SpringerProtocols: Abstract: SNP Databases

3. SNP Databases

By: Christopher Phillips¹

Abstract

Full Text

Download PDF (438K)

Researchers interested in obtaining detailed information on SNPs now work in a golden age of online database availability: never has so much data and such a wealth of information been freely accessible for such a substantial proportion of the 18 million single nucleotide polymorphism (SNP) loci currently characterized in the human genome. This chapter describes the major SNP databases available for human genetics studies. Tools and strategies are outlined that can help researchers properly formulate a database query to be able to access the most appropriate information needed for their research aims, including medical or population genetics analysis – an approach that is getting increased attention given the expanding scale of online SNP data.

Affiliation(s): (1) Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Galicia, Spain

Book Title: Single Nucleotide Polymorphisms: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 578 | Pub. Date: Sep-01-2008 | Page Range: 43-71 | DOI: 10.1007/978-1-60327-411-1_3

Subject: Genetics/Genomics

Key Words: Single nucleotide polymorphism - database - search - query - National Center for Biotechnology Information - dbSNP Entrez - HapMap

References

Download References

1.	The International HapMap Consortium. (2005) A haplotype map of the human genome. Nature 437, 1299–1320.

2.	The International HapMap Consortium. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861.

3.	Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B. et al. (2002) The structure of haplotype blocks in the human genome. Science 296, 2225–2229.

4.	Wall, J. D. and Pritchard, J. K. (2003) Haplotype blocks and linkage disequilibrium in the human genome. Nat. Rev. Genet 4, 587–597.

5.	Ashurst, J. L., Chen, C. K., Gilbert, J. G., Jekosch K., Keenan S., Meidl P. et al. (2005) The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res. 33, D459–465.

6.	Yang, N., Li, H., Criswell, L. A., Gregersen, P. K., Alarcon-Riquelme, M. E., Kittles, R. et al. (2005) Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers. Hum. Genet. 118, 382–392.

7.	de Bakker, P. I., Yelensky, R., Pe'er, I., Gabriel, S. B., Daly, M. J. and Altshuler, D. (2005) Efficiency and power in genetic association studies. Nat. Genet. 37, 1217–1223.

8.	de Bakker, P. I. W., Noel, N. P., Burtt, N. P., Graham, R. R., Guiducci, C., Yelensky, R., Drake, J.A. et al. (2006) Transferability of tag SNPs in genetic association studies in multiple populations. Nat. Genet. 38, 1298–1303.

9.	Riva, A. and Kohane, I. S. (2002) SNPper: retrieval and analysis of human SNPs. Bioinformatics 18, 1681–1685.

10.	Conde, L., Vaquerizas, J. M., Santoyo, J., Shahrour, F., Ruiz-Llorente, S., Robledo, M. et al. (2004) PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Res. 32, W242–248.

11.	Conde L., Vaquerizas J.M., Dopazo H., Arbiza L., Reumers J., Rousseau F. et al. (2006) PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res. 34, W621–625.

12.	Ramensky, V., Bork, P., and Sunyaev, S. (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30, 3894–3900.

13.	Cartegni, L., Wang, J., Zhu, Z., Zhang, M. Q., and Krainer, A. R. (2003) ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res. 31, 3568–3571.

14.	Voight, B. F., Kudaravalli, S., Wen, X. and Pritchard, J. K. (2006) A map of recent positive selection in the human genome. PLoS Biol 4, 446–458.

15.	Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F. et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832–837.

16.	Haiman, C. A. and Stram, D. O. (2008) Utilizing HapMap and tagging SNPs. Methods Mol. Med. 141, 37–54.

17.	Zhang, J., Rowe, W.L., Clark, A.G. and Buetow, K.H. (2003) Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations. Am. J. Hum. Genet. 73, 1073–1081.

18.	Bersaglieri, T., Sabeti, P. C., Patterson, N., Vanderploeg, T., Schaffner, S.F., Drake J.A. et al. (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet. 74, 1111–1120.

19.	Bandelt, H. J., Salas, A. and Bravi, C. M. (2006) What is a ‘novel’ mtDNA mutation–and does ‘novelty’ really matter? J. Hum. Genet. 51, 1073–1082.

Comments (Loading...)

Post comment/View all comments