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 journalArticlepeer-review

2 Scopus citations


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
Issue number1
StatePublished - Jan 2013
Externally publishedYes

Bibliographical note

Funding Information:
We thank Drs Zhen Wang and Guangyong Zhen for their helpful comments and suggestions. This work was supported by grants from State key basic research program (973) ( 2011CB910204 , 2011CBA00801 ), the Knowledge Innovation Program of the Chinese Academy of Sciences ( KSCX2-YW-R-112 , KSCX2-YW-R-190 , 2011KIP204 ), and National Natural Science Foundation of China ( 90913009 , 30900272 ). Conflict of interest statement The authors declare no conflict of interest.


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


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