COBT: A gene-based rare variant burden test for case-only study designs using aggregated genotypes from public reference cohorts

More than 4000 rare genetic diseases affect 1 in 16 people, yet ∼50% of patients remain undiagnosed after genetic testing. Identifying genotype-phenotype associations is challenged by small cohorts and high clinical and genetic heterogeneity. Rare variant burden tests increase statistical power in case-control studies, but are limited in rare disease research due to the lack of matched controls in retrospective studies. Recently proposed case-only aggregation tests assess the number of individuals with damaging variants under dominant or recessive models, but fail to capture additive effects, hypomorphic variants, or heterogeneous inheritance modes. Here, we present the Case-Only Burden Test (COBT), a gene-based burden test for case-only designs accounting for multiple variants per individual and their putative additive effects. COBT uses a Poisson model to test for excess variants in a gene compared to expectations from general population mutation rates. We validated the model’s assumptions and goodness-of-fit on a control cohort from the 1000 Genomes Project, where COBT showed low false-positive rates and outperformed alternative case-only tests. Applied to 478 ciliopathy patients, COBT re-identified known causal genes and highlighted novel candidate variants in unsolved cases. COBT enables gene discovery in case-only rare disease cohorts and is available at https://github.com/RausellLab/COBT .