Scanning for Genomic Regions Subject to Selective Sweeps Using SNP-MaP Strategy
10.1016/S1672-0229(10)60027-7
- Author:
Deng LIBIN
1
,
2
,
3
;
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
2. Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
3. 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.
