-03-23 Illumina, Inc. Automatically identifying failure sources in nucleotide sequencing from base-call-error patterns
WO2023059654A1 (en) 2021-10-05 2023-04-13 Personalis, Inc. Customized assays for personalized cancer monitoring
CN114242167B (zh) * 2021-12-10 2024-03-26 天津金匙医学科技有限公司 一种宏基因组血液样本绝对定量的产品、方法及其应用
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
WO2026006629A1 (en) 2024-06-27 2026-01-02 Personalis, Inc. System and method for management of compressed sequencing files

Family Cites Families (177)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4994373A (en) 1983-01-27 1991-02-19 Enzo Biochem, Inc. Method and structures employing chemically-labelled polynucleotide probes
US4719179A (en) 1984-11-30 1988-01-12 Pharmacia P-L Biochemicals, Inc. Six base oligonucleotide linkers and methods for their use
US4883750A (en) 1984-12-13 1989-11-28 Applied Biosystems, Inc. Detection of specific sequences in nucleic acids
US5525464A (en) 1987-04-01 1996-06-11 Hyseq, Inc. Method of sequencing by hybridization of oligonucleotide probes
US6270961B1 (en) 1987-04-01 2001-08-07 Hyseq, Inc. Methods and apparatus for DNA sequencing and DNA identification
US5202231A (en) 1987-04-01 1993-04-13 Drmanac Radoje T Method of sequencing of genomes by hybridization of oligonucleotide probes
US5124246A (en) 1987-10-15 1992-06-23 Chiron Corporation Nucleic acid multimers and amplified nucleic acid hybridization assays using same
US5091302A (en) 1989-04-27 1992-02-25 The Blood Center Of Southeastern Wisconsin, Inc. Polymorphism of human platelet membrane glycoprotein iiia and diagnostic and therapeutic applications thereof
US5800992A (en) 1989-06-07 1998-09-01 Fodor; Stephen P.A. Method of detecting nucleic acids
US6346413B1 (en) 1989-06-07 2002-02-12 Affymetrix, Inc. Polymer arrays
US6379895B1 (en) 1989-06-07 2002-04-30 Affymetrix, Inc. Photolithographic and other means for manufacturing arrays
US5143854A (en) 1989-06-07 1992-09-01 Affymax Technologies N.V. Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof
US5744101A (en) 1989-06-07 1998-04-28 Affymax Technologies N.V. Photolabile nucleoside protecting groups
US5427930A (en) 1990-01-26 1995-06-27 Abbott Laboratories Amplification of target nucleic acids using gap filling ligase chain reaction
CA2036946C (en) 1990-04-06 2001-10-16 Kenneth V. Deugau Indexing linkers
JP3080178B2 (ja) 1991-02-18 2000-08-21 東洋紡績株式会社 核酸配列の増幅方法およびそのための試薬キット
US5426180A (en) 1991-03-27 1995-06-20 Research Corporation Technologies, Inc. Methods of making single-stranded circular oligonucleotides
JP3085409B2 (ja) 1991-03-29 2000-09-11 東洋紡績株式会社 標的核酸配列の検出方法およびそのための試薬キット
US5474796A (en) 1991-09-04 1995-12-12 Protogene Laboratories, Inc. Method and apparatus for conducting an array of chemical reactions on a support surface
US6589726B1 (en) 1991-09-04 2003-07-08 Metrigen, Inc. Method and apparatus for in situ synthesis on a solid support
ZA927323B (en) 1991-09-24 1993-08-30 Keygene Nv Selective restriction fragment amplification: A general method for DNA fingerprinting
US5632957A (en) 1993-11-01 1997-05-27 Nanogen Molecular biological diagnostic systems including electrodes
US5403708A (en) 1992-07-06 1995-04-04 Brennan; Thomas M. Methods and compositions for determining the sequence of nucleic acids
GB9214873D0 (en) 1992-07-13 1992-08-26 Medical Res Council Process for categorising nucleotide sequence populations
WO1994003624A1 (en) 1992-08-04 1994-02-17 Auerbach Jeffrey I Methods for the isothermal amplification of nucleic acid molecules
US6261808B1 (en) 1992-08-04 2001-07-17 Replicon, Inc. Amplification of nucleic acid molecules via circular replicons
US5834202A (en) 1992-08-04 1998-11-10 Replicon, Inc. Methods for the isothermal amplification of nucleic acid molecules
US6096880A (en) 1993-04-15 2000-08-01 University Of Rochester Circular DNA vectors for synthesis of RNA and DNA
US5714320A (en) 1993-04-15 1998-02-03 University Of Rochester Rolling circle synthesis of oligonucleotides and amplification of select randomized circular oligonucleotides
US6077668A (en) 1993-04-15 2000-06-20 University Of Rochester Highly sensitive multimeric nucleic acid probes
US6401267B1 (en) 1993-09-27 2002-06-11 Radoje Drmanac Methods and compositions for efficient nucleic acid sequencing
NZ275194A (en) 1993-09-27 1997-09-22 Arch Dev Corp Method and kit for nucleic acid sequencing
SE9400522D0 (sv) 1994-02-16 1994-02-16 Ulf Landegren Method and reagent for detecting specific nucleotide sequences
US5641658A (en) 1994-08-03 1997-06-24 Mosaic Technologies, Inc. Method for performing amplification of nucleic acid with two primers bound to a single solid support
US5710000A (en) 1994-09-16 1998-01-20 Affymetrix, Inc. Capturing sequences adjacent to Type-IIs restriction sites for genomic library mapping
US6013445A (en) 1996-06-06 2000-01-11 Lynx Therapeutics, Inc. Massively parallel signature sequencing by ligation of encoded adaptors
FR2726286B1 (fr) 1994-10-28 1997-01-17 Genset Sa Procede d'amplification d'acides nucleiques en phase solide et trousse de reactifs utile pour la mise en oeuvre de ce procede
US5866337A (en) 1995-03-24 1999-02-02 The Trustees Of Columbia University In The City Of New York Method to detect mutations in a nucleic acid using a hybridization-ligation procedure
US5750341A (en) 1995-04-17 1998-05-12 Lynx Therapeutics, Inc. DNA sequencing by parallel oligonucleotide extensions
US5648245A (en) 1995-05-09 1997-07-15 Carnegie Institution Of Washington Method for constructing an oligonucleotide concatamer library by rolling circle replication
DK0862656T3 (da) 1995-11-21 2001-04-09 Univ Yale Unimolekylær segmentamplifikation og -detektering
US5854033A (en) 1995-11-21 1998-12-29 Yale University Rolling circle replication reporter systems
DE69636080T2 (de) 1995-12-05 2006-11-30 Erland Jorn Koch Eine in Kaskaden verlaufende Vervielfältigungsreaktion von Nukleinsäuren
US5851804A (en) 1996-05-06 1998-12-22 Apollon, Inc. Chimeric kanamycin resistance gene
GB9620209D0 (en) 1996-09-27 1996-11-13 Cemu Bioteknik Ab Method of sequencing DNA
US5935793A (en) 1996-09-27 1999-08-10 The Chinese University Of Hong Kong Parallel polynucleotide sequencing method using tagged primers
US6297006B1 (en) 1997-01-16 2001-10-02 Hyseq, Inc. Methods for sequencing repetitive sequences and for determining the order of sequence subfragments
US6309824B1 (en) 1997-01-16 2001-10-30 Hyseq, Inc. Methods for analyzing a target nucleic acid using immobilized heterogeneous mixtures of oligonucleotide probes
US5994068A (en) 1997-03-11 1999-11-30 Wisconsin Alumni Research Foundation Nucleic acid indexing
JP2001517948A (ja) 1997-04-01 2001-10-09 グラクソ、グループ、リミテッド 核酸配列決定法
US5888737A (en) 1997-04-15 1999-03-30 Lynx Therapeutics, Inc. Adaptor-based sequence analysis
US20040229221A1 (en) 1997-05-08 2004-11-18 Trustees Of Columbia University In The City Of New York Method to detect mutations in a nucleic acid using a hybridization-ligation procedure
US6124120A (en) 1997-10-08 2000-09-26 Yale University Multiple displacement amplification
JP2001519538A (ja) 1997-10-10 2001-10-23 プレジデント・アンド・フェローズ・オブ・ハーバード・カレッジ 核酸アレイのレプリカ増幅
US6136537A (en) 1998-02-23 2000-10-24 Macevicz; Stephen C. Gene expression analysis
DE19812729A1 (de) 1998-03-24 1999-09-30 Bosch Gmbh Robert Elektromotor, insbesondere mit einem Lüfterrad zur Bildung eines Axial- oder Radiallüfters
WO1999049079A1 (en) 1998-03-25 1999-09-30 Ulf Landegren Rolling circle replication of padlock probes
US6004755A (en) 1998-04-07 1999-12-21 Incyte Pharmaceuticals, Inc. Quantitative microarray hybridizaton assays
US6284497B1 (en) 1998-04-09 2001-09-04 Trustees Of Boston University Nucleic acid arrays and methods of synthesis
US6355419B1 (en) 1998-04-27 2002-03-12 Hyseq, Inc. Preparation of pools of nucleic acids based on representation in a sample
US6255469B1 (en) 1998-05-06 2001-07-03 New York University Periodic two and three dimensional nucleic acid structures
WO2000004193A1 (en) 1998-07-20 2000-01-27 Yale University Method for detecting nucleic acids using target-mediated ligation of bipartite primers
US6787308B2 (en) 1998-07-30 2004-09-07 Solexa Ltd. Arrayed biomolecules and their use in sequencing
AU770831B2 (en) 1998-07-30 2004-03-04 Solexa Ltd. Arrayed biomolecules and their use in sequencing
US6232067B1 (en) 1998-08-17 2001-05-15 The Perkin-Elmer Corporation Adapter directed expression analysis
US6653077B1 (en) 1998-09-04 2003-11-25 Lynx Therapeutics, Inc. Method of screening for genetic polymorphism
WO2000015779A2 (en) 1998-09-15 2000-03-23 Yale University Molecular cloning using rolling circle amplification
US6235502B1 (en) 1998-09-18 2001-05-22 Molecular Staging Inc. Methods for selectively isolating DNA using rolling circle amplification
US6610492B1 (en) 1998-10-01 2003-08-26 Variagenics, Inc. Base-modified nucleotides and cleavage of polynucleotides incorporating them
US7272507B2 (en) 1999-10-26 2007-09-18 Michael Paul Strathmann Applications of parallel genomic analysis
CA2356697C (en) 1999-01-06 2010-06-22 Cornell Research Foundation, Inc. Accelerating identification of single nucleotide polymorphisms and alignment of clones in genomic sequencing
EP1144684B1 (en) 1999-01-06 2009-08-19 Callida Genomics, Inc. Enhanced sequencing by hybridization using pools of probes
GB9901475D0 (en) 1999-01-22 1999-03-17 Pyrosequencing Ab A method of DNA sequencing
US6514768B1 (en) 1999-01-29 2003-02-04 Surmodics, Inc. Replicable probe array
US6521428B1 (en) 1999-04-21 2003-02-18 Genome Technologies, Llc Shot-gun sequencing and amplification without cloning
AU7569600A (en) 1999-05-20 2000-12-28 Illumina, Inc. Combinatorial decoding of random nucleic acid arrays
US6573369B2 (en) 1999-05-21 2003-06-03 Bioforce Nanosciences, Inc. Method and apparatus for solid state molecular analysis
US7501245B2 (en) 1999-06-28 2009-03-10 Helicos Biosciences Corp. Methods and apparatuses for analyzing polynucleotide sequences
AU6387000A (en) 1999-07-29 2001-02-19 Genzyme Corporation Serial analysis of genetic alterations
US6472156B1 (en) 1999-08-30 2002-10-29 The University Of Utah Homogeneous multiplex hybridization analysis by color and Tm
US6274320B1 (en) 1999-09-16 2001-08-14 Curagen Corporation Method of sequencing a nucleic acid
US7211390B2 (en) 1999-09-16 2007-05-01 454 Life Sciences Corporation Method of sequencing a nucleic acid
US7244559B2 (en) 1999-09-16 2007-07-17 454 Life Sciences Corporation Method of sequencing a nucleic acid
WO2001023610A2 (en) 1999-09-29 2001-04-05 Solexa Ltd. Polynucleotide sequencing
US6297016B1 (en) 1999-10-08 2001-10-02 Applera Corporation Template-dependent ligation with PNA-DNA chimeric probes
US6287778B1 (en) 1999-10-19 2001-09-11 Affymetrix, Inc. Allele detection using primer extension with sequence-coded identity tags
EP1238105A2 (en) 1999-12-02 2002-09-11 Molecular Staging Inc. Generation of single-strand circular dna from linear self-annealing segments
AU2282801A (en) 1999-12-29 2001-07-09 Mergen Ltd. Methods for amplifying and detecting multiple polynucleotides on a solid phase support
GB0002389D0 (en) 2000-02-02 2000-03-22 Solexa Ltd Molecular arrays
US6221603B1 (en) 2000-02-04 2001-04-24 Molecular Dynamics, Inc. Rolling circle amplification assay for nucleic acid analysis
WO2001057268A2 (en) 2000-02-07 2001-08-09 Illumina, Inc. Nucleic acid detection methods using universal priming
JP2003521252A (ja) 2000-02-07 2003-07-15 イルミナ インコーポレイテッド ユニバーサルプライミングを用いる核酸検出方法
US6913884B2 (en) 2001-08-16 2005-07-05 Illumina, Inc. Compositions and methods for repetitive use of genomic DNA
WO2001062982A2 (en) 2000-02-25 2001-08-30 Mosaic Technologies, Inc. Methods for multi-stage solid phase amplification of nucleic acids
US20020004204A1 (en) 2000-02-29 2002-01-10 O'keefe Matthew T. Microarray substrate with integrated photodetector and methods of use thereof
US6413722B1 (en) 2000-03-22 2002-07-02 Incyte Genomics, Inc. Polymer coated surfaces for microarray applications
AU2001268468A1 (en) 2000-06-13 2001-12-24 The Trustees Of Boston University Use of nucleotide analogs in the analysis of oligonucleotide mixtures and in highly multiplexed nucleic acid sequencing
JP3930227B2 (ja) 2000-06-14 2007-06-13 ペンタックス株式会社 磁気式エンコーダおよび磁気式エンコーダを搭載した測量機
US6783943B2 (en) 2000-12-20 2004-08-31 The Regents Of The University Of California Rolling circle amplification detection of RNA and DNA
WO2002061143A2 (en) 2001-01-31 2002-08-08 Ambion, Inc. Comparative analysis of nucleic acids using population tagging
EP2801624B1 (en) 2001-03-16 2019-03-06 Singular Bio, Inc Arrays and methods of use
GB0114853D0 (en) 2001-06-18 2001-08-08 Medical Res Council Happier Mapping
US7297778B2 (en) 2001-07-25 2007-11-20 Affymetrix, Inc. Complexity management of genomic DNA
GB2378245A (en) 2001-08-03 2003-02-05 Mats Nilsson Nucleic acid amplification method
US6975943B2 (en) 2001-09-24 2005-12-13 Seqwright, Inc. Clone-array pooled shotgun strategy for nucleic acid sequencing
US6617137B2 (en) 2001-10-15 2003-09-09 Molecular Staging Inc. Method of amplifying whole genomes without subjecting the genome to denaturing conditions
GB0126887D0 (en) 2001-11-08 2002-01-02 Univ London Method for producing and identifying soluble protein domains
GB2382137A (en) 2001-11-20 2003-05-21 Mats Gullberg Nucleic acid enrichment
US7011945B2 (en) 2001-12-21 2006-03-14 Eastman Kodak Company Random array of micro-spheres for the analysis of nucleic acids
US20040002090A1 (en) 2002-03-05 2004-01-01 Pascal Mayer Methods for detecting genome-wide sequence variations associated with a phenotype
DE10224339A1 (de) 2002-05-29 2003-12-11 Axaron Bioscience Ag Verfahren zur hochparallelen Nukleinsäuresequenzierung
US20050019776A1 (en) 2002-06-28 2005-01-27 Callow Matthew James Universal selective genome amplification and universal genotyping system
AU2003267583A1 (en) 2002-09-19 2004-04-08 The Chancellor, Master And Scholars Of The University Of Oxford Molecular arrays and single molecule detection
WO2004033728A2 (en) 2002-10-11 2004-04-22 Erasmus Universiteit Rotterdam Nucleic acid amplification primers for pcr-based clonality studies
US6977153B2 (en) 2002-12-31 2005-12-20 Qiagen Gmbh Rolling circle amplification of RNA
DE602004026033D1 (de) 2003-01-29 2010-04-29 454 Corp Zweiendige sequenzierung
CA2515938A1 (en) 2003-02-12 2004-08-26 Genizon Svenska Ab Methods and means for nucleic acid sequencing
CN1791682B (zh) 2003-02-26 2013-05-22 凯利达基因组股份有限公司 通过杂交进行的随机阵列dna分析
US7718403B2 (en) 2003-03-07 2010-05-18 Rubicon Genomics, Inc. Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process
EP1616947B1 (en) 2003-03-28 2012-05-09 Japan as represented by Director General of National Rehabilitation Center for Persons with Disabilities METHOD OF SYNTHESIZING cDNA
WO2004090100A2 (en) 2003-04-04 2004-10-21 Agilent Technologies, Inc. Visualizing expression data on chromosomal graphic schemes
US7745116B2 (en) 2003-04-08 2010-06-29 Pacific Biosciences Of California, Inc. Composition and method for nucleic acid sequencing
US20040259118A1 (en) 2003-06-23 2004-12-23 Macevicz Stephen C. Methods and compositions for nucleic acid sequence analysis
EP1685380A2 (en) 2003-09-18 2006-08-02 Parallele Bioscience, Inc. System and methods for enhancing signal-to-noise ratios of microarray-based measurements
GB0324456D0 (en) 2003-10-20 2003-11-19 Isis Innovation Parallel DNA sequencing methods
ATE510024T1 (de) 2003-10-31 2011-06-15 Advanced Genetic Analysis Corp Ab Verfahren zur herstellung eines gepaarten tag aus einer nukleinsäuresequenz sowie verfahren zur verwendung davon
US7169560B2 (en) 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
US7972994B2 (en) 2003-12-17 2011-07-05 Glaxosmithkline Llc Methods for synthesis of encoded libraries
GB0400584D0 (en) 2004-01-12 2004-02-11 Solexa Ltd Nucleic acid chacterisation
GB0402895D0 (en) 2004-02-10 2004-03-17 Solexa Ltd Arrayed polynucleotides
ATE463584T1 (de) 2004-02-19 2010-04-15 Helicos Biosciences Corp Verfahren zur analyse von polynukleotidsequenzen
CA2557841A1 (en) 2004-02-27 2005-09-09 President And Fellows Of Harvard College Polony fluorescent in situ sequencing beads
KR100552706B1 (ko) 2004-03-12 2006-02-20 삼성전자주식회사 핵산 증폭 방법 및 장치
US20050214840A1 (en) 2004-03-23 2005-09-29 Xiangning Chen Restriction enzyme mediated method of multiplex genotyping
GB2413796B (en) 2004-03-25 2006-03-29 Global Genomics Ab Methods and means for nucleic acid sequencing
US7470517B2 (en) 2004-04-09 2008-12-30 Trustees Of Boston University Method for de novo detection of sequences in nucleic acids: target sequencing by fragmentation
US20050260609A1 (en) 2004-05-24 2005-11-24 Lapidus Stanley N Methods and devices for sequencing nucleic acids
EP1766090B1 (en) 2004-05-25 2011-04-27 Helicos Biosciences Corporation Methods for nucleic acid immobilisation
US20070117104A1 (en) 2005-11-22 2007-05-24 Buzby Philip R Nucleotide analogs
US7565346B2 (en) * 2004-05-31 2009-07-21 International Business Machines Corporation System and method for sequence-based subspace pattern clustering
US20060024711A1 (en) 2004-07-02 2006-02-02 Helicos Biosciences Corporation Methods for nucleic acid amplification and sequence determination
US7276720B2 (en) 2004-07-19 2007-10-02 Helicos Biosciences Corporation Apparatus and methods for analyzing samples
US20060012793A1 (en) 2004-07-19 2006-01-19 Helicos Biosciences Corporation Apparatus and methods for analyzing samples
WO2006073504A2 (en) 2004-08-04 2006-07-13 President And Fellows Of Harvard College Wobble sequencing
EP1647600A3 (en) 2004-09-17 2006-06-28 Affymetrix, Inc. (A US Entity) Methods for identifying biological samples by addition of nucleic acid bar-code tags
GB0422551D0 (en) 2004-10-11 2004-11-10 Univ Liverpool Labelling and sequencing of nucleic acids
JP2008520975A (ja) 2004-11-16 2008-06-19 ヘリコス バイオサイエンシーズ コーポレイション Ｔｉｒｆ単分子分析および核酸を配列決定する方法
US20060110744A1 (en) 2004-11-23 2006-05-25 Sampas Nicolas M Probe design methods and microarrays for comparative genomic hybridization and location analysis
EP2857523A1 (en) 2005-02-01 2015-04-08 Applied Biosystems, LLC Method for identifying a sequence in a polynucleotide
US20060223122A1 (en) 2005-03-08 2006-10-05 Agnes Fogo Classifying and predicting glomerulosclerosis using a proteomics approach
DK1907571T3 (en) 2005-06-15 2017-08-21 Complete Genomics Inc NUCLEIC ACID ANALYSIS USING INCIDENTAL MIXTURES OF NON-OVERLAPPING FRAGMENTS
US20070099212A1 (en) 2005-07-28 2007-05-03 Timothy Harris Consecutive base single molecule sequencing
DK1915446T3 (en) 2005-08-11 2017-09-11 Synthetic Genomics Inc IN VITRO RECOMBINATION PROCEDURE
US7666593B2 (en) 2005-08-26 2010-02-23 Helicos Biosciences Corporation Single molecule sequencing of captured nucleic acids
EP1951900B1 (en) 2005-10-07 2016-06-15 Callida Genomics, Inc. Self-assembled single molecule arrays and uses thereof
WO2007120208A2 (en) 2005-11-14 2007-10-25 President And Fellows Of Harvard College Nanogrid rolling circle dna sequencing
US20090125246A1 (en) 2006-01-11 2009-05-14 Neocodex S.L. Method and Apparatus for the Determination of Genetic Associations
EP1987162A4 (en) 2006-01-23 2009-11-25 Population Genetics Technologi NUCLEIC ACID ANALYSIS ABOUT SEQUENCE TOKENS
WO2007092538A2 (en) 2006-02-07 2007-08-16 President And Fellows Of Harvard College Methods for making nucleotide probes for sequencing and synthesis
SG170028A1 (en) 2006-02-24 2011-04-29 Callida Genomics Inc High throughput genome sequencing on dna arrays
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
JP2009529876A (ja) 2006-03-14 2009-08-27 ゲニゾン バイオサイエンシス インコーポレイテッド 核酸を配列決定するための方法および手段
AU2007237909A1 (en) 2006-04-19 2007-10-25 Applied Biosystems, Llc. Reagents, methods, and libraries for gel-free bead-based sequencing
WO2007133710A2 (en) 2006-05-11 2007-11-22 Raindance Technologies, Inc. Microfluidic devices and methods of use thereof
WO2008070352A2 (en) 2006-10-27 2008-06-12 Complete Genomics, Inc. Efficient arrays of amplified polynucleotides
US12180549B2 (en) 2007-07-23 2024-12-31 The Chinese University Of Hong Kong Diagnosing fetal chromosomal aneuploidy using genomic sequencing
US7897344B2 (en) 2007-11-06 2011-03-01 Complete Genomics, Inc. Methods and oligonucleotide designs for insertion of multiple adaptors into library constructs
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
CN102459592B (zh) * 2009-06-15 2017-04-05 考利达基因组股份有限公司 用于长片段阅读测序的方法和组合物
EP2480690A2 (en) 2009-09-23 2012-08-01 Existence Genetics LLC Genetic analysis
LT3241914T (lt) 2009-11-05 2019-04-25 The Chinese University Of Hong Kong Vaisiaus genomo analizė iš motinos biologinio mėginio
CN102725424B (zh) 2010-01-25 2014-07-09 Rd生物科技公司 靶核酸的自折叠扩增
WO2011097424A1 (en) 2010-02-05 2011-08-11 Siemens Healthcare Diagnostics Inc. Methods for increasing multiplex level by externalization of passive reference in polymerase chain reactions
EP2363502B1 (en) 2010-03-04 2017-02-15 miacom Diagnostics GmbH Enhanced multiplex FISH
CN107368705B (zh) 2011-04-14 2021-07-13 完整基因有限公司 分析生物体的基因组dna的方法和计算机系统
WO2012162161A1 (en) 2011-05-20 2012-11-29 Phthisis Diagnostics Microsporidia detection system and method

Also Published As

Publication number Publication date
WO2012142611A3 (en) 2016-03-03
JP6297972B2 (ja) 2018-03-20
AU2012242508A1 (en) 2013-05-02
US9524369B2 (en) 2016-12-20
US20160378916A1 (en) 2016-12-29
HK1201077A1 (en) 2015-08-21
US20130124100A1 (en) 2013-05-16
WO2012142611A2 (en) 2012-10-18
AU2016202139A1 (en) 2016-06-02
CN103987857A (zh) 2014-08-13
EP2997157A2 (en) 2016-03-23
US20150379192A9 (en) 2015-12-31
JP2014523233A (ja) 2014-09-11
CA2832643A1 (en) 2012-10-18
EP2997157A4 (en) 2017-03-29
AU2016202139B2 (en) 2017-10-26
AU2012242508B2 (en) 2016-01-07
CN103987857B (zh) 2018-04-27

Similar Documents

Publication Publication Date Title
AU2016202139B2 (en) Sequencing small amounts of complex nucleic acids
US20240287598A1 (en) Multiple tagging of individual long dna fragments
AU2012242525B2 (en) Processing and analysis of complex nucleic acid sequence data
AU2015264833B2 (en) Processing and analysis of complex nucleic acid sequence data
HK1246901B (en) Method and computer system for analyzing genomic dna of organisms
HK40041078B (en) Multiple tagging of long dna fragments
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
HK1219709B (en) Multiple tagging of long dna fragments
HK40015468B (en) Method for sequencing using universal short adapters for indexing of polynucleotide samples

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20170412

MPN Maintenance fee for patent paid

Free format text: FEE DESCRIPTION TEXT: MF (PATENT, 13TH ANNIV.) - STANDARD

Year of fee payment: 13

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20250324

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT DETERMINED COMPLIANT

Effective date: 20250324

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20250324

MPN Maintenance fee for patent paid

Free format text: FEE DESCRIPTION TEXT: MF (PATENT, 14TH ANNIV.) - STANDARD

Year of fee payment: 14

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20260324

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20260324