Recessive and rare variant effects on common diseases and the immune cell transcriptome

Studying genetic variation provides insight into the biology of phenotypes, improves risk prediction, and contributes to developing better therapeutics. Different types of variant effects contribute to the heritability of a trait, and in this thesis I focused on recessive effects and rare, loss-of-function variant (LoF) effects. Genes & Health (G&H) is a cohort of ~50,000 British South Asians with elevated rates of consanguinity and consequently, increased homozygosity, therefore making it a suitable cohort to study both recessive effects and LoFs. Little is known about recessive effects on common diseases. Therefore, we searched for common and rare variants that had a recessive effect on common diseases in G&H. We imputed variants into 44,190 genotyped individuals, using two imputation panels: a set of 4,982 exomes from within the cohort, and the TOPMed-r2 panel. We then performed association testing with 898 common diseases, identifying 207 loci that reached standard genome-wide significance (p-value 5x10-8) under the recessive model and were more significant than under the additive model. Of these, about 70% demonstrated a nominally-significant (p-value 0.05) dominance deviation p-value. I discuss several findings in detail in my thesis. Among subtypes of variants with recessive effects, homozygous LoFs are of interest as they can function like naturally-occurring gene ‘knockouts’. We performed a recall-by-genotype of 114 individuals in G&H with rare, putative LoFs affecting immune genes, for single-cell RNA-sequencing (scRNAseq) of peripheral blood mononuclear cells (PBMCs). Cell-type-specific LoF effects on transcription have yet to be studied at scale, and in my thesis I discuss the three phases to building this unique dataset: firstly, the curation of true LoFs from bioinformatically-called putative LoFs (which are enriched for errors), secondly, LoF effects on the immune transcriptome at rest, and thirdly, LoF effects on the immune transcriptome after stimulation (by interferon alpha for innate immune processes, and by anti-CD3 for adaptive immune processes). We showed that direct knockdown effects of LoFs on the genes they affect can be detected in RNA expression, and that LoFs were associated with pathway derangements. These effects were cell-type- and context-specific. In summary, during my PhD, I leveraged the increased homozygosity within G&H to first demonstrate widespread recessive effects of common and rare variants on common diseases, and secondly, to profile the direct and indirect effects of rare LoFs, including homozygous LoFs, on the immune transcriptome.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2024

Author dc:creator

• Heng, Teng Hiang

Advisors dc:contributor.advisor

• Martin, Hilary C
• Trynka, Gosia

• Human Genetics
• Recessive
• Rare variants
• Medical Genetics
• Complex Traits
• Immunology
• Single cell transcriptomics

Licence

• https://www.repository.cam.ac.uk/bitstreams/6997ad6e-2567-468b-99ef-aeb1f068be94/download
• http://purl.org/NET/rdflicense/allrightsreserved

Language dc:language

eng

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.115780

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/379810