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

doi:10.1016/j.ygeno.2012.09.003

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 journal › Article › peer-review

2 Scopus citations

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 language	English (US)
Pages (from-to)	20-23
Number of pages	4
Journal	Genomics
Volume	101
Issue number	1
DOIs	https://doi.org/10.1016/j.ygeno.2012.09.003
State	Published - Jan 2013
Externally published	Yes

Keywords

Coverage
Genome-wide association study
HapMap
Single-nucleotide polymorphism

ASJC Scopus subject areas

Genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.ygeno.2012.09.003

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title = "Evaluating coverage of exons by HapMap SNPs",

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.",

keywords = "Coverage, Genome-wide association study, HapMap, Single-nucleotide polymorphism",

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

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. ",

year = "2013",

month = jan,

doi = "10.1016/j.ygeno.2012.09.003",

language = "English (US)",

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AU - Dong, Xiao

AU - Zhong, Tingyan

AU - Xu, Tao

AU - Xia, Yunting

AU - Li, Biqing

AU - Li, Chao

AU - Yuan, Liyun

AU - Ding, Guohui

AU - Li, Yixue

N1 - 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.

PY - 2013/1

Y1 - 2013/1

N2 - 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.

AB - 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.

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KW - HapMap

KW - Single-nucleotide polymorphism

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Evaluating coverage of exons by HapMap SNPs

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

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