WO2011106738A3 - Use of tcr clonotypes as biomarkers for disease - Google Patents

Use of tcr clonotypes as biomarkers for disease Download PDF

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Publication number
WO2011106738A3
WO2011106738A3 PCT/US2011/026373 US2011026373W WO2011106738A3 WO 2011106738 A3 WO2011106738 A3 WO 2011106738A3 US 2011026373 W US2011026373 W US 2011026373W WO 2011106738 A3 WO2011106738 A3 WO 2011106738A3
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WO
WIPO (PCT)
Prior art keywords
disease
biomarkers
tcr clonotypes
exposure
cells
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PCT/US2011/026373
Other languages
French (fr)
Other versions
WO2011106738A2 (en
Inventor
Edus H. Warren
Christopher Scott Carlson
Harlan S. Robins
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Fred Hutchinson Cancer Research Center
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Publication of WO2011106738A2 publication Critical patent/WO2011106738A2/en
Publication of WO2011106738A3 publication Critical patent/WO2011106738A3/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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

Abstract

A method of detecting disease or risk of disease in subject using a biomarker or panel of biomarkers identified from exposure-specific clonotype sequences is described. The method for identifying the exposure-specific clonotype sequences from a subset of B cells or T cells from an immune cell sample is also described.
PCT/US2011/026373 2010-02-25 2011-02-25 Use of tcr clonotypes as biomarkers for disease WO2011106738A2 (en)

Applications Claiming Priority (2)

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US30826110P 2010-02-25 2010-02-25
US61/308,261 2010-02-25

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WO2011106738A2 WO2011106738A2 (en) 2011-09-01
WO2011106738A3 true WO2011106738A3 (en) 2011-12-01

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EP3498866A1 (en) 2014-11-25 2019-06-19 Adaptive Biotechnologies Corp. Characterization of adaptive immune response to vaccination or infection using immune repertoire sequencing
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WO2016161054A1 (en) * 2015-04-01 2016-10-06 Pharmacyclics Llc Massive parallel primer dimer-mediated multiplexed single cell-based amplification for concurrent evaluation of multiple target sequences in complex cell mixtures
WO2016161273A1 (en) 2015-04-01 2016-10-06 Adaptive Biotechnologies Corp. Method of identifying human compatible t cell receptors specific for an antigenic target
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US9217176B2 (en) 2008-11-07 2015-12-22 Sequenta, Llc Methods of monitoring conditions by sequence analysis
US9512487B2 (en) 2008-11-07 2016-12-06 Adaptive Biotechnologies Corp. Monitoring health and disease status using clonotype profiles
US9228232B2 (en) 2008-11-07 2016-01-05 Sequenta, LLC. Methods of monitoring conditions by sequence analysis
US9416420B2 (en) 2008-11-07 2016-08-16 Adaptive Biotechnologies Corp. Monitoring health and disease status using clonotype profiles
US8795970B2 (en) 2008-11-07 2014-08-05 Sequenta, Inc. Methods of monitoring conditions by sequence analysis
US8507205B2 (en) 2008-11-07 2013-08-13 Sequenta, Inc. Single cell analysis by polymerase cycling assembly
US8628927B2 (en) 2008-11-07 2014-01-14 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
US9523129B2 (en) 2008-11-07 2016-12-20 Adaptive Biotechnologies Corp. Sequence analysis of complex amplicons
US8691510B2 (en) 2008-11-07 2014-04-08 Sequenta, Inc. Sequence analysis of complex amplicons
US8748103B2 (en) 2008-11-07 2014-06-10 Sequenta, Inc. Monitoring health and disease status using clonotype profiles
US9347099B2 (en) 2008-11-07 2016-05-24 Adaptive Biotechnologies Corp. Single cell analysis by polymerase cycling assembly
US9043160B1 (en) 2009-11-09 2015-05-26 Sequenta, Inc. Method of determining clonotypes and clonotype profiles
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
US9371558B2 (en) 2012-05-08 2016-06-21 Adaptive Biotechnologies Corp. Compositions and method for measuring and calibrating amplification bias in multiplexed PCR reactions
US9150905B2 (en) 2012-05-08 2015-10-06 Adaptive Biotechnologies Corporation Compositions and method for measuring and calibrating amplification bias in multiplexed PCR reactions
CN104560978A (en) * 2015-01-20 2015-04-29 中国人民解放军第三军医大学 Multiplex-polymerase chain reaction (PCR) primer and method for constructing human B cell receptor (BCR) heavy-chain library based on high-throughput sequencing

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