Strategies for genetic model specification in the screening of genome-wide meta-analysis signals for further replication.

BACKGROUND: Meta-analysis is increasingly being employed as a screening procedure in large-scale association studies to select promising variants for follow-up studies. However, standard methods for meta-analysis require the assumption of an underlying genetic model, which is typically unknown a priori. This drawback can introduce model misspecifications, causing power to be suboptimal, or the evaluation of multiple genetic models, which augments the number of false-positive associations, ultimately leading to waste of resources with fruitless replication studies. We used simulated meta-analyses of large genetic association studies to investigate naïve strategies of genetic model specification to optimize screenings of genome-wide meta-analysis signals for further replication. METHODS: Different methods, meta-analytical models and strategies were compared in terms of power and type-I error. Simulations were carried out for a binary trait in a wide range of true genetic models, genome-wide thresholds, minor allele frequencies (MAFs), odds ratios and between-study heterogeneity (τ²). RESULTS: Among the investigated strategies, a simple Bonferroni-corrected approach that fits both multiplicative and recessive models was found to be optimal in most examined scenarios, reducing the likelihood of false discoveries and enhancing power in scenarios with small MAFs either in the presence or in absence of heterogeneity. Nonetheless, this strategy is sensitive to τ² whenever the susceptibility allele is common (MAF ≥ 30%), resulting in an increased number of false-positive associations compared with an analysis that considers only the multiplicative model. CONCLUSION: Invoking a simple Bonferroni adjustment and testing for both multiplicative and recessive models is fast and an optimal strategy in large meta-analysis-based screenings. However, care must be taken when examined variants are common, where specification of a multiplicative model alone may be preferable.

Critical interpretation of Cochran's Q test depends on power and prior assumptions about heterogeneity.

We describe how an appropriate interpretation of the Q-test depends on its power to detect a given typical amount of between-study variance (τ(2)) as well as prior beliefs on heterogeneity. We illustrate these concepts in an evaluation of 1011 meta-analyses of clinical trials with ⩾4 studies and binary outcomes. These concepts can be seen as an application of the Bayes theorem. Across the 1011 meta-analyses, power to detect typical heterogeneity was low in most situations. Thus, usually a non-significant Q test did not change perceptibly prior convictions on heterogeneity. Conversely, significant results for the Q test typically augmented considerably the probability of heterogeneity. The posterior probability of heterogeneity depends on what τ(2) we want to detect. With the same approach, one may also estimate the posterior probability for the presence of heterogeneity that is large enough to annul statistically significant summary effects; that is half the average within-study variance of the combined studies; and that is able to change the summary effect estimate of the meta-analysis by 20%. The discussed analyses are exploratory, and may depend heavily on prior assumptions when power for the Q-test is low. Statistical heterogeneity in meta-analyses should be cautiously interpreted considering the power to detect a specific τ(2) and prior assumptions about the presence of heterogeneity. Copyright © 2010 John Wiley & Sons, Ltd.

Discovery properties of genome-wide association signals from cumulatively combined data sets.

Genetic effects for common variants affecting complex disease risk are subtle. Single genome-wide association (GWA) studies are typically underpowered to detect these effects, and combination of several GWA data sets is needed to enhance discovery. The authors investigated the properties of the discovery process in simulated cumulative meta-analyses of GWA study-derived signals allowing for potential genetic model misspecification and between-study heterogeneity. Variants with null effects on average (but also between-data set heterogeneity) could yield false-positive associations with seemingly homogeneous effects. Random effects had higher than appropriate false-positive rates when there were few data sets. The log-additive model had the lowest false-positive rate. Under heterogeneity, random-effects meta-analyses of 2-10 data sets averaging 1,000 cases/1,000 controls each did not increase power, or the meta-analysis was even less powerful than a single study (power desert). Upward bias in effect estimates and underestimation of between-study heterogeneity were common. Fixed-effects calculations avoided power deserts and maximized discovery of association signals at the expense of much higher false-positive rates. Therefore, random- and fixed-effects models are preferable for different purposes (fixed effects for initial screenings, random effects for generalizability applications). These results may have broader implications for the design and interpretation of large-scale multiteam collaborative studies discovering common gene variants.