Although thousands of rare disorders are caused by single, deleterious, protein- coding variants, evidence suggests that common variants also contribute to risk for rare, neurodevelopmental disorders (NDDs). These are likely affecting the penetrance of protein-coding variants as well as expressivity, posing a major challenge in the interpretation of rare variants. An additional challenge is our incomplete understanding of which variants are likely to affect gene function. Due to the high burden of “variants of unknown significance” (VUS), there is a great need to develop molecular biomarkers of individual disorders which could be used as an intermediate phenotype to help determine whether a VUS is pathogenic or benign. For disorders which are due to mutations in spliceosomal components, global patterns of splicing changes may be a useful biomarker.

The research presented falls into three main projects. First, I investigated via genetically-predicted gene expression, whether cis-regulatory variants modify the penetrance of inherited, putatively damaging variants in NDD probands in the Deciphering Developmental Disorders (DDD) Study. To determine whether there were overall differences in predicted gene expression between probands and controls, I conducted a Transcriptome Association Study. I then tested whether the predicted gene expression of genes harbouring inherited, putatively damaging variants, is lower in undiagnosed NDD probands compared to controls. Finally, I investigated the modified penetrance of inherited, putatively damaging variants by comparing predicted gene expression between undiagnosed NDD probands and their unaffected, variant-transmitting parents.

Second, I further explored the role of common variants in severe NDDs using polygenic scores (PGS) in both DDD and the Genomics England (GEL) 100,000 Genomes project. I tested whether undiagnosed NDD probands over- or under- inherit PGS for NDDs and correlated traits. I found that NDD probands over-inherit PGS for NDDs and schizophrenia. To put these results into context, I compared unaffected parents of undiagnosed probands’ PGS to both controls and probands. I found that parents’ PGS are significantly different from controls’ PGS, but not from probands. Additionally, I explored sex differences in PGS, by examining both affected and unaffected individuals. I found preliminary evidence of a female protective effect in the context of common variation. Finally, I revisited the question of the modified penetrance of inherited, putatively damaging variants.

Third, using whole genome sequencing and bulk RNA sequencing of whole blood from GEL, I investigated differential splicing and gene expression in rare disorder probands with a pathogenic variant in the spliceosome. I found enrichment of differentially expressed genes for processes related to genes containing minor introns. Additionally, I found enrichment of genes involved in spliceosomal components among differentially spliced genes, suggesting a potential feedback loop for regulation of splicing.

These studies emphasise the importance of studying the convergence of common and rare variation, as well as the integration of functional data, in the context of rare disease genetics. Moreover, they highlight the need to collect phenotypic and genotypic data on parents and family members of rare disorder probands.