Scanning for Genomic Regions Subject to Selective Sweeps Using SNP-MaP Strategy
10.1016/S1672-0229(10)60027-7
- Author:
Deng LIBIN
1
;
Tang XIAOLI
;
Chen WEI
;
Lin JIARI
;
Lai ZHIQING
;
Liu ZUOQI
;
Zhang DAKE
Author Information
1. Faculty of Basic Medical Science, Nanchang University, Nanchang 330006, China;Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China;The Institute of Translational Medicine, Nanchang University, Nanchang 330006, China
- Keywords:
selective sweep;
SNP-MaP;
boxplot
- From:
Genomics, Proteomics & Bioinformatics
2010;08(4):256-261
- CountryChina
- Language:Chinese
-
Abstract:
Population genomic approaches,which take advantages of high-throughput genotyping,are powerful yet costly methods to scan for selective sweeps.DNA-pooling strategies have been widely used for association studies because it is a cost-effective alternative to large-scale individual genotyping.Here,we performed an SNP-MaP(single nucleotide polymorphism microarrays and pooling)analysis using samples from Eurasia to evaluate the efficiency of pooling strategy in genome-wide scans for selection.By conducting simulations of allelotype data,we first demonstrated that the boxplot with average heterozygosity(HET)is a promising method to detect strong selective sweeps with a moderate level of pooling error.Based on this,we used a sliding window analysis of HET to detect the large contiguous regions(LCRs)putatively under selective sweeps from Eurasia datasets.This survey identified 63 LCRs in a European population.These signals were further supported by the integrated haplotype score(iHS)test using HapMap Ⅱ data.We also confirrned the European-specific signatures of positive selection from several previously identified genes(KEL,TRPV5,TRPV6,EPHB6).In summary,our results not only revealed the high credibility of SNP-MaP strategy in scanning for selective sweeps,but also provided an insight into the population differentiation.
