A power-based sliding window approach to evaluate the clinical impact of rare genetic variants

Systematic determination of rare and novel variant pathogenicity remains a major challenge, even when there is an established association between a gene and phenotype. Here we present Power Window (PW), a novel sliding window technique that identifies the clinically impactful regions of a gene using population-scale clinico-genomic datasets. By sizing windows based on the number of variant carriers, rather than the number of variants or nucleotides, statistical power is held constant during analysis, enabling the localization of clinical impact as well as the removal of unassociated gene regions. This method can be used to focus on: specific variant types such as loss of function (LoF) or other coding; parts of a gene, such as those expressed in different tissues; or isolating gene regions with opposite directions of effect. Using a training set of 300K exomes from the UKBiobank (UKB), we developed PW-based LoF and coding models for well-established gene-disease associations and tested their accuracy in two additional cohorts (128k exomes from the UKB and 30k exomes from the Healthy Nevada Project (HNP)). The significant PW models retained a mean of 64% of the rare variant carriers in each gene (range 16-98%), with quantitative traits showing a mean effect size improvement of 48% compared to aggregating rare variants across the entire gene, and the odds ratios for binary traits improving by a mean of 2.4-fold. PW showcases that EHR-based statistical analyses can accurately distinguish between novel coding variants that will have high phenotypic penetrance in a population and those that will not, unlocking new potential for population genetic screening.