[go: up one dir, main page]

WO2001018245A3 - Detection of alterations in a gene by long range pcr using human mobile elements - Google Patents

Detection of alterations in a gene by long range pcr using human mobile elements Download PDF

Info

Publication number
WO2001018245A3
WO2001018245A3 PCT/IB2000/001283 IB0001283W WO0118245A3 WO 2001018245 A3 WO2001018245 A3 WO 2001018245A3 IB 0001283 W IB0001283 W IB 0001283W WO 0118245 A3 WO0118245 A3 WO 0118245A3
Authority
WO
WIPO (PCT)
Prior art keywords
gene
alteration
interest
test sample
genomic dna
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.)
Ceased
Application number
PCT/IB2000/001283
Other languages
French (fr)
Other versions
WO2001018245A2 (en
Inventor
Struan Grant
Thorarinn Blondal
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.)
Decode Genetics ehf
Original Assignee
Decode Genetics ehf
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 US09/470,673 external-priority patent/US6225093B1/en
Priority to EP00954856A priority Critical patent/EP1214449A2/en
Priority to BR0014017-1A priority patent/BR0014017A/en
Priority to JP2001521779A priority patent/JP2003508082A/en
Priority to CA002383857A priority patent/CA2383857A1/en
Priority to NZ517641A priority patent/NZ517641A/en
Application filed by Decode Genetics ehf filed Critical Decode Genetics ehf
Priority to AU67207/00A priority patent/AU6720700A/en
Priority to MXPA02002507A priority patent/MXPA02002507A/en
Publication of WO2001018245A2 publication Critical patent/WO2001018245A2/en
Anticipated expiration legal-status Critical
Publication of WO2001018245A3 publication Critical patent/WO2001018245A3/en
Ceased 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
    • C12Q1/686—Polymerase chain reaction [PCR]
    • 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
    • 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

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)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (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

Methods are described for detecting an alteration in a gene of interest, such as a deletion in the C4A gene (e.g., for detecting C4AQ0), by performing long range polymerase chain reaction amplification on a test sample comprising genomic DNA. The methods amplify target DNA comprising all or a portion of a human mobile element (e.g., a retroviral insert in intron 9 of the C4A gene), using primers designed such that PCR products are formed only if the test sample comprises genomic DNA comprising the alteration in the gene of interest; alternatively, the methods amplify target DNA using primers designed such that PCR products are formed only if the test sample comprises genomic DNA that does not comprise the alteration in the gene of interest. Alternatively, primers are designed such that PCR products have detectably different sizes, depending on whether or the test sample comprises genomic DNA that comprises the alteration in the gene of interest. The methods can be used to identify whether an individual is at risk for a disease or condition associated with the alteration in the gene of interest, as the presence of the alteration correlates with risk for the disease.
PCT/IB2000/001283 1999-09-07 2000-09-06 Detection of alterations in a gene by long range pcr using human mobile elements Ceased WO2001018245A2 (en)

Priority Applications (7)

Application Number Priority Date Filing Date Title
MXPA02002507A MXPA02002507A (en) 1999-09-07 2000-09-06 Detection of alterations in a gene by long range pcr using human mobile elements.
BR0014017-1A BR0014017A (en) 1999-09-07 2000-09-06 Method for detecting changes in a gene using wide-ranging pcr using mobile human elements
JP2001521779A JP2003508082A (en) 1999-09-07 2000-09-06 Detection of alterations in genes by long-range PCR using human mobility factors
CA002383857A CA2383857A1 (en) 1999-09-07 2000-09-06 Detection of alterations in a gene by long range pcr using human mobile elements
NZ517641A NZ517641A (en) 1999-09-07 2000-09-06 Detection of alterations in a gene by long range PCR using human mobile elements
EP00954856A EP1214449A2 (en) 1999-09-07 2000-09-06 Detection of alterations in a gene by long range pcr using human mobile elements
AU67207/00A AU6720700A (en) 1999-09-07 2000-09-06 Detection of alterations in a gene by long range pcr using human mobile elements

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US39124499A 1999-09-07 1999-09-07
US09/391,244 1999-09-07
US44353999A 1999-11-19 1999-11-19
US09/443,539 1999-11-19
US47159899A 1999-12-23 1999-12-23
US09/470,673 1999-12-23
US09/471,598 1999-12-23
US09/470,673 US6225093B1 (en) 1999-09-07 1999-12-23 Detection of C4A deletion by long range PCR

Publications (2)

Publication Number Publication Date
WO2001018245A2 WO2001018245A2 (en) 2001-03-15
WO2001018245A3 true WO2001018245A3 (en) 2002-04-18

Family

ID=27503328

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IB2000/001283 Ceased WO2001018245A2 (en) 1999-09-07 2000-09-06 Detection of alterations in a gene by long range pcr using human mobile elements

Country Status (9)

Country Link
EP (1) EP1214449A2 (en)
JP (1) JP2003508082A (en)
CN (1) CN1382221A (en)
AU (1) AU6720700A (en)
BR (1) BR0014017A (en)
CA (1) CA2383857A1 (en)
MX (1) MXPA02002507A (en)
NZ (1) NZ517641A (en)
WO (1) WO2001018245A2 (en)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002062197A2 (en) * 2000-12-19 2002-08-15 Hospital For Special Surgery Markers for disease susceptibility and targets for therapy
TWI340168B (en) 2003-05-07 2011-04-11 Tosoh Corp Method of detecting micrometastasis
EP2397561B1 (en) 2010-06-18 2017-08-02 Progenika Biopharma, S.A. Methods for determining the presence or absence of genetic segments
ES2833299T3 (en) 2014-02-04 2021-06-14 Jumpcode Genomics Inc Genome fractionation
EP3943615A1 (en) * 2014-02-27 2022-01-26 Jumpcode Genomics, Inc. Methods for analysis of somatic mobile elements, and uses thereof
US10968536B2 (en) 2015-02-25 2021-04-06 Jumpcode Genomics, Inc. Methods and compositions for sequencing
US11339427B2 (en) 2016-02-12 2022-05-24 Jumpcode Genomics, Inc. Method for target specific RNA transcription of DNA sequences
CN113820499B (en) * 2021-10-26 2024-06-25 深圳临研医学有限公司 Protein markers for diagnosing systemic lupus erythematosus

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5096557A (en) * 1990-07-11 1992-03-17 Genetype A.G. Internal standard for electrophoretic separations

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5096557A (en) * 1990-07-11 1992-03-17 Genetype A.G. Internal standard for electrophoretic separations

Non-Patent Citations (10)

* Cited by examiner, † Cited by third party
Title
BARBA G M R ET AL: "A new PCR-based typing of the Rodgers and Chido antigenic determinants of the fourth component of human complement.", EUROPEAN JOURNAL OF IMMUNOGENETICS, vol. 21, no. 5, 1994, pages 325 - 339, XP001052889, ISSN: 0960-7420 *
BRUNSBERG ULRICA ET AL: "Structure and organization of pig MHC class II DRB genes: Evidence for genetic exchange between loci.", IMMUNOGENETICS, vol. 44, no. 1, 1996, pages 1 - 8, XP002188283, ISSN: 0093-7711 *
CHENG S ET AL: "EFFECTIVE AMPLIFICATION OF LONG TARGETS FROM CLONED INSERTS AND HUMAN GENOMIC DNA", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE. WASHINGTON, US, vol. 91, no. 12, June 1994 (1994-06-01), pages 5695 - 5699, XP000982285, ISSN: 0027-8424 *
CHU XIAOLAN ET AL: "Length polymorphism of the human complement component C4 gene is due to an ancient retroviral integration.", EXPERIMENTAL AND CLINICAL IMMUNOGENETICS, vol. 12, no. 2, 1995, pages 74 - 81, XP001052890, ISSN: 0254-9670 *
DANGEL ANDREW W ET AL: "Complement component C4 gene intron 9 as a phylogenetic marker for primates: long terminal repeats of the endogenous retrovirus ERV-K(C4) are a molecular clock of evolution.", IMMUNOGENETICS, vol. 42, no. 1, 1995, pages 41 - 52, XP001053153, ISSN: 0093-7711 *
DANGEL ANDREW W ET AL: "The dichotomous size variation of human complement C4 genes is mediated by a novel family of endogenous retroviruses, which also establishes species-specific genomic patterns among Old World primates.", IMMUNOGENETICS, vol. 40, no. 6, 1994, pages 425 - 436, XP001053138, ISSN: 0093-7711 *
GOODMAN S ET AL: "RECOMBINANT ADENO-ASSOCIATED VIRUS-MEDIATED GENE TRANSFER INTO HEMATOPOIETIC PROGENITOR CELLS", BLOOD, W.B. SAUNDERS, PHILADELPHIA, VA, US, vol. 84, no. 5, 1 September 1994 (1994-09-01), pages 1492 - 1500, XP000609220, ISSN: 0006-4971 *
See also references of EP1214449A2 *
TANG J Q ET AL: "ALU-PCR COMBINED WITH NON-ALU PRIMERS REVEALS MULTIPLE POLYMORPHIC LOCI", MAMMALIAN GENOME, NEW YORK, NY, US, vol. 6, no. 5, 1995, pages 345 - 349, XP000607150, ISSN: 0938-8990 *
ULGIATI D ET AL: "COMPARATIVEANALYSIS OF THE DISEASE-ASSOCIATED COMPLEMENT C4 GENE FROM THE HLA-A1, B8, DR3 HAPLOTYPE", EXPERIMENTAL AND CLINICAL IMMUNOGENETICS, S.KARGER, BASEL, CH, vol. 13, no. 1, 1996, pages 43 - 54, XP001001407, ISSN: 0254-9670 *

Also Published As

Publication number Publication date
JP2003508082A (en) 2003-03-04
BR0014017A (en) 2002-12-31
MXPA02002507A (en) 2004-09-10
CN1382221A (en) 2002-11-27
CA2383857A1 (en) 2001-03-15
WO2001018245A2 (en) 2001-03-15
NZ517641A (en) 2004-02-27
EP1214449A2 (en) 2002-06-19
AU6720700A (en) 2001-04-10

Similar Documents

Publication Publication Date Title
WO2001007640A3 (en) Method for detecting single nucleotide polymorphisms
WO2004106547A3 (en) Fast method for detecting micro-organisms in food samples
WO2005047543A3 (en) Ligation assay
WO2004053105A3 (en) Direct SNP detection with unamplified DNA
WO2009032781A3 (en) Methods and compositions for universal size-specific polymerase chain reaction
WO1999014377A3 (en) Detection and identification of human papillomavirus by pcr and type-specific reverse hybridization
CA2075847A1 (en) Mycobacterium primers and probes
EP0776981A3 (en) Oligonucleotide primers for amplifying HCV nucleic acid
CA2482192A1 (en) Methods for detecting abnormally methylated nucleic acid in heterogeneous biological samples
WO2002086448A3 (en) Detection of microsatellite instability and its use in diagnosis of tumors
WO2003054209A3 (en) A method of reducing non-specific amplification in pcr
WO2002044416A3 (en) Sulfonated diarylrhodamine dyes as fluorescent labels
WO2006077102A3 (en) Method for the detection of hpv and probes, primers and kits
WO2005001142A3 (en) Methods and nucleic acids for the analysis of colorectal cell proliferative disorders
WO2001018245A3 (en) Detection of alterations in a gene by long range pcr using human mobile elements
WO2002064842A3 (en) Quantitative epstein barr virus pcr rapid assay
WO2003074739A3 (en) Automated allele determination using fluorometric genotyping
EP1312685A3 (en) Oligonucleotide array for detecting the methylation state
WO2001029264A3 (en) Nucleic acid primers and probes for detecting tumor cells
WO2004050911A3 (en) Method for lowering both sequence variations and increase of base lines effects in diagnostic hybridisation assay, assay for performing such a method and probe for use in the assay
WO2003054149A3 (en) Targeted genetic risk-stratification using microarrays
EP1266970A3 (en) Detecting nucleic acid deletion sequences
WO2002081644A3 (en) Haplotyping method for multiple distal nucleotide polymorphisms
WO2004013305A3 (en) Improved compositions for in vitro amplification of nucleic acids
WO2003054214A3 (en) Tsunami chain reaction - geometric dna amplification

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CR CU CZ DE DK DM DZ EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
WWE Wipo information: entry into national phase

Ref document number: 2383857

Country of ref document: CA

Ref document number: 67207/00

Country of ref document: AU

ENP Entry into the national phase

Ref document number: 2001 521779

Country of ref document: JP

Kind code of ref document: A

WWE Wipo information: entry into national phase

Ref document number: PA/a/2002/002507

Country of ref document: MX

Ref document number: 517641

Country of ref document: NZ

Ref document number: 00812602X

Country of ref document: CN

WWE Wipo information: entry into national phase

Ref document number: 2000954856

Country of ref document: EP

AK Designated states

Kind code of ref document: A3

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CR CU CZ DE DK DM DZ EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A3

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

WWP Wipo information: published in national office

Ref document number: 2000954856

Country of ref document: EP

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWP Wipo information: published in national office

Ref document number: 517641

Country of ref document: NZ

WWG Wipo information: grant in national office

Ref document number: 517641

Country of ref document: NZ

WWW Wipo information: withdrawn in national office

Ref document number: 2000954856

Country of ref document: EP