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EP2836611A4 - Détection et quantification de la contamination d'échantillons dans une analyse de répertoire immunologique - Google Patents

Détection et quantification de la contamination d'échantillons dans une analyse de répertoire immunologique

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Withdrawn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)
English (en)
Other versions
EP2836611A1 (fr
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/fr
Publication of EP2836611A4 publication Critical patent/EP2836611A4/fr
Withdrawn legal-status Critical Current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 Détection et quantification de la contamination d'échantillons dans une analyse de répertoire immunologique Withdrawn EP2836611A4 (fr)

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 (fr) 2012-04-13 2013-04-09 Détection et quantification de la contamination d'échantillons dans une analyse de répertoire immunologique

Publications (2)

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

Family

ID=49328112

Family Applications (1)

Application Number Title Priority Date Filing Date
EP13775514.6A Withdrawn EP2836611A4 (fr) 2012-04-13 2013-04-09 Détection et quantification de la contamination d'échantillons dans une analyse de répertoire immunologique

Country Status (7)

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

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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
US8748103B2 (en) 2008-11-07 2014-06-10 Sequenta, Inc. Monitoring health and disease status using clonotype profiles
GB2467704B (en) 2008-11-07 2011-08-24 Mlc Dx Inc A method for determining a profile of recombined DNA sequences in T-cells and/or B-cells
US9528160B2 (en) 2008-11-07 2016-12-27 Adaptive Biotechnolgies Corp. Rare clonotypes and uses thereof
US9365901B2 (en) 2008-11-07 2016-06-14 Adaptive Biotechnologies Corp. Monitoring immunoglobulin heavy chain evolution in B-cell acute lymphoblastic leukemia
PL2387627T3 (pl) 2009-01-15 2016-10-31 Profilowanie odporności adaptacyjnej i wytwarzanie przeciwciał monoklonalnych
KR20120044941A (ko) 2009-06-25 2012-05-08 프레드 헛친슨 켄서 리서치 센터 적응 면역의 측정방법
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
CA2853088C (fr) 2011-10-21 2018-03-13 Adaptive Biotechnologies Corporation Quantification de genomes de cellules immunitaires adaptatives dans un melange complexe de cellules
ES2867924T3 (es) 2011-12-09 2021-10-21 Adaptive Biotechnologies Corp Diagnóstico de tumores malignos linfoides y detección de enfermedad residual mínima
US9499865B2 (en) 2011-12-13 2016-11-22 Adaptive Biotechnologies Corp. Detection and measurement of tissue-infiltrating lymphocytes
ES2662128T3 (es) 2012-03-05 2018-04-05 Adaptive Biotechnologies Corporation Determinación de cadenas de receptor inmunitario emparejadas a partir de la frecuencia de subunidades coincidentes
JP5756247B1 (ja) 2012-05-08 2015-07-29 アダプティブ バイオテクノロジーズ コーポレイション マルチプレックスｐｃｒ反応における増幅バイアスを測定し校正する組成物及び方法
ES2660027T3 (es) 2012-10-01 2018-03-20 Adaptive Biotechnologies Corporation Evaluación de la inmunocompetencia por la diversidad de los receptores de inmunidad adaptativa y caracterización de la clonalidad
EP3511423B2 (fr) 2012-10-17 2024-05-29 Spatial Transcriptomics AB Procédés et produits pour optimiser la detection localisée ou spatiale de l'expression génique dans un échantillon de tissu
WO2015160439A2 (fr) 2014-04-17 2015-10-22 Adaptive Biotechnologies Corporation Quantification de génomes de cellules de l'immunité acquise dans un mélange complexe de cellules
LT3013983T (lt) 2013-06-25 2023-05-10 Prognosys Biosciences, Inc. Erdviniai koduoti biologiniai tyrimai, naudojant mikrofluidinį įrenginį
US9708657B2 (en) * 2013-07-01 2017-07-18 Adaptive Biotechnologies Corp. Method for generating clonotype profiles using sequence tags
EP3114240B1 (fr) 2014-03-05 2019-07-24 Adaptive Biotechnologies Corporation Procédés dans lesquels on utilise des molécules synthétiques contenant des randomères
US10066265B2 (en) 2014-04-01 2018-09-04 Adaptive Biotechnologies Corp. Determining antigen-specific t-cells
AU2015339191A1 (en) 2014-10-29 2017-05-18 Adaptive Biotechnologies Corp. Highly-multiplexed simultaneous 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
AU2015353581A1 (en) 2014-11-25 2017-06-15 Adaptive Biotechnologies Corporation Characterization of adaptive immune response to vaccination or infection using immune repertoire sequencing
WO2016138122A1 (fr) 2015-02-24 2016-09-01 Adaptive Biotechnologies Corp. Méthodes pour le diagnostic d'une maladie infectieuse et la détermination du statut hla à l'aide du séquençage du répertoire immunitaire
EP3277294B1 (fr) 2015-04-01 2024-05-15 Adaptive Biotechnologies Corp. Procédé d'identification des récepteurs de lymphocytes t spécifiques à compatibilité humaine pour une cible antigénique
SG11201707515SA (en) 2015-04-10 2017-10-30 Spatial Transcriptomics Ab Spatially distinguished, multiplex nucleic acid analysis of biological specimens
CN105095687B (zh) * 2015-06-26 2018-10-26 南方科技大学 一种免疫组库数据分析方法及终端
KR20240056636A (ko) * 2015-09-01 2024-04-30 더 리젠츠 오브 더 유니버시티 오브 캘리포니아 모듈 폴리펩타이드 라이브러리 및 이의 제조 및 사용 방법
CA3004310A1 (fr) * 2015-11-04 2017-05-11 Atreca, Inc. Ensembles combinatoires de codes-barres d'acides nucleiques pour l'analyse d'acides nucleiques associes a des cellules uniques
CN105740650B (zh) * 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 一种快速准确鉴定高通量基因组数据污染源的方法
US10428325B1 (en) 2016-09-21 2019-10-01 Adaptive Biotechnologies Corporation Identification of antigen-specific B cell receptors
WO2019046817A1 (fr) 2017-09-01 2019-03-07 Life Technologies Corporation Compositions et méthodes pour séquençage de répertoire immunologique
US11254980B1 (en) 2017-11-29 2022-02-22 Adaptive Biotechnologies Corporation Methods of profiling targeted polynucleotides while mitigating sequencing depth requirements
WO2020018836A1 (fr) 2018-07-18 2020-01-23 Life Technologies Corporation Compositions et méthodes destinées au séquençage de répertoire immunologique
WO2020131182A2 (fr) * 2018-09-26 2020-06-25 The University Of North Carolina At Chapel Hill Composés, compositions et méthodes d'amélioration de dosages
SG11202102424QA (en) 2018-12-17 2021-04-29 Illumina Inc Methods and means for preparing a library for sequencing
WO2020243579A1 (fr) 2019-05-30 2020-12-03 10X Genomics, Inc. Procédés de détection de l'hétérogénéité spatiale d'un échantillon biologique
CN110970091B (zh) * 2019-12-20 2023-05-23 北京优迅医学检验实验室有限公司 标签质控的方法及装置
CN111304309A (zh) * 2020-03-06 2020-06-19 上海韦翰斯生物医药科技有限公司 一种测序平台标签序列污染的检测方法
WO2021247543A2 (fr) 2020-06-02 2021-12-09 10X Genomics, Inc. Procédés de banques d'acides nucléiques
EP4158054B1 (fr) 2020-06-02 2025-04-16 10X Genomics, Inc. Trancriptomique spatiale pour les récepteurs d'antigènes
ES2981265T3 (es) 2020-06-08 2024-10-08 10X Genomics Inc Métodos para determinar un margen quirúrgico y métodos de uso del mismo

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999020798A1 (fr) * 1997-10-23 1999-04-29 Exact Laboratories, Inc. Procedes de detection de contamination dans le diagnostic moleculaire utilisant la reaction pcr
WO2005113803A1 (fr) * 2004-05-19 2005-12-01 Amplion Limited Detection de la contamination d'amplicons lors de la pcr presentant deux temperatures de recuit differentes
WO2011139371A1 (fr) * 2010-05-06 2011-11-10 Sequenta, Inc. Surveillance de l'état de santé et du stade d'une maladie à l'aide de profils de clonotype

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US7537897B2 (en) * 2006-01-23 2009-05-26 Population Genetics Technologies, Ltd. Molecular counting
ES2546848T3 (es) * 2006-03-10 2015-09-29 Epigenomics Ag Un método para identificar una muestra biológica para el análisis de la metilación
US8748103B2 (en) * 2008-11-07 2014-06-10 Sequenta, Inc. Monitoring health and disease status using clonotype profiles
GB2467704B (en) * 2008-11-07 2011-08-24 Mlc Dx Inc A method for determining a profile of recombined DNA sequences in T-cells and/or B-cells
US20140057799A1 (en) * 2010-12-16 2014-02-27 Gigagen System and Methods for Massively 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 (fr) * 1997-10-23 1999-04-29 Exact Laboratories, Inc. Procedes de detection de contamination dans le diagnostic moleculaire utilisant la reaction pcr
WO2005113803A1 (fr) * 2004-05-19 2005-12-01 Amplion Limited Detection de la contamination d'amplicons lors de la pcr presentant deux temperatures de recuit differentes
WO2011139371A1 (fr) * 2010-05-06 2011-11-10 Sequenta, Inc. Surveillance de l'état de santé et du stade d'une maladie à l'aide de profils de clonotype

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 (fr) 2015-02-18
SG11201406538VA (en) 2014-11-27
AU2013246050B2 (en) 2017-03-16
CA2869481A1 (fr) 2013-10-17
JP2015512655A (ja) 2015-04-30
WO2013155119A1 (fr) 2013-10-17
CN104395481A (zh) 2015-03-04
AU2013246050A1 (en) 2014-10-23

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