Illuminating the distribution of extreme evolutionary constraint in the human genome from fetal demise to severe developmental disorders

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Abstract Natural selection purges deleterious mutations from populations in genomic regions impacting survival or reproductive capacity. Recent genetic studies of massive population cohorts have revealed a continuous distribution across the human genome of this constraint on deleterious mutations. Large-scale association studies have found mutations in strongly constrained genomic regions to be major risk factors in many childhood developmental disorders (DDs), suggesting that highly constrained sequences are likely to play key roles in development. However, genetic studies of fetal demise after the first trimester (FD), an extreme outcome of DDs, have thus far been limited in scope and size. The establishment by my mentors of an international Fetal Genomics Consortium to sequence 10,500 samples (3,500 FD cases and their family members) ascertained for FD of suspected genetic etiology now offers an unprecedented opportunity to illuminate the most extreme consequences of mutation across individual genes and dosage sensitive genomic segments critical for human development. In this fellowship, I will integrate whole-genome sequencing and autopsy data from this cohort together with data from previously established DD cohorts to discover and functionally characterize mutationally intolerant loci in the human genome. I will first define patterns of genetic variation in FD across constraint metrics (loss-of-function, missense, and noncoding) and genomic variation classes (point mutations, indels, structural variants, and repeat expansions), and investigate biases in these patterns with respect to fetal sex and mutational parent-of-origin. I will then adapt a statistical framework for disease association capable of integrating evidence from all coding and noncoding variant classes with prioritization of constrained regions, which I will apply to perform novel gene discovery in FD (Aim 1). I will leverage these findings to generate functional predictions of mutationally intolerant loci by defining the biological networks of activity and the cell types in which they are likely to operate early in development (Aim 2). Finally, I will test these functional hypotheses across DDs that do not result in FD, including liveborn fetal structural abnormalities, neurodevelopmental disorders, and congenital anomalies (Aim 3). In parallel with these research aims, an exceptional team of six mentors and advisors across multiple disciplines, career stages, and institutions will provide didactic training, hands-on research support, regular opportunities for presentation in seminars and conferences, and a variety of soft skill development sessions that directly align with my career objectives during my PhD training. Collectively, the aims outlined in this proposal will take advantage of unique tools and resources to yield novel insights into the etiology of the extremes along the continuum of developmental anomalies and evolutionary constraint, and will serve as an outstanding training opportunity for me in computational, statistical, and functional disease genomics.