Analysis of Inbred Mouse strains' High-Impact Genotype-phenotype Hypotheses (AIMHIGH) reveals novel disease-causing candidate genes

Abstract

Inbred mouse strains reveal the molecular basis of mammalian traits and diseases, particularly recessive ones. We utilized mouse community curated resources to set up an automated screen to discover novel testable gene function hypotheses. Using 11,832 community contributed strain-differentiating experiments and trait presence/absence scoring, we searched for all experiments where strains can be split by their phenotypic values (e.g., high vs. low responders). Then, using 48 sequenced strains, we found one or more candidate gene for each experiment where homozygous high-impact variants (such as stopgain, frameshifts) segregate strains into these same binary grouping. Our approach rediscovered 212 known gene-phenotype relationships, almost always highlighting potentially novel causal variants, as well as thousands of gene function hypotheses. To help find the most exciting hypotheses, we improved the state of the art in machine learning driven literature-based discovery (LBD). Reading on our top 3 ranked candidate genes per experiment reveals 80% of rediscovered relationships, compared to 5% reading at random. We proposed 1,842 novel gene-phenotype testable hypotheses using our approach. We built a web portal at aimhigh.stanford.edu to allow researchers to view all our testable hypotheses in detail. Our open-source code can be rerun as more sequenced strains and phenotyping experiments become available.