The Genetics of Primary Immunodeficiency in Children

Studies of children with recurrent infection demonstrate that primary immunodeficiency (PID) has a significant genetic component. In PID, over 300 genes of high penetrance inherited mostly in autosomal recessive manner have already been identified. However, many children, including those with early onset immunodeficiency have not received a genetic diagnosis, despite use of targeted sequencing methods. I performed bioinformatic analysis in whole genome sequencing data in patients with immunodeficiency. These analyses were initially in a small cohort of affected children at Great Ormond Street in whom a genetic diagnosis was not known. I devised and utilised bioinformatic programs to identify novel genetic variants in this cohort. I evaluated the performance of whole genome sequence analyses with targeted gene panel analyses, which is the most utilised method of genetic diagnosis. To expand my analysis, I looked at a larger cohort of young people and adults with immunodeficiency as part of the large national collaborative project NIHR Bioresource Rare Diseases BRIDGE-PID project. I quantified the burden of rare coding variation in a case cohort compared to controls and used rare variant association analysis to identify potential novel candidate genes in primary immunodeficiency. The final chapter focuses on 2 novel genetic variants found in the cohort and our initial functional testing to verify genetic diagnosis. The work presented in this thesis demonstrates novel genetic causes of immunodeficiency and their functional implications. The results of my work have improved understanding of the genetic architecture of primary immunodeficiencies and has clinical utility in the diagnosis and subsequent treatment of immunodeficiency

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene's tolerance to haploinsufficiency and dominant loss of function. We analyzed the distribution of truncating variants across 16,260 autosomal protein coding genes in 11,546 individuals. We observed 39,893 truncating variants affecting 12,062 genes, which significantly differed from an expectation of 12,916 genes under a model of neutral de novo mutation (p<10-4). Extrapolating this to increasing numbers of sequenced individuals, we estimate that 10.8% of human genes do not tolerate heterozygous truncating variants. An additional 10 to 15% of truncated genes may be rescued by incomplete penetrance or compensatory mutations, or because the truncating variants are of limited functional impact. The study of protein truncating variants delineates the essential genome and, more generally, identifies rare heterozygous variants as an unexplored source of diversity of phenotypic traits and diseases

List of human genes and their probabilities of being intolerant to heterozygous protein truncating variants.

<p>Recalculation of the Supplementary Table 2 (doi:10.1371/journal.pcbi.1004647.s002) of the journal article "The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome" by Bartha and Rausell published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1004647). Probabilities in this dataset were computed using human variation data from the Exome Aggregation Consortium (http://exac.broadinstitute.org/).</p> <p>Methods described in that article is relevant for this dataset. All author and affiliation information in that article is relevant for this dataset.</p> <p>Credit for the original human variation data is for the Exome Aggregation Consortium (http://exac.broadinstitute.org/, doi:10.1038/nature19057).</p