Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-11-08
2005-11-08
Allen, Marianne P. (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S019000, C435S006120
Reexamination Certificate
active
06963805
ABSTRACT:
The present invention provides methods for determining sequence similarity (conserved sequences) between nucleic acids from a first organism and nucleic acids from a second, different organism without having to know a priori the nucleic acid sequence from the second, different organism. The first nucleic acid can be from any organism where the sequence of the nucleic acid is known and the second nucleic acid can be from any organism. The method involves determining which bases from the second nucleic acid are identical to the first nucleic acid, and allows one to determine the sequence of portions of the second nucleic acid. The invention is useful for identifying putative functional regions or putative organism-sequences in a genome.
REFERENCES:
patent: 5405783 (1995-04-01), Pirrung et al.
patent: 5800992 (1998-09-01), Fodor et al.
patent: 5837832 (1998-11-01), Chee et al.
patent: 5925525 (1999-07-01), Fodor et al.
patent: 5968740 (1999-10-01), Fodor et al.
patent: 6013449 (2000-01-01), Hacia et al.
patent: 6251601 (2001-06-01), Bao et al.
patent: 6383742 (2002-05-01), Drmanac et al.
patent: 6391550 (2002-05-01), Lockhart et al.
patent: 0785280 (1997-07-01), None
patent: 0848067 (1998-06-01), None
patent: WO 95/00530 (1995-01-01), None
Frazer et al., Genome Research, 11:1651-1659, 2001.
Hacia, J.G., et al.; Detection of Heterozygous Mutations in BRCA1 Using High Density Oligonucleotide Arrays and Two-Colour Fluorescence Analysis, Nature Genetics, 1996, 14:4:441-447.
Loots et al., “Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons”,Science, vol. 288 pp. 136-140 (Apr. 7, 2000).
Murphy et al., “Database Searches for Binding Sites”,Science, vol. 288 (5475) pp 2319 ;(Jun. 30, 2000).
Oeltjen, J.C. et al., “Large-Scale Comparative Sequence Analysis of the Human and Murine Bruton's Tyrosine Kinase Loci Reveals Conserved Regulatory Domains” Genome Research; 7:315-329 (1997).
Hardison, R.C. et al., “Long Human-Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome”, Genome Research; 7:959-966 (1997).
Karet, G. et al., “Unraveling Human Diversity”, The SNP Consortium; S5-S12, Nov./Dec. 2000.
Hinde, A., “Evolution, not Revolution” Trends Biotechnol.; 18:230-231 (2000).
Cargill, M. et al., “Mining for SNPs: Putting the Common Variants-Common Diease Hypothesis to the Test”, Pharmacogenomics; 1-27-37 (2000).
Wang, D.G. et al., “Large-Scale Identification, Mapping, and Genotyping of Single Nucleotide Polymorphisms in the Human Genome”, Science; 280:1077-1082 (1998).
Pennacchio, L.A. et al., “Genomics Strategies to Identify Mammalian Regulatory Sequences”, Nature; 2:100-109 (2001).
Wynn, S.L. et al., “Organization and Conservation of the GART/SON/DONSON Locus in Mouse and Human Genomes”, Genomics; 68:57-62 (2000).
Wiltshire, T. et al., “Perfect Conserved Linkage Across the Entire Mouse Chromosome 10 Region Homologous to Human Chromosome 21”Genome Research; 9:1214-1222 (1999).
Ansari-Lari, M. A. et al., “Comparative Sequence Analysis of a Gene-Rich Cluster at Human Chromosome 12p13 and its Syntenic Region in Mouse Chromosome 6”Genome Research; 8:29-40 (1998).
Onyango, P. et al., “Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain”, Genome Research; 10:1697-1710 (2000).
Hardison, R., “Conserved Noncoding Sequences are Reliable Guides to Regulatory Elements”, Trend Genet,; 16-369-72 (2000).
Dubchak, I. et al., “Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons”, Genome Research; 10:1304-1306 (2000).
Hacia, J.G. et al., “Determination of Ancestral Alleles for Human Single-Nucleotide Polymorphisms Using High-Density Oligonucleotide Arrays”, Nature Genetics; 22:164-167 (1999).
Hacia, J.G. et al., “Evolutionary Sequence Comparsions Using High-Density Oligonucleotide Arrays”, Nature Genetics; 18:155-158 (1998).
Chen et al., “Genomic Divergences Between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees,” Am. J. Hum. Genet. 68:444-456, 2001.
Fujiyama et al., “Construction and Analysis of a Human-Chimpanzee Comparative Clone Map,” Science, vol. 295, pp. 131-134, Jan. 4, 2002.
Gagneux et al., “Genetic Differences between Humans and Great Apes,” Molecular Phylogenetics an Evolution, vol. 18, No. 1, pp. 2-13, Jan. 2001.
Hacia et al., “Genome of the apes”, Trends in Genetics, vol. 17, No. 11, pp. 637-645, Nov. 2001.
Hattori et al., “The DNA sequence of human chromosome 21,” Nature, vol. 405, pp. 311-319, May 18, 2000.
King et al., “Evolution at Two Levels in Humans and Chimpanzees,” Science, vol. 188, No. 4184, pp. 107-116, Apr. 11, 1975.
Koop et al., “A Molecular View of Primate Phylogeny and Important Systematic and Evolutionary Questions,” Mol. Biol. Evol. 6(6):580-612. pp. 580-612, 1989.
Nickerson et al., “Molecular Definition of Pericentric Inversion Breakpoints Occurring during the Evolution of Humans and Chimpanzees,” Genomics 50, 368-372 (1998).
Ueda et al., “Human-Specific Sequences: Isolation of Species-Specific DNA Regions by Genome Subtraction,” Genomics 8, 7-12 (1990).
Yunis et al. “The Origin of Man: A Chromosomal Pictorial Legacy,” Science, vol. 215, pp. 1525-1530, Mar. 19, 1982.
Frazer Kelly A.
Patil Nila
Sheehan John
Allen Marianne P.
Arnold Deana A.
Perlegen Sciences, Inc.
Shaver Gulshan H.
LandOfFree
Methods for identifying the evolutionarily conserved sequences does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Methods for identifying the evolutionarily conserved sequences, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods for identifying the evolutionarily conserved sequences will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3476324