Association of exome sequences with plasma C-reactive protein levels in >9000 participants

Abstract

C-reactive protein (CRP) concentration is a heritable systemic marker of inflammation that is associated with cardiovascular disease risk. Genome-wide association studies have identified CRP-associated common variants associated in ∼25 genes. Our aims were to apply exome sequencing to (1) assess whether the candidate loci contain rare coding variants associated with CRP levels and (2) perform an exome-wide search for rare variants in novel genes associated with CRP levels. We exome-sequenced 6050 European-Americans (EAs) and 3109 African-Americans (AAs) from the NHLBI-ESP and the CHARGE consortia, and performed association tests of sequence data with measured CRP levels. In single-variant tests across candidate loci, a novel rare (minor allele frequency = 0.16%) CRP-coding variant (rs77832441-A; p.Thr59Met) was associated with 53% lower mean CRP levels (P = 2.9 × 10(-6)). We replicated the association of rs77832441 in an exome array analysis of 11 414 EAs (P = 3.0 × 10(-15)). Despite a strong effect on CRP levels, rs77832441 was not associated with inflammation-related phenotypes including coronary heart disease. We also found evidence for an AA-specific association of APOE-ε2 rs7214 with higher CRP levels. At the exome-wide significance level (P < 5.0 × 10(-8)), we confirmed associations for reported common variants of HNF1A, CRP, IL6R and TOMM40-APOE. In gene-based tests, a burden of rare/lower frequency variation in CRP in EAs (P ≤ 6.8 × 10(-4)) and in retinoic acid receptor-related orphan receptor α (RORA) in AAs (P = 1.7 × 10(-3)) were associated with CRP levels at the candidate gene level (P < 2.0 × 10(-3)). This inquiry did not elucidate novel genes, but instead demonstrated that variants distributed across the allele frequency spectrum within candidate genes contribute to CRP levels.

Decreased plasma C‐reactive protein levels in APOE ε4 allele carriers

“…This is consistent with the north‐south gradient, which has demonstrated that the APOE ε 4 allele frequency is the highest in Finland and Sweden 36. Although the link between the APOE ε 4 allele and low levels of plasma hs‐CRP is corroborated by several studies, most of the previous reports derive from considerably smaller cohorts, lacking convincing statistical power 37, 38, 39, 40, 41. To our knowledge, only one study has so far shown the link between APOE genotypes and hs‐CRP levels in a large population cohort of the same scale 41.…”

Genetics of Coronary Artery Disease

“…In contrast, C-reactive protein, Lp-PLA2, high-density lipoprotein (HDL) cholesterol, fibrinogen, and homocysteine, despite being robust risk markers, have not been shown to be causal. the general population 72 nor rare exonic variants associated with CRP levels 73 associate with CAD risk, demonstrating that CRP is not a causal risk factor and hence not a relevant drug target. Similarly, although data from epidemiological and clinical studies supported a potentially important role of lipoprotein-associated phospholipase A2 in atherosclerosis and its sequelae, 74,75 the genetic variants near PLA2G7 and CETP associated with LP-PLA2 levels and activity did not confer CAD risk.…”

The effect of phenotypic outliers and non-normality on rare-variant association testing

“…12,16 However, many quantitative phenotypes are not normally distributed in healthy populations (even after controlling for confounders that may contribute to non-normality). 17,18 We show that rare-variant association tests are uniquely susceptible to biases caused by outliers and non-normality.…”