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Joint Association Testing of Common and Rare Genetic Variants Using Hierarchical Modeling


  • Niall J. Cardin,

  • Joel A. Mefford,

  • John S. Witte

    Corresponding author
    • Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, California
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Correspondence to: John S. Witte, Department of Epidemiology and Biostatistics, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, Room 388, San Francisco, CA 94158-9001. E-mail:


New sequencing technologies provide an opportunity for assessing the impact of rare and common variants on complex diseases. Several methods have been developed for evaluating rare variants, many of which use weighted collapsing to combine rare variants. Some approaches require arbitrary frequency thresholds below which to collapse alleles, and most assume that effect sizes for each collapsed variant are either the same or a function of minor allele frequency. Some methods also further assume that all rare variants are deleterious rather than protective. We expect that such assumptions will not hold in general, and as a result performance of these tests will be adversely affected. We propose a hierarchical model, implemented in the new program CHARM, to detect the joint signal from rare and common variants within a genomic region while properly accounting for linkage disequilibrium between variants. Our model explores the scale, rather than the center of the odds ratio distribution, allowing for both causative and protective effects. We use cross-validation to assess the evidence for association in a region. We use model averaging to widen the range of disease models under which we will have good power. To assess this approach, we simulate data under a range of disease models with effects at common and/or rare variants. Overall, our method had more power than other well-known rare variant approaches; it performed well when either only rare, or only common variants were causal, and better than other approaches when both common and rare variants contributed to disease.