EP2836611A4 - Detection and quantitation of sample contamination in immune repertoire analysis - Google Patents

Detection and quantitation of sample contamination in immune repertoire analysis

Info

Publication number
EP2836611A4
EP2836611A4 EP13775514.6A EP13775514A EP2836611A4 EP 2836611 A4 EP2836611 A4 EP 2836611A4 EP 13775514 A EP13775514 A EP 13775514A EP 2836611 A4 EP2836611 A4 EP 2836611A4
Authority
EP
European Patent Office
Prior art keywords
quantitation
detection
immune repertoire
sample contamination
repertoire analysis
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.)
Withdrawn
Application number
EP13775514.6A
Other languages
German (de)
French (fr)
Other versions
EP2836611A1 (en
Inventor
Thomas Asbury
Victoria Carlton
Malek Faham
Stephen Macevicz
Martin Head
Thomas Willis
Jianbiao Zheng
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.)
Adaptive Biotechnologies Corp
Original Assignee
Sequenta 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
Priority claimed from US13/834,794 external-priority patent/US9528160B2/en
Priority claimed from US13/835,093 external-priority patent/US9506119B2/en
Application filed by Sequenta Inc filed Critical Sequenta Inc
Publication of EP2836611A1 publication Critical patent/EP2836611A1/en
Publication of EP2836611A4 publication Critical patent/EP2836611A4/en
Withdrawn legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6848—Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction

Landscapes

  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
EP13775514.6A 2012-04-13 2013-04-09 Detection and quantitation of sample contamination in immune repertoire analysis Withdrawn EP2836611A4 (en)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US201261624002P 2012-04-13 2012-04-13
US201261658317P 2012-06-11 2012-06-11
US201261738277P 2012-12-17 2012-12-17
US201361768269P 2013-02-22 2013-02-22
US13/834,794 US9528160B2 (en) 2008-11-07 2013-03-15 Rare clonotypes and uses thereof
US13/835,093 US9506119B2 (en) 2008-11-07 2013-03-15 Method of sequence determination using sequence tags
PCT/US2013/035857 WO2013155119A1 (en) 2012-04-13 2013-04-09 Detection and quantitation of sample contamination in immune repertoire analysis

Publications (2)

Publication Number Publication Date
EP2836611A1 EP2836611A1 (en) 2015-02-18
EP2836611A4 true EP2836611A4 (en) 2015-12-30

Family

ID=49328112

Family Applications (1)

Application Number Title Priority Date Filing Date
EP13775514.6A Withdrawn EP2836611A4 (en) 2012-04-13 2013-04-09 Detection and quantitation of sample contamination in immune repertoire analysis

Country Status (7)

Country Link
EP (1) EP2836611A4 (en)
JP (1) JP2015512655A (en)
CN (1) CN104395481A (en)
AU (1) AU2013246050B2 (en)
CA (1) CA2869481A1 (en)
SG (1) SG11201406538VA (en)
WO (1) WO2013155119A1 (en)

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CN104195227B (en) 2008-11-07 2017-04-12 适应生物技术公司 Methods of monitoring conditions by sequence analysis
US8748103B2 (en) 2008-11-07 2014-06-10 Sequenta, Inc. Monitoring health and disease status using clonotype profiles
US9365901B2 (en) 2008-11-07 2016-06-14 Adaptive Biotechnologies Corp. Monitoring immunoglobulin heavy chain evolution in B-cell acute lymphoblastic leukemia
US9506119B2 (en) 2008-11-07 2016-11-29 Adaptive Biotechnologies Corp. Method of sequence determination using sequence tags
US9528160B2 (en) 2008-11-07 2016-12-27 Adaptive Biotechnolgies Corp. Rare clonotypes and uses thereof
US9394567B2 (en) 2008-11-07 2016-07-19 Adaptive Biotechnologies Corporation Detection and quantification of sample contamination in immune repertoire analysis
US8628927B2 (en) 2008-11-07 2014-01-14 Sequenta, Inc. Monitoring health and disease status using clonotype profiles
US8685898B2 (en) 2009-01-15 2014-04-01 Imdaptive, Inc. Adaptive immunity profiling and methods for generation of monoclonal antibodies
CA2765949C (en) 2009-06-25 2016-03-29 Fred Hutchinson Cancer Research Center Method of measuring adaptive immunity
US9043160B1 (en) 2009-11-09 2015-05-26 Sequenta, Inc. Method of determining clonotypes and clonotype profiles
GB201106254D0 (en) 2011-04-13 2011-05-25 Frisen Jonas Method and product
US10385475B2 (en) 2011-09-12 2019-08-20 Adaptive Biotechnologies Corp. Random array sequencing of low-complexity libraries
AU2012325791B2 (en) 2011-10-21 2018-04-05 Adaptive Biotechnologies Corporation Quantification of adaptive immune cell genomes in a complex mixture of cells
ES2683037T3 (en) 2011-12-09 2018-09-24 Adaptive Biotechnologies Corporation Diagnosis of lymphoid malignant tumors and detection of minimal residual disease
US9499865B2 (en) 2011-12-13 2016-11-22 Adaptive Biotechnologies Corp. Detection and measurement of tissue-infiltrating lymphocytes
US10077478B2 (en) 2012-03-05 2018-09-18 Adaptive Biotechnologies Corp. Determining paired immune receptor chains from frequency matched subunits
SG10201507700VA (en) 2012-05-08 2015-10-29 Adaptive Biotechnologies Corp Compositions and method for measuring and calibrating amplification bias in multiplexed pcr reactions
AU2013327423B2 (en) 2012-10-01 2017-06-22 Adaptive Biotechnologies Corporation Immunocompetence assessment by adaptive immune receptor diversity and clonality characterization
US10150996B2 (en) 2012-10-19 2018-12-11 Adaptive Biotechnologies Corp. Quantification of adaptive immune cell genomes in a complex mixture of cells
CN118240918A (en) 2013-06-25 2024-06-25 普罗格诺西斯生物科学公司 Spatially encoded bioanalytical analysis using microfluidic devices
US9708657B2 (en) * 2013-07-01 2017-07-18 Adaptive Biotechnologies Corp. Method for generating clonotype profiles using sequence tags
ES2741740T3 (en) 2014-03-05 2020-02-12 Adaptive Biotechnologies Corp Methods that use synthetic molecules that contain random nucleotide segments
US10066265B2 (en) 2014-04-01 2018-09-04 Adaptive Biotechnologies Corp. Determining antigen-specific t-cells
ES2784343T3 (en) 2014-10-29 2020-09-24 Adaptive Biotechnologies Corp Simultaneous, highly multiplexed detection of nucleic acids encoding paired adaptive immune receptor heterodimers from many samples
US10246701B2 (en) 2014-11-14 2019-04-02 Adaptive Biotechnologies Corp. Multiplexed digital quantitation of rearranged lymphoid receptors in a complex mixture
CA2968543C (en) 2014-11-25 2024-04-02 Adaptive Biotechnologies Corporation Characterization of adaptive immune response to vaccination or infection using immune repertoire sequencing
WO2016138122A1 (en) 2015-02-24 2016-09-01 Adaptive Biotechnologies Corp. Methods for diagnosing infectious disease and determining hla status using immune repertoire sequencing
EP3277294B1 (en) 2015-04-01 2024-05-15 Adaptive Biotechnologies Corp. Method of identifying human compatible t cell receptors specific for an antigenic target
EP4119677B1 (en) 2015-04-10 2023-06-28 Spatial Transcriptomics AB Spatially distinguished, multiplex nucleic acid analysis of biological specimens
CN105095687B (en) * 2015-06-26 2018-10-26 南方科技大学 Immune repertoire data analysis method and terminal
IL257453B (en) * 2015-09-01 2022-07-01 Univ California Modular polypeptide libraries and methods of making and using same
JP7064439B2 (en) * 2015-11-04 2022-05-10 アトレカ インコーポレイテッド A set of nucleic acid barcode combinations for the analysis of nucleic acids associated with a single cell
CN105740650B (en) * 2016-03-02 2019-04-05 广西作物遗传改良生物技术重点开放实验室 A method of quick and precisely identifying high-throughput genomic data pollution sources
US10428325B1 (en) 2016-09-21 2019-10-01 Adaptive Biotechnologies Corporation Identification of antigen-specific B cell receptors
WO2019046817A1 (en) 2017-09-01 2019-03-07 Life Technologies Corporation Compositions and methods for immune repertoire sequencing
US11254980B1 (en) 2017-11-29 2022-02-22 Adaptive Biotechnologies Corporation Methods of profiling targeted polynucleotides while mitigating sequencing depth requirements
WO2020131182A2 (en) * 2018-09-26 2020-06-25 The University Of North Carolina At Chapel Hill Compounds, compositions, and methods for improving assays
CN112867800B (en) * 2018-12-17 2024-07-12 Illumina公司 Methods and means for preparing sequencing libraries
EP3976820A1 (en) 2019-05-30 2022-04-06 10X Genomics, Inc. Methods of detecting spatial heterogeneity of a biological sample
CN110970091B (en) * 2019-12-20 2023-05-23 北京优迅医学检验实验室有限公司 Label quality control method and device
CN111304309A (en) * 2020-03-06 2020-06-19 上海韦翰斯生物医药科技有限公司 Detection method for sequencing platform tag sequence pollution
WO2021247568A1 (en) 2020-06-02 2021-12-09 10X Genomics, Inc. Spatial trancriptomics for antigen-receptors
WO2021247543A2 (en) 2020-06-02 2021-12-09 10X Genomics, Inc. Nucleic acid library methods
WO2021252499A1 (en) 2020-06-08 2021-12-16 10X Genomics, Inc. Methods of determining a surgical margin and methods of use thereof

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999020798A1 (en) * 1997-10-23 1999-04-29 Exact Laboratories, Inc. Methods for detecting contamination in molecular diagnostics using pcr
WO2005113803A1 (en) * 2004-05-19 2005-12-01 Amplion Limited Detection of amplicon contamination during pcr exhibiting two different annealing temperatures
WO2011139371A1 (en) * 2010-05-06 2011-11-10 Sequenta, Inc. Monitoring health and disease status using clonotype profiles

Family Cites Families (5)

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WO2007087312A2 (en) * 2006-01-23 2007-08-02 Population Genetics Technologies Ltd. Molecular counting
ES2546848T3 (en) * 2006-03-10 2015-09-29 Epigenomics Ag A method to identify a biological sample for methylation analysis
CN104195227B (en) * 2008-11-07 2017-04-12 适应生物技术公司 Methods of monitoring conditions by sequence analysis
US8748103B2 (en) * 2008-11-07 2014-06-10 Sequenta, Inc. Monitoring health and disease status using clonotype profiles
DK2652155T3 (en) * 2010-12-16 2017-02-13 Gigagen Inc Methods for Massive Parallel Analysis of Nucleic Acids in Single Cells

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999020798A1 (en) * 1997-10-23 1999-04-29 Exact Laboratories, Inc. Methods for detecting contamination in molecular diagnostics using pcr
WO2005113803A1 (en) * 2004-05-19 2005-12-01 Amplion Limited Detection of amplicon contamination during pcr exhibiting two different annealing temperatures
WO2011139371A1 (en) * 2010-05-06 2011-11-10 Sequenta, Inc. Monitoring health and disease status using clonotype profiles

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
MEGAN L MCCLOSKEY ET AL: "Encoding PCR Products with Batch-stamps and Barcodes", BIOCHEMICAL GENETICS, KLUWER ACADEMIC PUBLISHERS-PLENUM PUBLISHERS, NE, vol. 45, no. 11-12, 23 October 2007 (2007-10-23), pages 761 - 767, XP019548696, ISSN: 1573-4927, DOI: 10.1007/S10528-007-9114-X *
See also references of WO2013155119A1 *

Also Published As

Publication number Publication date
EP2836611A1 (en) 2015-02-18
AU2013246050A1 (en) 2014-10-23
JP2015512655A (en) 2015-04-30
SG11201406538VA (en) 2014-11-27
CA2869481A1 (en) 2013-10-17
WO2013155119A1 (en) 2013-10-17
AU2013246050B2 (en) 2017-03-16
CN104395481A (en) 2015-03-04

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