Genomics Inform.  2012 Jun;10(2):81-87. 10.5808/GI.2012.10.2.81.

Identifying Copy Number Variants under Selection in Geographically Structured Populations Based on F-statistics

Affiliations
  • 1Division of Biostatistics, Department of Medical Lifescience, The Catholic University of Korea, College of Medicine, Seoul 137-040, Korea. hhsong@catholic.ac.kr
  • 2Department of Microbiology, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 137-040, Korea. yejun@catholic.ac.kr
  • 3Department of Statistics, Hankuk University of Foreign Studies, Yongin 449-791, Korea.

Abstract

Large-scale copy number variants (CNVs) in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered. Although the examination of relatively large numbers of specific ethnic groups has recently started in regard to inter-ethnic group differences in CNVs, identifying and understanding particular instances of natural selection have not been performed. The traditional FST measure, obtained from differences in allele frequencies between populations, has been used to identify CNVs loci subject to geographically varying selection. Here, we review advances and the application of multinomial-Dirichlet likelihood methods of inference for identifying genome regions that have been subject to natural selection with the FST estimates. The contents of presentation are not new; however, this review clarifies how the application of the methods to CNV data, which remains largely unexplored, is possible. A hierarchical Bayesian method, which is implemented via Markov Chain Monte Carlo, estimates locus-specific FST and can identify outlying CNVs loci with large values of FST. By applying this Bayesian method to the publicly available CNV data, we identified the CNV loci that show signals of natural selection, which may elucidate the genetic basis of human disease and diversity.

Keyword

Bayes theorem; DNA copy number variations; population structure; selection; Wright's FST

MeSH Terms

Bayes Theorem
Coat Protein Complex I
DNA Copy Number Variations
Ethnic Groups
Gene Frequency
Genome
Humans
Markov Chains
Selection, Genetic
Coat Protein Complex I
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