<i>Cis</i>-epistasis at the <i>LPA</i> locus and risk of cardiovascular diseases

Zeng, Lingyao, Moser, Sylvain, Mirza-Schreiber, Nazanin, Lamina, Claudia, Coassin, Stefan, Nelson, Christopher P, Annilo, Tarmo, Franzen, Oscar, Kleber, Marcus E, Mack, Salome
et al (show 25 more authors) (2022) <i>Cis</i>-epistasis at the <i>LPA</i> locus and risk of cardiovascular diseases. CARDIOVASCULAR RESEARCH, 118 (4). pp. 1088-1102.

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<h4>Aims</h4>Coronary artery disease (CAD) has a strong genetic predisposition. However, despite substantial discoveries made by genome-wide association studies (GWAS), a large proportion of heritability awaits identification. Non-additive genetic effects might be responsible for part of the unaccounted genetic variance. Here, we attempted a proof-of-concept study to identify non-additive genetic effects, namely epistatic interactions, associated with CAD.<h4>Methods and results</h4>We tested for epistatic interactions in 10 CAD case-control studies and UK Biobank with focus on 8068 SNPs at 56 loci with known associations with CAD risk. We identified a SNP pair located in cis at the LPA locus, rs1800769 and rs9458001, to be jointly associated with risk for CAD [odds ratio (OR) = 1.37, P = 1.07 × 10-11], peripheral arterial disease (OR = 1.22, P = 2.32 × 10-4), aortic stenosis (OR = 1.47, P = 6.95 × 10-7), hepatic lipoprotein(a) (Lp(a)) transcript levels (beta = 0.39, P = 1.41 × 10-8), and Lp(a) serum levels (beta = 0.58, P = 8.7 × 10-32), while individual SNPs displayed no association. Further exploration of the LPA locus revealed a strong dependency of these associations on a rare variant, rs140570886, that was previously associated with Lp(a) levels. We confirmed increased CAD risk for heterozygous (relative OR = 1.46, P = 9.97 × 10-32) and individuals homozygous for the minor allele (relative OR = 1.77, P = 0.09) of rs140570886. Using forward model selection, we also show that epistatic interactions between rs140570886, rs9458001, and rs1800769 modulate the effects of the rs140570886 risk allele.<h4>Conclusions</h4>These results demonstrate the feasibility of a large-scale knowledge-based epistasis scan and provide rare evidence of an epistatic interaction in a complex human disease. We were directed to a variant (rs140570886) influencing risk through additive genetic as well as epistatic effects. In summary, this study provides deeper insights into the genetic architecture of a locus important for cardiovascular diseases.

Item Type: Article
Uncontrolled Keywords: Statistical genetics, Epistasis, Coronary artery diseases, LPA
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Population Health
Depositing User: Symplectic Admin
Date Deposited: 07 Dec 2021 10:24
Last Modified: 18 Oct 2023 01:40
DOI: 10.1093/cvr/cvab136
Open Access URL: https://doi.org/10.1093/cvr/cvab136
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URI: https://livrepository.liverpool.ac.uk/id/eprint/3144854