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... Show moreGenotype 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 advance online publication, 21 December 2011; doi:10.1038/ejhg.2011.231. Show less
Blom, J.W.; Ruijter, W. de; Witteman, J.C.M.; Assendelft, W.J.J.; Breteler, M.M.B.; Hofman, A.; Gussekloo, J. 2011
There are indications that in persons of older age, systolic blood pressure (SBP) is no longer associated with mortality. This raises the question whether the predictive value of SBP changes from... Show moreThere are indications that in persons of older age, systolic blood pressure (SBP) is no longer associated with mortality. This raises the question whether the predictive value of SBP changes from younger to older age groups. Analysis in the Rotterdam Study, a population-based prospective cohort study among 4,612 participants aged ≥55 years without previous cardiovascular disease and with a median follow-up of 14.9 (interquartile range, 11.1-15.8) years. Within four age groups (55-64, 65-74, 75-84, ≥85 years), the predictive value of baseline SBP for mortality was studied. From age 55 to ≥85 years, risk of all-cause mortality associated with SBP ≥160 mmHg decreased from HR 1.7 (95%CI 1.2-2.2) to HR 0.7 (95%CI 0.4-1.1), p for trend <0.001. For participants with SBP 140-159 mmHg, the risk decreased from HR 1.2 (95%CI 0.9-1.5) to HR 0.7 (95%CI 0.5-1.1), p for trend <0.001. Analyses in the 5-year age groups showed an increased risk with higher SBPs up to age 75 years. After 75 years, a trend towards SBP no longer being associated with an increased mortality risk was seen in our study. These findings need to be considered with recently reported beneficial effects of antihypertensive treatment in this age group. Show less
Chambers, J.C.; Zhang, W.H.; Sehmi, J.; Li, X.Z.; Wass, M.N.; Harst, P. van der; ... ; Meta-Anal Glucose Insulin-Related 2011
