Mapping causal genetic processes in non-Mendelian pediatric rare disease

总结 基因组测序导致儿科罕见疾病诊断的快速进步，但目前 60-70%的病例无法诊断。解释疾病变异的努力 倾向于集中在一个相对较小的一组罕见的或从头编码变异牵连孟德尔罕见 疾病;在这个提议中，我们概述了大大扩展变异解释方法的方法， 外显子组和包含复杂的非孟德尔疾病过程。我们之前已经提供了 整合功能基因组资源和计算工具，将变异与罕见疾病联系起来 表型我们的大规模i2 QTL诱导的多能干细胞（iPSC）资源提供了一个图谱， 在1，490个细胞系中的发育基因调控，揭示了差异同种型表达，新的 已知罕见疾病基因的剪接和调控作用，包括那些在体细胞中不表达的基因。 组织中此外，我们最近发布了IOGC模型，用于连接罕见变异，以通过 多个分子表型的全基因组测定，提供了一种系统的方法来揭示大效应 编码区和非编码区的罕见变异。结合人口规模的疾病生物库，我们 我已经展示了这些变体如何提供一个强大的系统来映射组合的下游后果 在顺式和反式调节网络上，识别与基因表达相关的失调的核心疾病基因模块， 对疾病风险的极端影响。在这项提案中，我们将进行全面的基因组和功能 对来自中西部参加儿童基因组答案（GA 4K）的儿科患者进行评估 儿童慈善医院的倡议，患有外显子组测序无法解释的疑似罕见疾病 （N= 1 860）。我们已经开始在疾病组织和患者中生成功能谱- 使用多种分子测定法衍生iPSC，目前包括WGS（N= 1，860）、PacBio Long-Read HiFi WGS（N=384）、单细胞ATAC-seq（N=433）和单细胞RNA-seq（N=528）。这些分析将允许 我们系统地评估它们在鉴定与下游分子相关的罕见变异中的用途， 罕见疾病中的失调。然后，我们将开发新的统计方法， 疾病变异-功能图，揭示解释复杂罕见疾病的因果诊断变异 表型这项建议建立在PI以前在综合功能基因组学研究方面的贡献之上 在NIH未诊断疾病网络和GTEx联盟中。现在，在多样化的，大规模的 GA 4K倡议，PI正在努力促进儿科罕见疾病的下一代诊断 基因组学与研究和临床团队合作。总的来说，我们希望我们的研究计划将导致 通过精确识别潜在的病因， 遗传疾病过程。

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.