A meta-analysis of genome-wide data from five European isolates reveals an association of COL22A1, SYT1, and GABRR2 with serum creatinine level

Abstract

Background: Serum creatinine (S CR) is the most important biomarker for a quick and non-invasive assessment of kidney function in population-based surveys. A substantial proportion of the inter-individual variability in S CR level is explicable by genetic factors.

Methods: We performed a meta-analysis of genome-wide association studies of S CR undertaken in five population isolates ('discovery cohorts'), all of which are part of the European Special Population Network (EUROSPAN) project. Genes showing the strongest evidence for an association with SCR (candidate loci) were replicated in two additional population-based samples ('replication cohorts').

Results: After the discovery meta-analysis, 29 loci were selected for replication. Association between SCR level and polymorphisms in the collagen type XXII alpha 1 (COL22A1) gene, on chromosome 8, and in the synaptotagmin-1 (SYT1) gene, on chromosome 12, were successfully replicated in the replication cohorts (p value = 1.0 x 10(-6) and 1.7 x 10(-4), respectively). Evidence of association was also found for polymorphisms in a locus including the gamma-aminobutyric acid receptor rho-2 (GABRR2) gene and the ubiquitin-conjugating enzyme E2-J1 (UBE2J1) gene (replication p value = 3.6 x 10(-3)). Previously reported findings, associating glomerular filtration rate with SNPs in the uromodulin (UMOD) gene and in the schroom family member 3 (SCHROOM3) gene were also replicated.

Conclusions: While confirming earlier results, our study provides new insights in the understanding of the genetic basis of serum creatinine regulatory processes. In particular, the association with the genes SYT1 and GABRR2 corroborate previous findings that highlighted a possible role of the neurotransmitters GABAA receptors in the regulation of the glomerular basement membrane and a possible interaction between GABAA receptors and synaptotagmin-I at the podocyte level.

Figure 1

Workflow of the discovery and replication stages of the study (for details, see the Statistical Analysis section).

Figure 2

Manhattan plot of -log₁₀ (p values) from the meta-analysis of five GWA studies. GWA results were combined across all studies by fixed-effects meta-analysis using inverse variance weighting. Square dots indicate SNPs satisfying criteria for selection of candidate regions. SNPs within replicated regions are colored in dark red and SNPs within non-replicated regions in pink. The genomic control factor of λ = 1.004, assessed by the quantile-quantile plot in the upper-right panel, indicates that cryptic relatedness and population structure have been modeled appropriately.

Figure 3

Results of the false discovery rate analysis. -log₁₀ (Fisher p value) of the replication analysis (orange) and -log₁₀ (significance thresholds) for FDR (black) are plotted for each candidate locus. According to [41], FDR thresholds have been calculated as i/m × α, with α = 0.05, m = no. of test (i.e.: no. of regions, 29), and i ranging between 1 and 29. After sorting the Fisher p values in ascending order, the first k tests for which the p value is ≤ threshold are significant.

Figure 4

Forest plots of betas and standard errors, with 95% confidence intervals, for the most significant SNPs in the three replicated loci (A, B, and C) and for the most significant SNP of the discovery meta-analysis (D). The pooled estimate was obtained with a fixed-effect meta-analysis using the metafor package in R http://www.wvbauer.com/index.htm.

Figure 5

Genomic structure and association results at the COL22A1 locus. Upper panel: -log₁₀(p values) are plotted by physical position for the EUROSPAN discovery meta-analysis (red squares), the popgen (blue squares) and the Korcula (green squares) replication cohorts. Middle panel: linkage disequilibrium (LD) as quantified by r² (the higher the LD, the darker the color, with black indicating perfect LD), based upon the HapMap-CEU database, Phase III/Release 2, (NCBI build 36). Lower panel: genes located in the plotted region, with coding exons indicated by black rectangles and orientation.

Figure 6

Genomic structure and association results at the GABRR2-UBE2J1 locus. Upper panel: -log₁₀(p values) are plotted by physical position for the EUROSPAN discovery meta-analysis (red squares), the popgen (blue squares) and the Korcula (green squares) replication cohorts. Middle panel: linkage disequilibrium (LD) as quantified by r² (the higher the LD, the darker the color, with black indicating perfect LD), based upon the HapMap-CEU database, Phase III/Release 2, (NCBI build 36). Lower panel: genes located in the plotted region, with coding exons indicated by black rectangles and orientation.