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WO2008026927A3 - Process for displaying t- and b-cell receptor repertoires - Google Patents

Process for displaying t- and b-cell receptor repertoires Download PDF

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Publication number
WO2008026927A3
WO2008026927A3 PCT/NL2007/050429 NL2007050429W WO2008026927A3 WO 2008026927 A3 WO2008026927 A3 WO 2008026927A3 NL 2007050429 W NL2007050429 W NL 2007050429W WO 2008026927 A3 WO2008026927 A3 WO 2008026927A3
Authority
WO
WIPO (PCT)
Prior art keywords
repertoire
allergen
ndn
gene segments
oligonucleotide
Prior art date
Application number
PCT/NL2007/050429
Other languages
French (fr)
Other versions
WO2008026927A2 (en
Inventor
Vries Nikolaas De
Original Assignee
Amc Amsterdam
Vries Nikolaas De
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.)
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Publication date
Application filed by Amc Amsterdam, Vries Nikolaas De filed Critical Amc Amsterdam
Publication of WO2008026927A2 publication Critical patent/WO2008026927A2/en
Publication of WO2008026927A3 publication Critical patent/WO2008026927A3/en

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    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (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)

Abstract

The current invention provides a process for determining the TCR or BCR receptor gene rearrangements and allows visualization of the repertoire of V(D)J rearranged CDR3 domains on an oligonucleotide array on a solid carrier. The method visualizes the end-result of the V(D)J recombination process and in particular the delet ion and insertion process that takes place in the NDN hypervariable region, where 1 up to 13 nucleotides are deleted from the V, D and/or J gene segments, by using a labeled annealer oligonucleotide that hybridizes on or in close proximity of the NDN region. The method allows detection of the full repertoire or a selected part of the repertoire, by choosing and combining primers that are specific for certain V, D and/or J gene segments flanking the CDR3 on either side. The method of the invention may be used or applied for the diagnosis of an immune response against a pathogen, allergen or auto-allergen.
PCT/NL2007/050429 2006-08-30 2007-08-30 Process for displaying t- and b-cell receptor repertoires WO2008026927A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
EP06119814 2006-08-30
EP06119814.9 2006-08-30

Publications (2)

Publication Number Publication Date
WO2008026927A2 WO2008026927A2 (en) 2008-03-06
WO2008026927A3 true WO2008026927A3 (en) 2008-04-24

Family

ID=37709507

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/NL2007/050429 WO2008026927A2 (en) 2006-08-30 2007-08-30 Process for displaying t- and b-cell receptor repertoires

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Country Link
WO (1) WO2008026927A2 (en)

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US9150905B2 (en) 2012-05-08 2015-10-06 Adaptive Biotechnologies Corporation Compositions and method for measuring and calibrating amplification bias in multiplexed PCR reactions
US9181590B2 (en) 2011-10-21 2015-11-10 Adaptive Biotechnologies Corporation Quantification of adaptive immune cell genomes in a complex mixture of cells
US9217176B2 (en) 2008-11-07 2015-12-22 Sequenta, Llc Methods of monitoring conditions by sequence analysis
US9365901B2 (en) 2008-11-07 2016-06-14 Adaptive Biotechnologies Corp. Monitoring immunoglobulin heavy chain evolution in B-cell acute lymphoblastic leukemia
US9416420B2 (en) 2008-11-07 2016-08-16 Adaptive Biotechnologies Corp. Monitoring health and disease status using clonotype profiles
US9499865B2 (en) 2011-12-13 2016-11-22 Adaptive Biotechnologies Corp. Detection and measurement of tissue-infiltrating lymphocytes
US9512487B2 (en) 2008-11-07 2016-12-06 Adaptive Biotechnologies Corp. Monitoring health and disease status using clonotype profiles

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ES2443582T3 (en) 2003-06-27 2014-02-19 International Institute Of Cancer Immunology, Inc. Method for diagnosing cancer comprising the measurement of WT1-specific CTL precursor cells
EP3173480A3 (en) 2007-03-05 2017-08-16 International Institute of Cancer Immunology, Inc. Cancer antigen-specific t-cell receptor gene, peptide encoded by the gene, and use of them
US8691510B2 (en) 2008-11-07 2014-04-08 Sequenta, Inc. Sequence analysis of complex amplicons
US9528160B2 (en) 2008-11-07 2016-12-27 Adaptive Biotechnolgies Corp. Rare clonotypes and uses thereof
US9506119B2 (en) 2008-11-07 2016-11-29 Adaptive Biotechnologies Corp. Method of sequence determination using sequence tags
ES2568509T3 (en) 2009-01-15 2016-04-29 Adaptive Biotechnologies Corporation Adaptive immunity profiling and methods for the generation of monoclonal antibodies
KR20140146180A (en) 2009-06-25 2014-12-24 프레드 헛친슨 켄서 리서치 센터 Method of measuring adaptive immunity
US9043160B1 (en) 2009-11-09 2015-05-26 Sequenta, Inc. Method of determining clonotypes and clonotype profiles
US9803246B2 (en) 2011-06-28 2017-10-31 International Institute Of Cancer Immunology, Inc. Receptor gene for peptide cancer antigen-specific T cell
US10385475B2 (en) 2011-09-12 2019-08-20 Adaptive Biotechnologies Corp. Random array sequencing of low-complexity libraries
CA2858070C (en) 2011-12-09 2018-07-10 Adaptive Biotechnologies Corporation Diagnosis of lymphoid malignancies and minimal residual disease detection
EP2788507A4 (en) * 2011-12-09 2015-07-08 Sequenta Inc Method of measuring immune activation
CN103184216B (en) * 2011-12-27 2015-03-18 深圳华大基因科技有限公司 Primer composition for amplifying coding sequence of immunoglobulin heavy chain CDR3 and use thereof
GB201203720D0 (en) 2012-03-02 2012-04-18 Babraham Inst Method of identifying VDJ recombination products
WO2013131074A1 (en) * 2012-03-02 2013-09-06 Diogenix, Inc. Methods and reagents for evaluating autoimmune disease and determining antibody repertoire
ES2662128T3 (en) 2012-03-05 2018-04-05 Adaptive Biotechnologies Corporation Determination of paired immune receptor chains from the frequency of matching subunits
AU2013327423B2 (en) 2012-10-01 2017-06-22 Adaptive Biotechnologies Corporation Immunocompetence assessment by adaptive immune receptor diversity and clonality characterization
WO2015160439A2 (en) 2014-04-17 2015-10-22 Adaptive Biotechnologies Corporation Quantification of adaptive immune cell genomes in a complex mixture of cells
US9708657B2 (en) 2013-07-01 2017-07-18 Adaptive Biotechnologies Corp. Method for generating clonotype profiles using sequence tags
EP3114240B1 (en) 2014-03-05 2019-07-24 Adaptive Biotechnologies Corporation Methods using randomer-containing synthetic molecules
US10066265B2 (en) 2014-04-01 2018-09-04 Adaptive Biotechnologies Corp. Determining antigen-specific t-cells
CA2966201A1 (en) 2014-10-29 2016-05-06 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
WO2016086029A1 (en) 2014-11-25 2016-06-02 Adaptive Biotechnologies Corporation Characterization of adaptive immune response to vaccination or infection using immune repertoire sequencing
CA2976580A1 (en) 2015-02-24 2016-09-01 Adaptive Biotechnologies Corp. Methods for diagnosing infectious disease and determining hla status using immune repertoire sequencing
WO2016161273A1 (en) 2015-04-01 2016-10-06 Adaptive Biotechnologies Corp. Method of identifying human compatible t cell receptors specific for an antigenic target
US10428325B1 (en) 2016-09-21 2019-10-01 Adaptive Biotechnologies Corporation Identification of antigen-specific B cell receptors
US11319590B2 (en) * 2017-01-31 2022-05-03 Ludwig Institute For Cancer Research Ltd. Enhanced immune cell receptor sequencing methods
GB201718238D0 (en) * 2017-11-03 2017-12-20 Univ Oxford Innovation Ltd Method and system for determining the disease status of a subject
US11254980B1 (en) 2017-11-29 2022-02-22 Adaptive Biotechnologies Corporation Methods of profiling targeted polynucleotides while mitigating sequencing depth requirements
CN108229100B (en) * 2018-05-22 2018-08-24 至本医疗科技（上海）有限公司 DNA resets region and corresponding RNA product detections method, equipment and storage medium
AU2019284211B2 (en) * 2018-06-11 2025-04-03 Monoquant Pty Ltd Amplification method and primers for use therein
CN111808195A (en) * 2020-06-30 2020-10-23 中国科学院心理研究所 A method for obtaining B cell antibody gene against N-methyl-D-aspartate receptor encephalitis and its immune repertoire
WO2025058951A1 (en) * 2023-09-14 2025-03-20 Rutgers, The State University Of New Jersey Methods for profiling immune repertoires

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Patent Citations (8)

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US20040229252A1 (en) * 2003-02-19 2004-11-18 Affmetrix, Inc. Genotyping the T cell receptor
WO2005098021A1 (en) * 2004-04-06 2005-10-20 Flinders Technologies Pty. Ltd. Detecting targets using nucleic acids having both a variable region and a conserved region

Non-Patent Citations (1)

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Cited By (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9217176B2 (en) 2008-11-07 2015-12-22 Sequenta, Llc Methods of monitoring conditions by sequence analysis
US9228232B2 (en) 2008-11-07 2016-01-05 Sequenta, LLC. Methods of monitoring conditions by sequence analysis
US9347099B2 (en) 2008-11-07 2016-05-24 Adaptive Biotechnologies Corp. Single cell analysis by polymerase cycling assembly
US9365901B2 (en) 2008-11-07 2016-06-14 Adaptive Biotechnologies Corp. Monitoring immunoglobulin heavy chain evolution in B-cell acute lymphoblastic leukemia
US9416420B2 (en) 2008-11-07 2016-08-16 Adaptive Biotechnologies Corp. Monitoring health and disease status using clonotype profiles
US9512487B2 (en) 2008-11-07 2016-12-06 Adaptive Biotechnologies Corp. Monitoring health and disease status using clonotype profiles
US9523129B2 (en) 2008-11-07 2016-12-20 Adaptive Biotechnologies Corp. Sequence analysis of complex amplicons
US9181590B2 (en) 2011-10-21 2015-11-10 Adaptive Biotechnologies Corporation Quantification of adaptive immune cell genomes in a complex mixture of cells
US9279159B2 (en) 2011-10-21 2016-03-08 Adaptive Biotechnologies Corporation Quantification of adaptive immune cell genomes in a complex mixture of cells
US9499865B2 (en) 2011-12-13 2016-11-22 Adaptive Biotechnologies Corp. Detection and measurement of tissue-infiltrating lymphocytes
US9150905B2 (en) 2012-05-08 2015-10-06 Adaptive Biotechnologies Corporation Compositions and method for measuring and calibrating amplification bias in multiplexed PCR reactions
US9371558B2 (en) 2012-05-08 2016-06-21 Adaptive Biotechnologies Corp. Compositions and method for measuring and calibrating amplification bias in multiplexed PCR reactions

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