Title:
IDENTIFICATION OF GENOMIC SIGNATURE FOR DIFFERENTIATING HIGHLY SIMILAR SEQUENCE VARIANTS OF AN ORGANISM
Document Type and Number:
WIPO Patent Application WO/2010/016071
Kind Code:
A3
Abstract:
The present invention provides a process of identification of genomic signature for differentiating highly similar sequence variants of an organism. The present invention also provides unique genomic signature of an organism that can be used as a tool or an identifier of a species of an organism for differentiating highly similar sequence variants of the organism. The present invention further provides the nucleotide probe and/or primers useful for identification the genomic signature of an organism.
Inventors:
SWATI SUBODH (IN)
TUTEJA AMIT (IN)
SUBODH SWATI (IN)
KRISHNAMOORTHY NARAYANASAMY (IN)
TUTEJA AMIT (IN)
SUBODH SWATI (IN)
KRISHNAMOORTHY NARAYANASAMY (IN)
Application Number:
PCT/IN2009/000442
Publication Date:
July 29, 2010
Filing Date:
August 05, 2009
Export Citation:
Assignee:
SWATI SUBODH (IN)
TUTEJA AMIT (IN)
SUBODH SWATI (IN)
KRISHNAMOORTHY NARAYANASAMY (IN)
TUTEJA AMIT (IN)
SUBODH SWATI (IN)
KRISHNAMOORTHY NARAYANASAMY (IN)
International Classes:
C12Q1/68; C12Q1/70
Domestic Patent References:
| WO1997040193A2 | 1997-10-30 |
Foreign References:
| US20060286566A1 | 2006-12-21 | |||
| EP1193313A1 | 2002-04-03 |
Other References:
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URWIN R ET AL: "Multi-locuas sequence typing: a tool for global epidemiology", TRENDS IN MICROBIOLOGY, ELSEVIER SCIENCE LTD., KIDLINGTON, GB, vol. 11, no. 10, 1 January 2003 (2003-01-01), pages 479 - 487, XP003017264, ISSN: 0966-842X
BUKH J ET AL: "SEQUENCE ANALYSIS OF THE CORE GENE OF 14 HEPATITIS C VIRUS GENOTYPES", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE, WASHINGTON, DC, US, vol. 91, no. 17, 16 August 1994 (1994-08-16), pages 8239 - 8243, XP002047846, ISSN: 0027-8424
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HUSSAIN MUNIRA ET AL: "Rapid and sensitive assays for determination of hepatitis B virus (HBV) genotypes and detection of HBV precore and core promoter variants.", JOURNAL OF CLINICAL MICROBIOLOGY AUG 2003, vol. 41, no. 8, August 2003 (2003-08-01), pages 3699 - 3705, XP002565052, ISSN: 0095-1137
YEH S-H ET AL: "Quantification and genotyping of hepatitis B virus in a single reaction by real-time PCR and melting curve analysis", JOURNAL OF HEPATOLOGY, MUNKSGAARD INTERNATIONAL PUBLISHERS, COPENHAGEN, DK, vol. 41, no. 4, 1 October 2004 (2004-10-01), pages 659 - 666, XP004586587, ISSN: 0168-8278
LIU WEN-CHUN ET AL: "Simultaneous quantification and genotyping of hepatitis B virus for genotypes A to G by real-time PCR and two-step melting curve analysis.", JOURNAL OF CLINICAL MICROBIOLOGY DEC 2006, vol. 44, no. 12, December 2006 (2006-12-01), pages 4491 - 4497, XP002565053, ISSN: 0095-1137
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PAI REKHA ET AL: "Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus pneumoniae isolates", JOURNAL OF CLINICAL MICROBIOLOGY JAN 2006,, vol. 44, no. 1, 1 January 2006 (2006-01-01), pages 124 - 131, XP002560719
OKAMOTO H ET AL: "TYPING HEPATITIS B VIRUS BY HOMOLOGY IN NUCLEOTIDE SEQUENCE: COMPARISON OF SURFACE ANTIGEN SUBTYPES", JOURNAL OF GENERAL VIROLOGY, SOCIETY FOR GENERAL MICROBIOLOGY, SPENCERS WOOD, GB, vol. 69, no. 10, 1 October 1988 (1988-10-01), pages 2575 - 2583, XP000672123, ISSN: 0022-1317
BAAR DE M P ET AL: "ONE-TUBE REAL-TIME ISOTHERMAL AMPLIFICATION ASSAY TO IDENTIFY AND DISTINGUISH HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 SUBTYPES A,B, AND C AND CIRCULATING RECOMBINANT FORMS AE AND AG", JOURNAL OF CLINICAL MICROBIOLOGY, AMERICAN SOCIETY FOR MICROBIOLOGY, WASHINGTON, DC, US LNKD- DOI:10.1128/JCM.39.5.1895-1902.2001, vol. 39, no. 5, 1 May 2001 (2001-05-01), pages 1895 - 1902, XP001011572, ISSN: 0095-1137
WEI M ET AL: "Simple subtyping assay for human immunodeficiency virus type 1 subtypes B, C, CRF01-AE, CRF07-BC, and CRF08-BC", JOURNAL OF CLINICAL MICROBIOLOGY, AMERICAN SOCIETY FOR MICROBIOLOGY, WASHINGTON, DC, US LNKD- DOI:10.1128/JCM.42.9.4261-4267.2004, vol. 42, no. 9, 1 September 2004 (2004-09-01), pages 4261 - 4267, XP002998793, ISSN: 0095-1137
HOELSCHER MICHAEL ET AL: "Detection of HIV-1 subtypes, recombinants, and dual infections in east Africa by a multi-region hybridization assay.", AIDS (LONDON, ENGLAND) 18 OCT 2002 LNKD- PUBMED:12370505, vol. 16, no. 15, 18 October 2002 (2002-10-18), pages 2055 - 2064, XP002581538, ISSN: 0269-9370
KIJAK ET AL: "Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2", VIROLOGY, ACADEMIC PRESS,ORLANDO, US LNKD- DOI:10.1016/J.VIROL.2006.07.055, vol. 358, no. 1, 9 January 2007 (2007-01-09), pages 178 - 191, XP005762428, ISSN: 0042-6822
URWIN R ET AL: "Multi-locuas sequence typing: a tool for global epidemiology", TRENDS IN MICROBIOLOGY, ELSEVIER SCIENCE LTD., KIDLINGTON, GB, vol. 11, no. 10, 1 January 2003 (2003-01-01), pages 479 - 487, XP003017264, ISSN: 0966-842X
BUKH J ET AL: "SEQUENCE ANALYSIS OF THE CORE GENE OF 14 HEPATITIS C VIRUS GENOTYPES", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE, WASHINGTON, DC, US, vol. 91, no. 17, 16 August 1994 (1994-08-16), pages 8239 - 8243, XP002047846, ISSN: 0027-8424
KIRSCHBERG OLIVER ET AL: "A multiplex-PCR to identify hepatitis B virus--enotypes A-F.", JOURNAL OF CLINICAL VIROLOGY : THE OFFICIAL PUBLICATION OF THE PAN AMERICAN SOCIETY FOR CLINICAL VIROLOGY JAN 2004, vol. 29, no. 1, January 2004 (2004-01-01), pages 39 - 43, XP002565051, ISSN: 1386-6532
HUSSAIN MUNIRA ET AL: "Rapid and sensitive assays for determination of hepatitis B virus (HBV) genotypes and detection of HBV precore and core promoter variants.", JOURNAL OF CLINICAL MICROBIOLOGY AUG 2003, vol. 41, no. 8, August 2003 (2003-08-01), pages 3699 - 3705, XP002565052, ISSN: 0095-1137
YEH S-H ET AL: "Quantification and genotyping of hepatitis B virus in a single reaction by real-time PCR and melting curve analysis", JOURNAL OF HEPATOLOGY, MUNKSGAARD INTERNATIONAL PUBLISHERS, COPENHAGEN, DK, vol. 41, no. 4, 1 October 2004 (2004-10-01), pages 659 - 666, XP004586587, ISSN: 0168-8278
LIU WEN-CHUN ET AL: "Simultaneous quantification and genotyping of hepatitis B virus for genotypes A to G by real-time PCR and two-step melting curve analysis.", JOURNAL OF CLINICAL MICROBIOLOGY DEC 2006, vol. 44, no. 12, December 2006 (2006-12-01), pages 4491 - 4497, XP002565053, ISSN: 0095-1137
MOROZOV V ET AL: "Homologous recombination between different genotypes of hepatitis B virus", GENE, ELSEVIER, AMSTERDAM, NL, vol. 260, no. 1-2, 30 December 2000 (2000-12-30), pages 55 - 65, XP004227524, ISSN: 0378-1119
PAI REKHA ET AL: "Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus pneumoniae isolates", JOURNAL OF CLINICAL MICROBIOLOGY JAN 2006,, vol. 44, no. 1, 1 January 2006 (2006-01-01), pages 124 - 131, XP002560719
OKAMOTO H ET AL: "TYPING HEPATITIS B VIRUS BY HOMOLOGY IN NUCLEOTIDE SEQUENCE: COMPARISON OF SURFACE ANTIGEN SUBTYPES", JOURNAL OF GENERAL VIROLOGY, SOCIETY FOR GENERAL MICROBIOLOGY, SPENCERS WOOD, GB, vol. 69, no. 10, 1 October 1988 (1988-10-01), pages 2575 - 2583, XP000672123, ISSN: 0022-1317
BAAR DE M P ET AL: "ONE-TUBE REAL-TIME ISOTHERMAL AMPLIFICATION ASSAY TO IDENTIFY AND DISTINGUISH HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 SUBTYPES A,B, AND C AND CIRCULATING RECOMBINANT FORMS AE AND AG", JOURNAL OF CLINICAL MICROBIOLOGY, AMERICAN SOCIETY FOR MICROBIOLOGY, WASHINGTON, DC, US LNKD- DOI:10.1128/JCM.39.5.1895-1902.2001, vol. 39, no. 5, 1 May 2001 (2001-05-01), pages 1895 - 1902, XP001011572, ISSN: 0095-1137
WEI M ET AL: "Simple subtyping assay for human immunodeficiency virus type 1 subtypes B, C, CRF01-AE, CRF07-BC, and CRF08-BC", JOURNAL OF CLINICAL MICROBIOLOGY, AMERICAN SOCIETY FOR MICROBIOLOGY, WASHINGTON, DC, US LNKD- DOI:10.1128/JCM.42.9.4261-4267.2004, vol. 42, no. 9, 1 September 2004 (2004-09-01), pages 4261 - 4267, XP002998793, ISSN: 0095-1137
HOELSCHER MICHAEL ET AL: "Detection of HIV-1 subtypes, recombinants, and dual infections in east Africa by a multi-region hybridization assay.", AIDS (LONDON, ENGLAND) 18 OCT 2002 LNKD- PUBMED:12370505, vol. 16, no. 15, 18 October 2002 (2002-10-18), pages 2055 - 2064, XP002581538, ISSN: 0269-9370
KIJAK ET AL: "Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2", VIROLOGY, ACADEMIC PRESS,ORLANDO, US LNKD- DOI:10.1016/J.VIROL.2006.07.055, vol. 358, no. 1, 9 January 2007 (2007-01-09), pages 178 - 191, XP005762428, ISSN: 0042-6822
Attorney, Agent or Firm:
VARADHACHARI, Lakshmikumaran et al. (Safdarjung Enclave, New Delhi 9, IN)
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