WO2009076055A3 - Multiplexed genomic gain and loss assays - Google Patents

Multiplexed genomic gain and loss assays Download PDF

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Publication number
WO2009076055A3
WO2009076055A3 PCT/US2008/084540 US2008084540W WO2009076055A3 WO 2009076055 A3 WO2009076055 A3 WO 2009076055A3 US 2008084540 W US2008084540 W US 2008084540W WO 2009076055 A3 WO2009076055 A3 WO 2009076055A3
Authority
WO
WIPO (PCT)
Prior art keywords
template dna
nucleic acid
dna
acid sequence
individual
Prior art date
Application number
PCT/US2008/084540
Other languages
French (fr)
Other versions
WO2009076055A2 (en
Inventor
Karl Edwin Adler
Mack J Schermer
Original Assignee
Perkinelmer Las Inc
Karl Edwin Adler
Mack J Schermer
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 Perkinelmer Las Inc, Karl Edwin Adler, Mack J Schermer filed Critical Perkinelmer Las Inc
Priority to EP08859169.8A priority Critical patent/EP2227564B1/en
Priority to CN200880125035.0A priority patent/CN101918596B/en
Priority to CA2707957A priority patent/CA2707957C/en
Priority to MX2010006061A priority patent/MX2010006061A/en
Priority to ES08859169.8T priority patent/ES2511029T3/en
Priority to AU2008335527A priority patent/AU2008335527B2/en
Priority to BRPI0819053A priority patent/BRPI0819053B1/en
Publication of WO2009076055A2 publication Critical patent/WO2009076055A2/en
Publication of WO2009076055A3 publication Critical patent/WO2009076055A3/en
Priority to HK11102276.8A priority patent/HK1148316A1/en

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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
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • 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
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/60—Detection means characterised by use of a special device
    • C12Q2565/625—Detection means characterised by use of a special device being a nucleic acid test strip device, e.g. dipsticks, strips, tapes, CD plates
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Abstract

Encoded bead multiplex assays for chromosomal gains and losses are provided that provide the benefits of complex, large template DNA sources, such as BAC DNA, as the probe material without bead networking or other assay performance problems. Reagents for assaying DNA are described herein which include a plurality of encoded particles having attached amplicons amplified from a template DNA sequence. Each individual attached amplicon includes a nucleic acid sequence identical to a random portion of the template DNA sequence, wherein the amplicons together represent substantially the entire template DNA and wherein the nucleic acid sequence identical to a random portion of the template DNA sequence of each individual amplicon is shorter than the entire template DNA.
PCT/US2008/084540 2007-12-05 2008-11-24 Multiplexed genomic gain and loss assays WO2009076055A2 (en)

Priority Applications (8)

Application Number Priority Date Filing Date Title
EP08859169.8A EP2227564B1 (en) 2007-12-05 2008-11-24 Multiplexed genomic gain and loss assays
CN200880125035.0A CN101918596B (en) 2007-12-05 2008-11-24 Multiple gene group obtains and loss assays
CA2707957A CA2707957C (en) 2007-12-05 2008-11-24 Multiplexed genomic gain and loss assays
MX2010006061A MX2010006061A (en) 2007-12-05 2008-11-24 Multiplexed genomic gain and loss assays.
ES08859169.8T ES2511029T3 (en) 2007-12-05 2008-11-24 Multiplexed genomic gain and loss tests
AU2008335527A AU2008335527B2 (en) 2007-12-05 2008-11-24 Multiplexed genomic gain and loss assays
BRPI0819053A BRPI0819053B1 (en) 2007-12-05 2008-11-24 method for analyzing a DNA sample, method for preparing a set of coded DNA analysis matrices, DNA analysis reagent, DNA analysis multiplex reagent and DNA analysis kit
HK11102276.8A HK1148316A1 (en) 2007-12-05 2011-03-07 Multiplexed genomic gain and loss assays

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US99248907P 2007-12-05 2007-12-05
US60/992,489 2007-12-05
US12/055,919 US7932037B2 (en) 2007-12-05 2008-03-26 DNA assays using amplicon probes on encoded particles
US12/055,919 2008-03-26

Publications (2)

Publication Number Publication Date
WO2009076055A2 WO2009076055A2 (en) 2009-06-18
WO2009076055A3 true WO2009076055A3 (en) 2009-07-30

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2008/084540 WO2009076055A2 (en) 2007-12-05 2008-11-24 Multiplexed genomic gain and loss assays

Country Status (11)

Country Link
US (3) US7932037B2 (en)
EP (3) EP2227564B1 (en)
KR (1) KR101602305B1 (en)
CN (1) CN101918596B (en)
AU (1) AU2008335527B2 (en)
BR (1) BRPI0819053B1 (en)
CA (1) CA2707957C (en)
ES (3) ES2666167T3 (en)
HK (1) HK1148316A1 (en)
MX (1) MX2010006061A (en)
WO (1) WO2009076055A2 (en)

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Also Published As

Publication number Publication date
EP2719775A1 (en) 2014-04-16
ES2666167T3 (en) 2018-05-03
US20130157899A1 (en) 2013-06-20
BRPI0819053B1 (en) 2017-02-07
ES2587604T3 (en) 2016-10-25
EP2227564A4 (en) 2011-01-19
EP3050976A1 (en) 2016-08-03
AU2008335527A1 (en) 2009-06-18
HK1148316A1 (en) 2011-09-02
KR20100120641A (en) 2010-11-16
US9127307B2 (en) 2015-09-08
KR101602305B1 (en) 2016-03-10
ES2511029T3 (en) 2014-10-22
US20110172117A1 (en) 2011-07-14
CN101918596B (en) 2015-09-09
MX2010006061A (en) 2011-04-11
AU2008335527B2 (en) 2014-08-14
EP3050976B1 (en) 2018-01-17
CA2707957C (en) 2016-11-08
BRPI0819053A2 (en) 2015-05-05
EP2719775B1 (en) 2016-04-06
US8404463B2 (en) 2013-03-26
CN101918596A (en) 2010-12-15
CA2707957A1 (en) 2009-06-18
US20090148841A1 (en) 2009-06-11
EP2227564B1 (en) 2014-07-02
US7932037B2 (en) 2011-04-26
EP2227564A2 (en) 2010-09-15
WO2009076055A2 (en) 2009-06-18

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