Mapping causal genetic processes in non-Mendelian pediatric rare disease

Summary Genome sequencing has led to rapid advances in the diagnosis of pediatric rare diseases, but current approaches fail to diagnose 60-70% of all cases. Efforts toward the interpretation of disease variants has tended to focus on a relatively small set of rare or de novo coding variants implicated in Mendelian rare disease; in this proposal, we outline approaches to substantially expand variant interpretation methods beyond the exome and encompassing complex, non-Mendelian disease processes. We have previously provided integrated functional genomic resources and computational tools to connect variants to rare disease phenotypes. Our large-scale i2QTL induced Pluripotent Stem Cell (iPSC) resource provides a map of developmental gene regulation across 1,490 cell lines, uncovering differential isoform expression, novel splicing and regulatory effects in known rare disease genes, including in those not expressed in somatic tissues. Furthermore, we recently released the IOGC model for connecting rare variants to function through genomewide assays of multiple molecular phenotypes, providing a systematic method to uncover large-effect rare variants in both coding and non-coding regions. Integrated with population-scale disease biobanks, we have shown how these variants provide a powerful system to map the combined downstream consequences on both cis- and trans-regulatory networks, identifying dysregulated core disease gene modules associated with extreme effects on disease risk. In this proposal, we will conduct a comprehensive genomic and functional assessment of pediatric patients from across the Midwest enrolled in the Genomic Answers for Kids (GA4K) initiative at Children’s Mercy Hospital who have a suspected rare disease not explained by exome sequencing (N=1,860). We have already embarked on generating functional profiles across disease tissues and patient- derived iPSCs using multiple molecular assays, currently consisting of WGS (N=1,860), PacBio Long-Read HiFi WGS (N=384), single-cell ATAC-seq (N=433) and single-cell RNA-seq (N=528). These assays will allow us to systematically evaluate their use in identifying rare variants associated with downstream molecular dysregulation in rare disease. We will then develop new statistical approaches integrating our pediatric rare disease variant-to-function maps to uncover causal diagnostic variation explaining complex rare disease phenotypes. This proposal builds on the PI’s previous contributions in integrated functional genomics research within the NIH Undiagnosed Diseases Network and GTEx consortiums. Now, within the diverse, large-scale GA4K initiative, the PI is leading efforts to catalyze next-generation diagnostics in pediatric rare disease genomics in collaboration with research and clinical teams. Overall, we expect our research program will lead to the improved diagnosis of pediatric rare diseases through the precise identification of underlying causal genetic disease processes.