MAX-rank: a simple and robust genome-wide scan for case-control association studies

doi:10.1007/s00439-008-0514-8

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	MAX-rank: a simple and robust genome-wide scan for case-control association studies
	Li, Qizhai2,3 ; Yu, Kai 2; Li, Zhaohai 4,5; Zheng, Gang 1
	2008-07-01
发表期刊	HUMAN GENETICS
ISSN	0340-6717
卷号	123 期号:6 页码:617-623
摘要	In genome-wide association studies (GWAS), single-marker analysis is usually employed to identify the most significant single nucleotide polymorphisms (SNPs). The trend test has been proposed for analysis of case-control association. Three trend tests, optimal for the recessive, additive and dominant models respectively, are available. When the underlying genetic model is unknown, the maximum of the three trend test results (MAX) has been shown to be robust against genetic model misspecification. Since the asymptotic distribution of MAX depends on the allele frequency of the SNP, using the P-value of MAX for ranking may be different from using the MAX statistic. Calculating the P-value of MAX for 300,000 (300 K) or more SNPs is computationally intensive and the software and program to obtain the P-value of MAX are not widely available. On the other hand, the MAX statistic is very easy to calculate without complex computer programs. Thus, we study whether or not one could use the MAX statistic instead of its P-value to rank SNPs in GWAS. The approaches using the MAX and its P-value to rank SNPs are referred to as MAX-rank and P-rank. By applying MAX-rank and P-rank to simulated and four real datasets from GWAS, we found the ranks of SNPs with true association are very similar using both approaches. Thus, we recommend to use MAX-rank for genome-wide scans. After the top-ranked SNPs are identified, their P-values based on MAX can be calculated and compared with the significance level.
DOI	10.1007/s00439-008-0514-8
语种	英语
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000256659100004
出版者	SPRINGER
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/5467
专题	系统科学研究所
通讯作者	Zheng, Gang
作者单位	1.NHLBI, Off Biostat Res, Bethesda, MD 20892 USA 2.NCI, Biostat Branch, Bethesda, MD 20892 USA 3.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 4.George Washington Univ, Dept Stat, Washington, DC 20052 USA 5.NICHHD, Biometry & Math Stat Branch, Rockville, MD 20852 USA
推荐引用方式 GB/T 7714	Li, Qizhai,Yu, Kai,Li, Zhaohai,et al. MAX-rank: a simple and robust genome-wide scan for case-control association studies[J]. HUMAN GENETICS,2008,123(6):617-623.
APA	Li, Qizhai,Yu, Kai,Li, Zhaohai,&Zheng, Gang.(2008).MAX-rank: a simple and robust genome-wide scan for case-control association studies.HUMAN GENETICS,123(6),617-623.
MLA	Li, Qizhai,et al."MAX-rank: a simple and robust genome-wide scan for case-control association studies".HUMAN GENETICS 123.6(2008):617-623.