How to deal with the early GWAS data when imputing and combining different arrays is necessary

被引：19
作者：
Uh, Hae-Won [1 ,2 ]
Deelen, Joris [1 ,2 ]
Beekman, Marian [1 ]
Helmer, Quinta
Rivadeneira, Fernando [2 ,3 ,4 ]
Hottenga, Jouke-Jan [5 ]
Boomsma, Dorret I. [5 ]
Hofman, Albert [2 ,3 ,4 ]
Uitterlinden, Andre G. [2 ,3 ,4 ]
Slagboom, P. E. [1 ,2 ]
Bohringer, Stefan
Houwing-Duistermaat, Jeanine J.
机构：
[1] Leiden Univ, Med Ctr, Dept Med Stat & Bioinformat, Sect Mol Epidemiol, NL-2300 RC Leiden, Netherlands
[2] Leiden Univ, Med Ctr, Netherlands Consortium Hlth Ageing, NL-2300 RC Leiden, Netherlands
[3] Erasmus MC, Dept Epidemiol, Rotterdam, Netherlands
[4] Erasmus MC, Dept Internal Med, Rotterdam, Netherlands
[5] Vrije Univ Amsterdam, Dept Biol Psychol, Amsterdam, Netherlands
来源：
EUROPEAN JOURNAL OF HUMAN GENETICS | 2012年 / 20卷 / 05期
关键词：
GWAS; imputation; quality control; GENOME-WIDE ASSOCIATION; IMPUTATION;
D O I：
10.1038/ejhg.2011.231
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Genotype imputation has become an essential tool in the analysis of genome-wide association scans. This technique allows investigators to test association at ungenotyped genetic markers, and to combine results across studies that rely on different genotyping platforms. In addition, imputation is used within long-running studies to reuse genotypes produced across generations of platforms. Typically, genotypes of controls are reused and cases are genotyped on more novel platforms yielding a case-control study that is not matched for genotyping platforms. In this study, we scrutinize such a situation and validate GWAS results by actually retyping top-ranking SNPs with the Sequenom MassArray platform. We discuss the needed quality controls (QCs). In doing so, we report a considerable discrepancy between the results from imputed and retyped data when applying recommended QCs from the literature. These discrepancies appear to be caused by extrapolating differences between arrays by the process of imputation. To avoid false positive results, we recommend that more stringent QCs should be applied. We also advocate reporting the imputation quality measure (R-T(2)) for the post-imputation QCs in publications. European Journal of Human Genetics (2012) 20, 572-576; doi:10.1038/ejhg.2011.231; published online 21 December 2011
引用
收藏
页码：572 / 576
页数：5
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