- 作者: Tulio C Lins; Breno S Abreu; Rinaldo W Pereira
- 作者服務機構: Programa de Pos-Graduacao em Ciencias Genomicas e Biotecnologia, Universidade Catolica de Brasilia, Brasilia, DF, Brazil
- 中文摘要: --
- 英文摘要:
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 a prediction accuracy algorithm. Transferability of tagSNPs and
relative loss of prediction were evaluated according to the difference between the
Brazilian sample and the pooled and single HapMap population estimates.
Results :
Each population presented different levels of prediction per gene. On average, the
Brazilian (BRA) sample displayed a lower power of prediction when compared to
HapMap and the pooled sample. There was a relative loss of prediction for BRA when
using single HapMap populations, but a pooled HapMap dataset generated minor loss of
variability prediction and lower standard deviations, except at the VDR locus at which
loss was minor using CEU tagSNPs.
Conclusions :
Studies that involve tagSNP selection for an admixed population should not be
generally correlated with any specific HapMap population and can be better represented
with a pooled dataset in most cases. - 中文關鍵字: --
- 英文關鍵字: --