Document Detail


Scanning for genomic regions subject to selective sweeps using SNP-MaP strategy.
MedLine Citation:
PMID:  21382594     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Libin Deng; Xiaoli Tang; Wei Chen; Jiari Lin; Zhiqing Lai; Zuoqi Liu; Dake Zhang
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Genomics, proteomics & bioinformatics     Volume:  8     ISSN:  2210-3244     ISO Abbreviation:  Genomics Proteomics Bioinformatics     Publication Date:  2010 Dec 
Date Detail:
Created Date:  2011-03-08     Completed Date:  2011-05-23     Revised Date:  2013-04-17    
Medline Journal Info:
Nlm Unique ID:  101197608     Medline TA:  Genomics Proteomics Bioinformatics     Country:  China    
Other Details:
Languages:  eng     Pagination:  256-61     Citation Subset:  IM    
Copyright Information:
Copyright © 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.
Affiliation:
Facuity of Basic Medical Science, Nanchang University, Nanchang 330006, China.
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MeSH Terms
Descriptor/Qualifier:
Computer Simulation
European Continental Ancestry Group / genetics
Genetics, Population / methods*
Genome, Human*
Genomics / methods*
Haplotypes
Heterozygote
Humans
Polymorphism, Single Nucleotide
Selection, Genetic

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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