Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome

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	Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome
	Zhao ZM*1,2,3; Zhang FK 1; zzhao@vcu.cdu
	2006
发表期刊	GENE
ISSN	0378-1119
卷号	366 期号:2 页码:316-324
合作性质	其它
摘要	We analyzed n-mers (n=3-8) in the local environment of 8,249,446 human SNPs and compared their distribution with that in the genome reference sequences. The results revealed that the short sequences, which contained at least one CpG dinucleotide, occurred more frequently in the local SNP sequences than in the genome sequences. To exclude the hypermutability effect of the methylated CpG dinucleotides on the sequence context of SNPs, we examined the distribution patterns for each of the six categories of substitution. We observed the similar pattern (i.e., CpG-containing n-mers vs. non-CpG-containing n-mers) in SNP categories A/G, C/T and C/G but the opposite pattern in category A/T. We next identified 34,928 putative CpG islands in the human genome and located 133,591 SNPs within these islands. In the CpG islands, CpG SNPs were 3.92-fold less prevalent relative to the presence of CpG dinucleotides. Conversely, in the human genome, the frequency of CpG dinucleotides at the polymorphic sites was 6.09 times that in the genome reference sequences. These results support the previous views of mutational suppression at the CpG sites in the CpG islands and hypermutability of the methylated CpG dinucleotides that are prevalent in the non-CpG island sequences in the human genome. Our study represents a comprehensive investigation of the sequence context of SNPs in the human genome and in human CpG islands.
关键词	Snps Short Sequence Cpg Dinucleotide Cpg Islands Gc Content
资助者	This project was supported by Thomas F. and Kate Miller Jeffress Memorial Trust Fund. ; This project was supported by Thomas F. and Kate Miller Jeffress Memorial Trust Fund. ; This project was supported by Thomas F. and Kate Miller Jeffress Memorial Trust Fund. ; This project was supported by Thomas F. and Kate Miller Jeffress Memorial Trust Fund.
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收录类别	SCI
语种	英语
资助者	This project was supported by Thomas F. and Kate Miller Jeffress Memorial Trust Fund. ; This project was supported by Thomas F. and Kate Miller Jeffress Memorial Trust Fund. ; This project was supported by Thomas F. and Kate Miller Jeffress Memorial Trust Fund. ; This project was supported by Thomas F. and Kate Miller Jeffress Memorial Trust Fund.
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/5369
专题	其他
通讯作者	zzhao@vcu.cdu
作者单位	1.Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA 2.Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA 3.Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
推荐引用方式 GB/T 7714	Zhao ZM*,Zhang FK,zzhao@vcu.cdu. Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome[J]. GENE,2006,366(2):316-324.
APA	Zhao ZM*,Zhang FK,&zzhao@vcu.cdu.(2006).Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome.GENE,366(2),316-324.
MLA	Zhao ZM*,et al."Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome".GENE 366.2(2006):316-324.

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