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Brynedal, B.

Publications and source records attributed to Brynedal, B..

2 recordsLinked to original sources

Understanding genetic interactions and assessing the utility of the additive and multiplicative models through simulations

Interaction analysis is used to investigate the magnitude of an effect which two risk factors have on disease risk, and on each other. To study interactions, both additive and multiplicative models have been used, although their interpretations are not universally understood. In this study, we set out to investigate the resulting interactions of several risk factors relationships in additive or multiplicative scenarios using simulations, in the context of case-control studies. Our simulation set up showed that independent risk factors approach additive relative risk at low disease prevalence. However, risk factors that contribute to the same chain of events (i.e. have synergy) lead to multiplicative relative risk. Additionally, thresholds on the number of required risk factors for a disease (the multifactorial threshold model) lead to intermediaries between additive and multiplicative risks. We proposed a novel measure of interaction consistent with additive, multiplicative and multifactorial threshold models. Finally, we demonstrate the utility of the simulation strategy and discovered relationships on real data by analyzing and interpreting gene-gene odds ratios from a case-control rheumatoid arthritis study.

genetics↗

The association between the HLA-DRB1 shared epitope alleles and the risk of rheumatoid arthritis is influenced by massive gene-gene interactions.

In anti-citrullinated protein antibody positive rheumatoid arthritis (ACPA-positive RA), a particular subset of HLA-DRB1 alleles, called shared epitope alleles (SE), is the highest genetic risk factor. Here, we aimed to investigate whether gene-gene interactions influence this HLA-DRB1 related major disease risk; specifically, we set out to test if non-HLA SNPs, conferring low diseases risk on their own, can modulate the HLA-DRB1 SE effect to develop ACPA-positive RA.\n\nTo address this question, we computed the attributable proportion (AP) due to additive interaction at genome-wide level for two independent ACPA-positive RA cohorts: the Swedish EIRA and the North American NARAC. We found a strong enrichment of significant interactions (AP p-values<0.05) between the HLA-DRB1 SE alleles and a group of SNPs associated with ACPA-positive RA in both cohorts (Kolmogorov-Smirnov [KS] test D=0.35 for EIRA and D=0.25 for NARAC, p<2.2e-16 for both). Interestingly, 201 out of 1,492 SNPs in consistent interaction for both cohorts, were eQTLs in SE alleles context in PBMCs from ACPA-positive RA patients. Finally, we observed that the effect size of HLA-DRB1 SE alleles for disease decreases from 5.2 to 2.5 after discounting the risk alleles of the two top interacting SNPs (rs2476601 and rs10739581, AP FDR corrected p <0.05).\n\nOur data demonstrate that the association between the HLA-DRB1 SE alleles and the risk of ACPA-positive RA is modulated by massive genetic interactions with non-HLA genetic variants.

genetics↗