Rapid analysis of variations in a genome

Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Preparing compound containing saccharide radical

Reexamination Certificate

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C435S006120, C435S091100, C536S024300, C536S024330

Reexamination Certificate

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06977162

ABSTRACT:
The invention provides a method useful for determining the sequence of large numbers of loci of interest on a single or multiple chromosomes. The method utilizes an oligonucleotide primer that contains a recognition site for a restriction enzyme such that digestion with the restriction enzyme generates a 5′ overhang containing the locus of interest. The 5′ overhang is used as a template to incorporate nucleotides, which can be detected. The method is especially amenable to the analysis of large numbers of sequences, such as single nucleotide polymorphisms, from one sample of nucleic acid.

REFERENCES:
patent: 4521509 (1985-06-01), Benkovic et al.
patent: 4683195 (1987-07-01), Mullis et al.
patent: 4683202 (1987-07-01), Mullis
patent: 4800159 (1989-01-01), Mullis et al.
patent: 4889818 (1989-12-01), Gelfand et al.
patent: 4965188 (1990-10-01), Mullis et al.
patent: 5023171 (1991-06-01), Ho et al.
patent: 5066584 (1991-11-01), Gyllensten et al.
patent: 5075216 (1991-12-01), Innis et al.
patent: 5079352 (1992-01-01), Gelfand et al.
patent: 5091310 (1992-02-01), Innis
patent: 5104792 (1992-04-01), Silver et al.
patent: 5432054 (1995-07-01), Saunders et al.
patent: 5538848 (1996-07-01), Livak et al.
patent: 5545552 (1996-08-01), Mathur
patent: 5565339 (1996-10-01), Bloch et al.
patent: 5618664 (1997-04-01), Kiessling
patent: 5631147 (1997-05-01), Lohman et al.
patent: 5641628 (1997-06-01), Bianchi
patent: 5648222 (1997-07-01), Tse et al.
patent: 5723591 (1998-03-01), Livak et al.
patent: 5744301 (1998-04-01), Birkenbach et al.
patent: 5831065 (1998-11-01), Brenner
patent: 5858671 (1999-01-01), Jones
patent: 5965363 (1999-10-01), Monforte et al.
patent: 5998141 (1999-12-01), Acton
patent: 6090553 (2000-07-01), Matson
patent: 6110709 (2000-08-01), Ausubel et al.
patent: 6124120 (2000-09-01), Lizardi
patent: 6180372 (2001-01-01), Franzen
patent: 6203989 (2001-03-01), Goldberg et al.
patent: 6225061 (2001-05-01), Becker et al.
patent: 6251639 (2001-06-01), Kurn
patent: 6258540 (2001-07-01), Lo et al.
patent: 6387621 (2002-05-01), Wittwer
patent: 6475736 (2002-11-01), Stanton, Jr.
patent: 6506561 (2003-01-01), Cheval et al.
patent: 6613517 (2003-09-01), Michelotti
patent: 2001/0051341 (2001-12-01), Lo et al.
patent: 2002/0045176 (2002-04-01), Lo et al.
patent: 2003/0044388 (2003-03-01), Dennis et al.
patent: 2003/0054386 (2003-03-01), Antonarakis et al.
patent: 2003/0082576 (2003-05-01), Jones et al.
patent: 2003/0099964 (2003-05-01), Pattil et al.
patent: 2003/0232348 (2003-12-01), Jones et al.
patent: 2004/0106102 (2004-06-01), Dhallan
patent: 2004/0137470 (2004-07-01), Dhallon
patent: 0 994 963 (2000-04-01), None
patent: 2 299 166 (1996-09-01), None
patent: WO 91/08304 (1991-06-01), None
patent: WO 95/06137 (1995-03-01), None
patent: WO 98/39474 (1998-09-01), None
patent: WO 02/04672 (2002-01-01), None
patent: WO 02/083839 (2002-10-01), None
patent: WO 03/074723 (2003-09-01), None
patent: WO 03/074740 (2003-09-01), None
patent: WO 03/106642 (2003-12-01), None
Written Opinion mailed on Mar. 10, 2005 for PCT patent application No. PCT/US03/06376 filed on Feb. 28, 2003. 3 pages.
Brown, E. L. et al. (1979). “Chemical Synthesis and Cloning of a Tyrosine tRNA Gene,”Methods in Enzymology68:109-151.
Center for Medical Genetics. (1998-2003). Human Insertion/Deletion Polymorphisms http://research.marshfieldclinicorg/genetics/. Last visited on Apr. 14, 2003. 3 pages.
Cooper, D. N. and Krawczak, M. eds.(1993). “Human Gene Mutation,”In Duchenne Muscular Dystrophy, Alzheimer's Disease, Cystic Fibrosis, and Huntington's Disease. BIOS Scientific Publishers Limited. (Table of Contents only).
Erlich, H. A. ed. (1989).PCR Technology: Principals and Applications of DNA Amplification, Stockton Press. pp. ix-x. (Table of Contents only).
Huber, M. et al. (2001). “Detection of Single Base Alterations in Genomic DNA by Solid Phase Polymerase Chain Reaction on Oligonucleotide Microarrays,”Analytical Biochemistry299:24-30.
Innis, M. A. ed., (1990).PCR Protocols: A Guide to Methods and Applications. Academic Press, Inc. pp. v-x. (Table of Contents only).
Kaneoka, H. et al. (1991). “Solid-Phase Direct DNA Sequencing of Allele-Specific Polymerase Chain Reaction-Amplified HLA-DR Genes,”Biotechniques10(1):30, 32 and 34 only.
McPherson, M. J. et al. eds., (1991).PCR: A Practical Approach, IRL Press at Oxford University Press. Total pp. 6. (Table of Contents).
Narang, S. A. et al. (1979). “Improved Phosphotriester Method for the Synthesis of Gene Fragments,”Methods in Enzymology68:90-98.
Poch, M. T. et al. (1997). “Sth132I, A Novel Class-IIS Restriction Endonuclease ofStreptococcus thermophilusST132,”Gene195:201-206.
Riordan, J. R. et al. (1989). “Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA,”Science245(4922):1066-1073.
Rommens, J. M. et al. (1989). “Identification of the Cystic Fibrosis Gene: Chromosome Walking and Jumping,”Science245:1059-1065.
Sambrook, J. and Russell, D. W. eds., (2001).Molecular Cloning Laboratory Manual. vol. 2 Third Edition, Cold Spring Harbor Laboratory Press. pp. v-xx. (Table of Contents only).
Sanger, F. et al. (1977). “DNA Sequencing with Chain-Terminating Inhibitors,”PNAS USA74(12):5463-5467.
Shah, J. S. et al. (1995). “Q-Beta Replicase-Amplified Assay for Detection ofMycobacterium tuberculosisDirectly from Clinical Specimens,”Journal of Clinical Microbiology. 33(6):1435-1441.
Shapero, M. H. et al. (2001). “SNP Genotyping by Multiplexed Solid-Phase Amplification and Fluorescent Minisequencing,”Genome Research11:1926-1934.
SNP Report for TSC0087315. (Aug. 2000). http://snp.cshl.org/snpsearch.shtml. Last visited on Apr. 14, 2003. 2 pages.
SNP Report for TSC0095512. (Aug. 2000). http://snp.cshl.org/snpsearch.shtml. Last visited on Apr. 14, 2003. 2 pages.
SNP Report for TSC0264580. (Aug. 2000). http://snp.cshl.org/snpsearch.shtml. Last visited on Apr. 14, 2003. 2 pages.
SNP Report for TSC0413944. (Aug. 2000). http://snp.cshl.org/snpsearch.shtml. Last visited on Apr. 14, 2003. 2 pages.
Wallace, R.W. (1997). “DNA on a Chip: Serving Up the Genome for Diagnostics and Research,”Molecular Medicine Today3:384-389.
Wang, D. G. et al. (1998). “Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome,”Science280:1077-1082.
Waterston, R.H. and McPherson, J.D. (2001). “A Map of Human Genome Sequence Variation Containing 1.42 Million Single Nucleotide Polymorphisms,”Nature409:928-933.
Blanchard, A. P. and Hood, L. (1996). “Sequence to Array: Probing the Genome's Secrets,”Nature Biotechnology14:1649.
Brenner, S. et al. (2000). “Gene Expression Analysis by Massively Parallel Signature Sequencing (MPSS) on Microbead Arrays,”Nature Biotechnology18:630-634.
Broude, N. et al. (2001). “High-Level Multiplex DNA Amplification,”Antisense&Nucleic Acid Drug Development11:327-332.
Chen, J. et al. (2000). “A Microsphere-Based Assay for Multiplexed Single Nucleotide Polymorphism Analysis Using Single Base Chain Extension,”Genome Research10:549-557.
Chicurel, M. (2001). “Faster, Better, Cheaper Genotyping,”Nature412:580-582.
Collins, F. S. and Mansoura, M. K. (2001). “The Human Genome Project: Revealing the Shared Inheritance of All Humankind,”7thBiennial Symposium on Minorities, the Medically Underserved and Cancer91(1):221-225.
Cutler, D. J. et al. (2001). “High-Throughput Variation Detection and Genotyping Using Microarrays,”Genome Research11:1913-1925.
Drábek, J. (2001). “A Commented Dictionary of Techniques for Genotyping,”Electrophoresis22:1024-1045.
Egholm, M. et al. (1992). “Peptide Nucleic Acids (PNA), Oligonucleotide Analogues with an Achiral Peptide Backbone,”Journal of the American Chemical Society114(5):1895-1897.
Gerhold, D. et al. (1999). “DNA Chips: Promising To

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