Evaluating coverage of exons by HapMap SNPs

Xiao Dong, Tingyan Zhong, Tao Xu, Yunting Xia, Biqing Li, Chao Li, Liyun Yuan, Guohui Ding, Yixue Li

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Genome-wide association (GWA) studies are currently one of the most powerful tools in identifying disease-associated genes or variants. In typical GWA studies, single-nucleotide polymorphisms (SNPs) are often used as genetic makers. Therefore, it is critical to estimate the percentage of genetic variations which can be covered by SNPs through linkage disequilibrium (LD). In this study, we use the concept of haplotype blocks to evaluate the coverage of five SNP sets including the HapMap and four commercial arrays, for every exon in the human genome. We show that although some Chips can reach similar coverage as the HapMap, only about 50% of exons are completely covered by haplotype blocks of HapMap SNPs. We suggest further high-resolution genotyping methods are required, to provide adequate genome-wide power for identifying variants.

Original languageEnglish (US)
Pages (from-to)20-23
Number of pages4
JournalGenomics
Volume101
Issue number1
DOIs
StatePublished - Jan 1 2013
Externally publishedYes

Fingerprint

HapMap Project
Single Nucleotide Polymorphism
Exons
Genome-Wide Association Study
Haplotypes
Linkage Disequilibrium
Human Genome
Genome
Genes

Keywords

  • Coverage
  • Genome-wide association study
  • HapMap
  • Single-nucleotide polymorphism

ASJC Scopus subject areas

  • Genetics

Cite this

Dong, X., Zhong, T., Xu, T., Xia, Y., Li, B., Li, C., ... Li, Y. (2013). Evaluating coverage of exons by HapMap SNPs. Genomics, 101(1), 20-23. https://doi.org/10.1016/j.ygeno.2012.09.003

Evaluating coverage of exons by HapMap SNPs. / Dong, Xiao; Zhong, Tingyan; Xu, Tao; Xia, Yunting; Li, Biqing; Li, Chao; Yuan, Liyun; Ding, Guohui; Li, Yixue.

In: Genomics, Vol. 101, No. 1, 01.01.2013, p. 20-23.

Research output: Contribution to journalArticle

Dong, X, Zhong, T, Xu, T, Xia, Y, Li, B, Li, C, Yuan, L, Ding, G & Li, Y 2013, 'Evaluating coverage of exons by HapMap SNPs', Genomics, vol. 101, no. 1, pp. 20-23. https://doi.org/10.1016/j.ygeno.2012.09.003
Dong X, Zhong T, Xu T, Xia Y, Li B, Li C et al. Evaluating coverage of exons by HapMap SNPs. Genomics. 2013 Jan 1;101(1):20-23. https://doi.org/10.1016/j.ygeno.2012.09.003
Dong, Xiao ; Zhong, Tingyan ; Xu, Tao ; Xia, Yunting ; Li, Biqing ; Li, Chao ; Yuan, Liyun ; Ding, Guohui ; Li, Yixue. / Evaluating coverage of exons by HapMap SNPs. In: Genomics. 2013 ; Vol. 101, No. 1. pp. 20-23.
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