The Use of Imputed Sibling Genotypes in Sibship-Based Association Analysis: On Modeling Alternatives, Power and Model Misspecification
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When phenotypic, but no genotypic data are available for relatives of participants in genetic association studies, previous research has shown that family-based imputed genotypes can boost the statistical power when included in such studies. Here, using simulations, we compared the performance of two statistical approaches suitable to model imputed genotype data: the mixture approach, which involves the full distribution of the imputed genotypes and the dosage approach, where the mean of the conditional distribution features as the imputed genotype. Simulations were run by varying sibship size, size of the phenotypic correlations among siblings, imputation accuracy and minor allele frequency of the causal SNP. Furthermore, as imputing sibling data and extending the model to include sibships of size two or greater requires modeling the familial covariance matrix, we inquired whether model misspecification affects power. Finally, the results obtained via simulations were empirically verified in two datasets with continuous phenotype data (height) and with a dichotomous phenotype (smoking initiation). Across the settings considered, the mixture and the dosage approach are equally powerful and both produce unbiased parameter estimates. In addition, the likelihood-ratio test in the linear mixed model appears to be robust to the considered misspecification in the background covariance structure, given low to moderate phenotypic correlations among siblings. Empirical results show that the inclusion in association analysis of imputed sibling genotypes does not always result in larger test statistic. The actual test statistic may drop in value due to small effect sizes. That is, if the power benefit is small, that the change in distribution of the test statistic under the alternative is relatively small, the probability is greater of obtaining a smaller test statistic. As the genetic effects are typically hypothesized to be small, in practice, the decision on whether family-based imputation could be used as a means to increase power should be informed by prior power calculations and by the consideration of the background correlation.
KeywordsFamily-based imputation Mixture model Dosage model Robustness
Camelia C. Minică and Jacqueline M. Vink are supported by the ERC starting Grant 284167. The statistical analyses were carried out on the Genetic Cluster Computer (http://www.geneticcluster.org) which is financially supported by the Netherlands Scientific Organization (NWO 480-05-003), the Dutch Brain Foundation and the Department of Psychology and Education of the VU University Amsterdam. Data collection and genotyping were funded by the Netherlands Organization for Scientific Research (NWO: MagW/ZonMW grants 904-61-090, 985-10-002, 904-61-193, 480-04-004, 400-05-717, Addiction-31160008 Middelgroot-911-09-032, Spinozapremie 56-464-14192), Center for Medical Systems Biology (CSMB, NWO Genomics), NBIC/BioAssist/RK(2008.024), Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-NL, 184.021.007), the VU University’s Institute for Health and Care Research (EMGO+) and Neuroscience Campus Amsterdam (NCA), the European Science Foundation (ESF, EU/QLRT-2001-01254), the European Community’s Seventh Framework Program (FP7/2007–2013), ENGAGE (HEALTH-F4-2007-201413); the European Science Council (ERC Advanced, 230374), Rutgers University Cell and DNA Repository (NIMH U24 MH068457-06), the Avera Institute, Sioux Falls, South Dakota (USA), the National Institutes of Health (NIH, R01D0042157-01A), the Genetic Association Information Network (GAIN) of the Foundation for the US National Institutes of Health, the (NIMH, MH081802) and by the Grand Opportunity Grants 1RC2MH089951-01 and 1RC2 MH089995-01 from the NIMH. The authors have no conflict of interest to declare.
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