a database of SNPs with high population differentiation for HapMap3 (original) (raw)
Title
FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3
Authors
Shiwei Duan1, Wei Zhang1, Nancy Jean Cox1, 2 and Mary Eileen Dolan1, 3, 4, *
Affiliation
1Section of Hematology/Oncology, Department of Medicine; 2Department of Human Genetics; 3Committee on Clinical Pharmacology and Pharmacogenomics; 4Cancer Research Center, The University of Chicago, IL 60637, USA
edolan@medicine.bsd.uchicago.edu; Corresponding author
Phone
773 702 4441
Fax
773 702 0963
Article Type
Database
Date
received September 16, 2008; revised October 10; accepted October 15, 2008; published November 09, 2008
Abstract
The International HapMap Project has recently made available genotypes and frequency data for phase 3 (NCBI build 36, dbSNP b129) of the HapMap providing an enriched genotype dataset for approximately 1.6 million single nucleotide polymorphisms (SNPs) from 1,115 individuals with ancestry from parts of Africa, Asia, Europe, North America and Mexico. In the present study, we aim to facilitate pharmacogenetics studies by providing a database of SNPs with high population differentiation through a genomewide test on allele frequency variation among 11 HapMap3 samples. Common SNPs with minor allele frequency greater than 5% from each of 11 HapMap3 samples were included in the present analysis. The population differentiation is measured in terms of fixation index (Fst), and the SNPs with Fst values over 0.5 were defined as highly differentiated SNPs. Our tests were carried out between all pairs of the 11 HapMap3 samples or among subgroups with the same continental ancestries. Altogether we carried out 64 genomewide Fst tests and identified 28,215 highly differentiated SNPs for 49 different combinations of HapMap3 samples in the current database.
Keywords
database; HapMap3; SNP; population differentiation; Fst; human genome
Availability
http://FstSNP-hapmap3.googlecode.com/
Citation
Duan et al., Bioinformation 3(3): 139-141 (2008)
Edited by
P. Kangueane
ISSN
0973-2063
Publisher
License
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.