TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population.

ABSTRACT:

Background

The application of a subset of single nucleotide polymorphisms, the tagSNPs, can be useful in capturing untyped SNPs information in a genomic region. TagSNP transferability from the HapMap dataset to admixed populations is of uncertain value due population structure, admixture, drift and recombination effects. In this work an empirical dataset from a Brazilian admixed sample was evaluated against the HapMap population to measure tagSNP transferability and the relative loss of variability prediction.

Methods

The transferability study was carried out using SNPs dispersed over four genomic regions: the PTPN22, HMGCR, VDR and CETP genes. Variability coverage and the prediction accuracy for tagSNPs in the selected genomic regions of HapMap phase II were computed using

SUBMITTER: Lins TC 

PROVIDER: S-EPMC2737315 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature