Exome-wide analysis of copy number variation shows association of the human leukocyte antigen region with asthma in UK Biobank

Fawcett, Katherine A.; Demidov, German; Shrine, Nick; Paynton, Megan L.; Ossowski, Stephan; Sayers, Ian; Wain, Louise V.; Hollox, Edward J.

Abstract

Background:
The role of copy number variants (CNVs) in susceptibility to asthma is not well understood. This is, in part, due to the difficulty of accurately measuring CNVs in large enough sample sizes to detect associations. The recent availability of whole-exome sequencing (WES) in large biobank studies provides an unprecedented opportunity to study the role of CNVs in asthma.
Methods:
We called common CNVs in 49,953 individuals in the first release of UK Biobank WES using ClinCNV software. CNVs were tested for association with asthma in a stage 1 analysis comprising 7098 asthma cases and 36,578 controls from the first release of sequencing data. Nominally-associated CNVs were then meta-analysed in stage 2 with an additional 17,280 asthma cases and 115,562 controls from the second release of UK Biobank exome sequencing, followed by validation and fine-mapping.
Results:
Five of 189 CNVs were associated with asthma in stage 2, including a deletion overlapping the HLA-DQA1 and HLA-DQB1 genes, a duplication of CHROMR/PRKRA, deletions within MUC22 and TAP2, and a duplication in FBRSL1. The HLA-DQA1, HLA-DQB1, MUC22 and TAP2 genes all reside within the human leukocyte antigen (HLA) region on chromosome 6. In silico analyses demonstrated that the deletion overlapping HLA-DQA1 and HLA-DQB1 is likely to be an artefact arising from under-mapping of reads from non-reference HLA haplotypes, and that the CHROMR/PRKRA and FBRSL1 duplications represent presence/absence of pseudogenes within the HLA region. Bayesian fine-mapping of the HLA region suggested that there are two independent asthma association signals. The variants with the largest posterior inclusion probability in the two credible sets were an amino acid change in HLA-DQB1 (glutamine to histidine at residue 253) and a multi-allelic amino acid change in HLA-DRB1 (presence/absence of serine, glycine or leucine at residue 11).
Conclusions:
At least two independent loci characterised by amino acid changes in the HLA-DQA1, HLA-DQB1 and HLA-DRB1 genes are likely to account for association of SNPs and CNVs in this region with asthma. The high divergence of haplotypes in the HLA can give rise to spurious CNVs, providing an important, cautionary tale for future large-scale analyses of sequencing data.

Citation

Fawcett, K. A., Demidov, G., Shrine, N., Paynton, M. L., Ossowski, S., Sayers, I., Wain, L. V., & Hollox, E. J. (2022). Exome-wide analysis of copy number variation shows association of the human leukocyte antigen region with asthma in UK Biobank. BMC Medical Genomics, 15(1), Article 119. https://doi.org/10.1186/s12920-022-01268-y

• Journal Article Type: Article
• Acceptance Date: May 10, 2022
• Online Publication Date: May 21, 2022
• Publication Date: 2022-12
• Deposit Date: Mar 14, 2024
• Publicly Available Date: Mar 15, 2024
• Journal: BMC Medical Genomics
• Electronic ISSN: 1755-8794
• Publisher: Springer Verlag
• Peer Reviewed: Peer Reviewed
• Volume: 15
• Issue: 1
• Article Number: 119
• DOI: https://doi.org/10.1186/s12920-022-01268-y
• Keywords: Copy number variants, Exome sequencing, UK Biobank, Asthma, Genetic association, Fine-mapping, Human leukocyte antigen
• Public URL: https://nottingham-repository.worktribe.com/output/23529223
• Publisher URL: https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-022-01268-y
• Additional Information: Received: 27 February 2022; Accepted: 10 May 2022; First Online: 21 May 2022; : ; : This study used anonymised data from UK Biobank, which comprises over 500,000 volunteer participants aged 40–69years recruited across Great Britain between 2006 and 2010. All participants provided written, informed consent. No individuals younger than 16years of age were recruited and therefore consent from parents or legal guardians was not appropriate. The protocol and consent were approved by the UK Biobank’s Research Ethics Committee. Our analysis was conducted under approved UK Biobank data application number 56607.; : Not applicable.; : LVW has research funding (outside of submitted work) from GSK and Orion Pharma and consultancy for Galapagos. All other authors declare that they have no competing interests.