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Genomics Proteomics Bioinformatics. 2010 Dec;8(4):256-61. doi: 10.1016/S1672-0229(10)60027-7.

Scanning for genomic regions subject to selective sweeps using SNP-MaP strategy.

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1
Facuity of Basic Medical Science, Nanchang University, Nanchang 330006, China.

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 confirmed 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.

PMID:
21382594
PMCID:
PMC5054161
DOI:
10.1016/S1672-0229(10)60027-7
[Indexed for MEDLINE]
Free PMC Article
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