Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Preparing compound containing saccharide radical
Reexamination Certificate
2007-08-28
2007-08-28
Horlick, Kenneth R. (Department: 1637)
Chemistry: molecular biology and microbiology
Micro-organism, tissue cell culture or enzyme using process...
Preparing compound containing saccharide radical
C435S006120, C435S091100, C435S091410, C435S091500, C435S091520, C435S195000
Reexamination Certificate
active
11256694
ABSTRACT:
The present invention relates to a method of detecting a base at a pre-determined position in a nucleic acid molecule by performing enzymatic detection reactions using base-specific detection oligomers, where each oligomer is specific for a particular base at the predetermined position, and then comparing the enzymatic detection reactions to determine which base is present at the position, with an enzyme-disabling agent being present during the enzymatic detection reaction. In preferred embodiments the enzymatic detection reaction is an oligomer elongation extension reaction, catalysed by, among others, polymerase or ligase. Also disclosed are methods of performing the assay in a liquid phase and on microarrays.
REFERENCES:
patent: 4654267 (1987-03-01), Ugelstad et al.
patent: 5302509 (1994-04-01), Franklin
patent: 5338671 (1994-08-01), Scalice et al.
patent: 5565340 (1996-10-01), Chenchik et al.
patent: 5587287 (1996-12-01), Scalice et al.
patent: 6020130 (2000-02-01), Gold et al.
patent: 6087095 (2000-07-01), Rosenthal et al.
patent: 6183998 (2001-02-01), Ivanov et al.
patent: 6190865 (2001-02-01), Jendrisak et al.
patent: 0 393 743 (1990-10-01), None
patent: 0 417 842 (1991-03-01), None
patent: 0 592 035 (1996-01-01), None
patent: 0 745 688 (1996-12-01), None
patent: WO98/13523 (1998-04-01), None
patent: WO98/28440 (1998-07-01), None
patent: WO 00/43540 (2000-07-01), None
patent: WO 00/53812 (2000-09-01), None
patent: WO 02/061428 (2002-08-01), None
patent: WO 02/006684 (2002-09-01), None
patent: WO 02/068684 (2002-09-01), None
Zhou G. et al., “Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER),” Oct. 1, 2001, Nucleic Acids Research, 29(19):E93.
Gerry NP et al., “Universal DNA microarray method for multiplex detection of low abundance point mutations,” Sep. 17, 1999, J Mol Biol., 292(2):251-62.
Landegren U. et al., “Detecting Genes with Ligases,” Feb. 1996, Methods, 9(1):84-90.
Bernard PS. et al., “Homogenous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes,” Oct. 1998, Am J Pathol., 153(4):1055-61.
Abu Al-Soud W. et al., “Capacity of nine thermostable DNA polymerases To mediate DNA amplification in the presence of PCR-inhibiting samples,” Appl Environ Microbiol, Oct. 1998;64(10):3748-53.
Lin Y. et al., “Inhibition of multiple thermostable DNA polymerases by a heterodimeric aptamer,” J Mol Biol., Aug. 8, 1997;271(1):100-11.
Ailenberg M. et al., “Controlled hot start and improved specificity in carrying out PCR utilizing touch-up and loop incorporated primers (TULIPS),” Biotechniques, Nov. 2000;29(5):1018-20, 1022-4.
Afshin Ahmadian et al., “A Brief History Of Genetic Variation Analysis”, BioTechniques, vol. 32, No. 5, pp. 1122-1137 (2002).
D. G.Wang et al., “Large-Scale Identification, Mapping, And Genotyping Of Single-Nucleotide Polymorphisms In The Human Genome”, Science, vol. 280, (5366) pp. 1077-1082 (1998).
J.N. Hirschhorn et al., “SBE-TAGS: An Array-Based-Method For Efficient Single-Nucleotide Polymorphism Genotyping”, Proc. Natl. Acad. Sci., vol. 97, No. 22. pp. 12164-12169 (2000).
T. Pastinen et al., “A System For Specific, High-Throughput Genotyping By Allele-Specific Primer Extension On Microarrays”, Genome Research, vol. 10, No. 7, pp. 1031-1042 (2000).
T. Pastinen et al., “Minisequencing: A Specific Tool For DNA Analysis And Diagnostic On Oligonucleotide Arrays”, Genome Research, vol. 7, No. 6, pp. 606-614 (1997).
S. J. Laken et al., “Genotyping By Mass Spectrometric Analysis Of Short DNA Fragments”, Nature Biotechnology, vol. 16, No. 13, pp. 1352-1356 (1998).
Afshin Ahmadian et al., “Single-Nucleotide Polymorphism Analysis By Pyrosequencing”, Analytical Biochemistry, vol. 280, No. 1, pp.103-110 (2000).
G. Scott Higgins et al., “Competitive Olignucleotide Single-Base Extension Combined With Mass Spectrometric Detection For Mutation Screening”, BioTechniques, vol. 23, No. 4, pp. 710-714 (1997).
Newton et al., “Amplification Refractory Mutation System For Prenatal Diagnosis And Carrier Assessment In Cystic- Fibrosis”, .The Lancet. vol. 23, No. 30, pp. 1481-1483 (1980).
B. Goergen et al., “Mutation Specific PCR And Direct Solid Phase Sequencing Assay For The Detection Of Hepatitis B Virus Pre-C/C Mutants in Anti-HBe-Positive, Chronic Hepatitis B”, Journal of Medical Virology, vol. 43, , No. 1, pp. 97-102 (1994).
Newton et al., “Analysis Of Any Point Mutation In DNA. The Amplification Refractory Mutation System (ARMS)”, Nucleic Acids Research, vol. 17, No. 7, pp. 2503-2516 (1989).
S. Ayyadevara et al., “Discrimination of Primer 3'-Nucleotide Mismatch By Taq DNA Polymerase During Polymerase Chain Reaction”, Analytical Biochemistry, vol. 284, No. 1, pp. 11-18 (2000).
J. P. Day et al., “Nucleotide Analogs Facilitate Base Conversion With 3' Mismatch Primers”, Nucleic Acids Research, vol. 27, No. 8, pp. 1810-1818 (1999).
S. Kwok et al., “Effects Of Primer-Template Mismatches On The Polymerase Chain Reaction: Human Immunodeficiency Virus Type 1 Model Studies”, Nucleic Acids Reseach, vol. 18, No. 4, pp. 999-1005 (1990).
Afshin Ahmadian et al., “Genotyping By Apyrase-Mediated Allele-Specific Extension”, Nucleic Acids Research, vol. 29, No. 24e121, pp. 1-5 (2001).
D. O'Meara et al., “SNP Typing By Apyrase-Mediated Allele-Specific Primer Extension On DNA Microarrays”, Nucleic Acids Research, vol. 30, No. 15e75, pp. 1-8 (2002).
M. Ronaghi et al., “Improved Performance of Pyrosequencing Using Single-Stranded DNA-Binding Protein”, Analytical Biochemistry, vol. 286, No. 2, pp. 282-288 (2000).
G. T.Tan et al., “Natural-Product Inhibitors Of Human DNA Ligase I”, Biochem. J., vol. 314, pp. 993-1000 (1996)..
P. Nyŕen et al., “Detection Of Single-Base Changes Using A Bioluminometric Primer Extension Assay”, Analytical Biochemistry, vol. 244, No. 2, pp. 367-373 (1997).
M. Ronaghi et al., “A Sequencing Method Based On Real-Time Pyrophosphate”, Science, vol. 281 (5375), pp. 363-365 (1998).
P. Nyŕen et al., “Enzymatic Method For Continuous Monitoring Of Inorganic Pyrophosphate Synthesis”, Analytical Biochemistry, vol. 151, No. 2, pp. 504-509 (1985).
Peter A.C. 't Hoen et al., “Fluorescent Labelling Of cRNA For Microarray Applications”, Nucleic Acids Research, vol. 31, No. 5e20, pp. 1-8 (2003).
G. T.Tran et al., “Parallel Genotyping Of Human SNPs Using Generic High-Density Oligonucleotide Tag Arrays”, Genome Research, vol. 10, No. 6, pp. 853-860 (2000).
D. O'Meara et al., “Capture Of Single-Stranded DNA Assisted By Oligonucleotide Modules”, Analytical Biochemistry, vol. 255, No. 2, pp. 195-203 (1998).
D. O'Meara et al., “Cooperative Oligonucleotides Mediating Direct Capture Of Hepatitis C Virus RNA From Serum”, Journal of Clinical Microbiology, vol. 36, No. 9, pp. 2454-2459 (1998).
K.J. Livak et al., “Oligonucleotide With Fluorescent Dyes At Opposite Ends Provide A Quenched Probe System Useful For Detecting PCR Product And Nucleic Acid Hybridization”, PCR Methods and Applications, vol. 4, No. 6, pp. 357-362 (1995).
C. Christopherson et al., “The Effects Of Internal Primer-Template Mismatches On RT-PCR: HIV-1 Model Studies”, Nucleic Acids Research, vol. 25, No. 3, pp. 654-658 (1997).
S.D. O'Dell et al., “SNP Genotyping By Combination Of 192-Well MADGE, ARMS And Computerized Gel Image Analysis”, BioTechniques, vol. 29, No. 3, pp. 500-506 (2000).
E. Huzltin et al., “Competitive enzymatic reaction to control allele-specific extensions”, Nucleic Acids Research, vol. 33, No. 5e48, pp. 1-10 (2005).
M. Kaller et al., “Tag-Array Based H
Ahmadian Afshin
Lundeberg Joakim
Baughman Molly E.
Horlick Kenneth R.
Winston & Strawn LLP
LandOfFree
Allele-specific mutation detection assay using an... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Allele-specific mutation detection assay using an..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Allele-specific mutation detection assay using an... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3900000