Abstract
SNP data has grown exponentially over the last two years, SNP database evolution has matched this growth, as initial development of several independent SNP databases has given way to one central SNP database, dbSNP. Other SNP databases have instead evolved to complement this central database by providing gene specific focus and an increased level of curation and analysis on subsets of data, derived from the central data set. By contrast, human mutation data, which has been collected over many years, is still stored in disparate sources, although moves are afoot to move to a similar central database. These developments are timely, human mutation and polymorphism data both hold complementary keys to a better understanding of how genes function and malfunction in disease. The impending availability of a complete human genome presents us with an ideal framework to integrate both these forms of data, as our understanding of the mechanisms of disease increase, the full genomic context of variation may become increasingly significant.
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Selected References
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- Altshuler D., Pollara V. J., Cowles C. R., Van Etten W. J., Baldwin J., Linton L., Lander E. S. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature. 2000 Sep 28;407(6803):513–516. doi: 10.1038/35035083. [DOI] [PubMed] [Google Scholar]
- Aparicio S., Morrison A., Gould A., Gilthorpe J., Chaudhuri C., Rigby P., Krumlauf R., Brenner S. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1684–1688. doi: 10.1073/pnas.92.5.1684. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brookes A. J., Lehväslaiho H., Siegfried M., Boehm J. G., Yuan Y. P., Sarkar C. M., Bork P., Ortigao F. HGBASE: a database of SNPs and other variations in and around human genes. Nucleic Acids Res. 2000 Jan 1;28(1):356–360. doi: 10.1093/nar/28.1.356. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chang H., Fujita T. PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Biochem Biophys Res Commun. 2001 Sep 14;287(1):288–291. doi: 10.1006/bbrc.2001.5576. [DOI] [PubMed] [Google Scholar]
- Cuticchia A. J. Future vision of the GDB human genome database. Hum Mutat. 2000;15(1):62–67. doi: 10.1002/(SICI)1098-1004(200001)15:1<62::AID-HUMU13>3.0.CO;2-R. [DOI] [PubMed] [Google Scholar]
- Hamosh A., Scott A. F., Amberger J., Valle D., McKusick V. A. Online Mendelian Inheritance in Man (OMIM). Hum Mutat. 2000;15(1):57–61. doi: 10.1002/(SICI)1098-1004(200001)15:1<57::AID-HUMU12>3.0.CO;2-G. [DOI] [PubMed] [Google Scholar]
- Kluijtmans L. A., van den Heuvel L. P., Boers G. H., Frosst P., Stevens E. M., van Oost B. A., den Heijer M., Trijbels F. J., Rozen R., Blom H. J. Molecular genetic analysis in mild hyperhomocysteinemia: a common mutation in the methylenetetrahydrofolate reductase gene is a genetic risk factor for cardiovascular disease. Am J Hum Genet. 1996 Jan;58(1):35–41. [PMC free article] [PubMed] [Google Scholar]
- Marth G. T., Korf I., Yandell M. D., Yeh R. T., Gu Z., Zakeri H., Stitziel N. O., Hillier L., Kwok P. Y., Gish W. R. A general approach to single-nucleotide polymorphism discovery. Nat Genet. 1999 Dec;23(4):452–456. doi: 10.1038/70570. [DOI] [PubMed] [Google Scholar]
- Marth G., Yeh R., Minton M., Donaldson R., Li Q., Duan S., Davenport R., Miller R. D., Kwok P. Y. Single-nucleotide polymorphisms in the public domain: how useful are they? Nat Genet. 2001 Apr;27(4):371–372. doi: 10.1038/86864. [DOI] [PubMed] [Google Scholar]
- Reich D. E., Cargill M., Bolk S., Ireland J., Sabeti P. C., Richter D. J., Lavery T., Kouyoumjian R., Farhadian S. F., Ward R. Linkage disequilibrium in the human genome. Nature. 2001 May 10;411(6834):199–204. doi: 10.1038/35075590. [DOI] [PubMed] [Google Scholar]
- Riggins G. J., Strausberg R. L. Genome and genetic resources from the Cancer Genome Anatomy Project. Hum Mol Genet. 2001 Apr;10(7):663–667. doi: 10.1093/hmg/10.7.663. [DOI] [PubMed] [Google Scholar]
- Risch N. J. Searching for genetic determinants in the new millennium. Nature. 2000 Jun 15;405(6788):847–856. doi: 10.1038/35015718. [DOI] [PubMed] [Google Scholar]
- Sherry S. T., Ward M. H., Kholodov M., Baker J., Phan L., Smigielski E. M., Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308–311. doi: 10.1093/nar/29.1.308. [DOI] [PMC free article] [PubMed] [Google Scholar]