Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders

Abstract

To characterize the role of rare complete human knockouts in autism spectrum disorders (ASDs), we identify genes with homozygous or compound heterozygous loss-of-function (LoF) variants (defined as nonsense and essential splice sites) from exome sequencing of 933 cases and 869 controls. We identify a 2-fold increase in complete knockouts of autosomal genes with low rates of LoF variation (≤ 5% frequency) in cases and estimate a 3% contribution to ASD risk by these events, confirming this observation in an independent set of 563 probands and 4,605 controls. Outside the pseudoautosomal regions on the X chromosome, we similarly observe a significant 1.5-fold increase in rare hemizygous knockouts in males, contributing to another 2% of ASDs in males. Taken together, these results provide compelling evidence that rare autosomal and X chromosome complete gene knockouts are important inherited risk factors for ASD.

Figure 1. Expression Patterns of the Complete Knockouts

(A) The enrichment of rare complete knockouts in cases versus controls. (B) The enrichment observed in rare complete knockouts is not observed in the common complete knockouts. The x-axis indicates the average number of events per individual in cases and controls and the numbers above the barplots indicate the total number of such events in cases and controls, with the odds ratios (OR) shown above.