Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction

doi:10.1038/srep43709

	Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction
	Wu, Yiming 1; Jing, Runyu 2; Dong, Yongcheng 3; Kuang, Qifan 1; Li, Yan 1; Huang, Ziyan 1; Gan, Wei 4; Xue, Yue 1; Li, Yizhou 1; Li, Menglong 1
	2017-03-06
发表期刊	SCIENTIFIC REPORTS
ISSN	2045-2322
卷号	7 页码:11
摘要	Genome-wide association studies (GWAS) have identified more than sixty single nucleotide polymorphisms (SNPs) associated with increased risk for type 2 diabetes (T2D). However, the identification of causal risk SNPs for T2D pathogenesis was complicated by the factor that each risk SNP is a surrogate for the hundreds of SNPs, most of which reside in non-coding regions. Here we provide a comprehensive annotation of 65 known T2D related SNPs and inspect putative functional SNPs probably causing protein dysfunction, response element disruptions of known transcription factors related to T2D genes and regulatory response element disruption of four histone marks in pancreas and pancreas islet. In new identified risk SNPs, some of them were reported as T2D related SNPs in recent studies. Further, we found that accumulation of modest effects of single sites markedly enhanced the risk prediction based on 1989 T2D samples and 3000 healthy controls. The AROC value increased from 0.58 to 0.62 by only using genotype score when putative risk SNPs were added. Besides, the net reclassification improvement is 10.03% on the addition of new risk SNPs. Taken together, functional annotation could provide a list of prioritized potential risk SNPs for the further estimation on the T2D susceptibility of individuals.
DOI	10.1038/srep43709
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[21375095] ; National Natural Science Foundation of China[21305096]
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000395545000001
出版者	NATURE PUBLISHING GROUP
引用统计	被引频次：5[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/7513
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Li, Yizhou; Li, Menglong
作者单位	1.Sichuan Univ, Coll Chem, Chengdu 610064, Peoples R China 2.Chinese Acad Sci, Shenzhen Inst Adv Technol, Ctr High Performance Comp, Shenzhen 518055, Peoples R China 3.Sichuan Univ, Coll Life Sci, Chengdu 610064, Peoples R China 4.Sichuan Univ, Coll Comp Sci, Chengdu 610064, Peoples R China
推荐引用方式 GB/T 7714	Wu, Yiming,Jing, Runyu,Dong, Yongcheng,et al. Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction[J]. SCIENTIFIC REPORTS,2017,7:11.
APA	Wu, Yiming.,Jing, Runyu.,Dong, Yongcheng.,Kuang, Qifan.,Li, Yan.,...&Li, Menglong.(2017).Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction.SCIENTIFIC REPORTS,7,11.
MLA	Wu, Yiming,et al."Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction".SCIENTIFIC REPORTS 7(2017):11.