Discovery of novel eGFR-associated multiple independent signals using a quasi-adaptive method

A decreased estimated glomerular filtration rate (eGFR) leading to chronic kidney disease is a significant public health problem. Kidney function is a heritable trait, and recent application of genome-wide association studies (GWAS) successfully identified multiple eGFR-associated genetic loci. To increase statistical power for detecting independent associations in GWAS loci, we improved our recently developed quasi-adaptive method estimating SNP-specific alpha levels for the conditional analysis, and applied it to the GWAS meta-analysis results of eGFR among 783,978 European-ancestry individuals. Among known eGFR loci, we revealed 19 new independent association signals that were subsequently replicated in the United Kingdom Biobank (n = 408,608). These associations have remained undetected by conditional analysis using the established conservative genome-wide significance level of 5 × 10–8. Functional characterization of known index SNPs and novel independent signals using colocalization of conditional eGFR association results and gene expression in cis across 51 human tissues identified two potentially causal genes across kidney tissues: TSPAN33 and TFDP2, and three candidate genes across other tissues: SLC22A2, LRP2, and CDKN1C. These colocalizations were not identified in the original GWAS. By applying our improved quasi-adaptive method, we successfully identified additional genetic variants associated with eGFR. Considering these signals in colocalization analyses can increase the precision of revealing potentially functional genes of GWAS loci.


Content description:
Figures 1-57: Represent regional association plots for loci with replicated novel independent signals identified by the quasi-adaptive method. Three plots were shown for each locus. The first plot shows a regional association plot based on eGFR association analysis performed on UKBB individual-level genotype data among European-ancestry participants with highlighted novel independent signal and known index SNP, respectively, as an LD reference variant (colored purple). The second plot is a regional association plot based on conditional eGFR association analysis conditioned on known index SNP performed on UKBB individual-level genotype data among European-ancestry participants with the novel independent signal as LD reference variant (colored purple). The third plot is a regional association plot based on conditional eGFR association analysis conditioned on a novel independent signal performed on UKBB individual-level genotype data among European-ancestry participants with known index SNP as LD reference variant (colored purple). The details of the conditional eGFR association analyses were explained for each plot separately.

Figures 58-59:
Colocalization of eGFR-associated known index SNPs with gene expression (cis eQTLs) across all tissues. Figure 58 and Figure 59 depict colocalization results based on unconditional and conditional eGFR association analyses, respectively. Genes with at least one posterior probability of colocalization (PP ≥ 80%) across tissues (x axis) are shown with the respective underlying variants and chromosome numbers (y axis). Colocalizations are illustrated as dots, where dot size corresponds to the PP and are colored according to the predicted change in gene expression relative to the lower eGFR. Color coding on y axis reflects locus.
Figures 60-76: Represent colocalization results for known index SNP and novel independent signal at each locus across all tissues. Plot A and Plot B show posterior probability of colocalization (PP of one common variant) based on eGFR association analysis (y axis) and conditional eGFR association analysis (x axis) for known index SNP and novel independent signal, respectively. The gray dash line represents PP = 80%, with high evidence for colocalization (PP > 80%) shown in color and low evidence (PP < 80%) shown in gray. The blue dashed line corresponds to the diagonal line. The details of the conditional eGFR association analyses were explained for each plot separately.
Figure 14: Regional association plot for secondary signal rs3730071 (12: 49168798_C/A) using conditional eGFR association analysis (conditioned on index SNP) Figure 15: Regional association plot for index SNP rs2634675 (12: 48740855_A/G) using conditional eGFR association analysis (conditioned on secondary signal).
Figure 17: Regional association plot for tertiary signal rs807574 (2:15807239_A/G) using conditional eGFR association analysis (conditioned on index SNP and secondary signal).
Figure 18: Regional association plot for index SNP rs807624 (2:15782471_G/T) using conditional eGFR association analysis (conditioned on secondary signal and tertiary signal).
Figure 20: Regional association plot for tertiary signal rs13227214 (7:128740355_C/G) using conditional eGFR association analysis (conditioned on index SNP and secondary signal).
Figure 21: Regional association plot for index SNP rs3757387 (7:128576086_T/C) using conditional eGFR association analysis (conditioned on secondary signal and tertiary signal).
Figure 23: Regional association plot for tertiary signal rs81205 (11:2798804_A/C) using conditional eGFR association analysis (conditioned on index SNP secondary signal and signal of 4 th ).
Figure 24: Regional association plot for index SNP rs233438 (11:2794392_G/A) using conditional eGFR association analysis (conditioned on secondary signal, tertiary signal, signal of 4 th ).
Figure 26: Regional association plot for tertiary signal rs1193692 (11: 65504069_A/C) using conditional eGFR association analysis (conditioned on index SNP and secondary signal).
Figure 27: Regional association plot for index SNP rs11227260 (11: 65461158_G/T) using conditional eGFR association analysis (conditioned on secondary signal and tertiary signal).    Figure 32: Regional association plot for signal of 4 th rs2075251 (2:170011458_T/A) using conditional eGFR association analysis (conditioned on index SNP, secondary signal, and tertiary signal).
Figure 33: Regional association plot for index SNP rs35472707 (2:169995581_C/T) using conditional eGFR association analysis (conditioned on secondary signal, tertiary signal, and signal of 4 th ).
Figure 35: Regional association plot for signal of 4 th rs6912283 (6:43364494_G/A) using conditional eGFR association analysis (conditioned on index SNP, secondary signal, and tertiary signal).
Figure 36: Regional association plot for index SNP rs881858 (6:43806609_G/A) using conditional eGFR association analysis (conditioned on secondary signal, tertiary signal, and signal of 4 th ).
Figure 50: Regional association plot for signal of 5 th rs76426793 (6:160566392_ T/A) using conditional eGFR association analysis (conditioned on index SNP, secondary signal, tertiary signal, and signal of 4 th ).
Figure 51: Regional association plot for index SNP rs12207180 (6:160633107_ T/A) using conditional eGFR association analysis (conditioned on secondary signal, tertiary signal, and signal of 4 th , and signal of 5 th ).
Figure 53: Regional association plot for signal of 5 th rs2695565 (7:156397312_ A/G) using conditional eGFR association analysis (conditioned on index SNP, secondary signal, tertiary signal, signal of 4 th and signal of 6 th ).
Figure 54: Regional association plot for index SNP rs2365286 (7:156258179_G/A) using conditional eGFR association analysis (conditioned on secondary signal, tertiary signal, signal of 4 th , signal of 5 th and signal of 6 th ).
Figure 56: Regional association plot for signal of 6 th rs6951593 (7:156270725_ A/G) using conditional eGFR association analysis (conditioned on index SNP, secondary signal, tertiary signal, signal of 4 th , and signal of 5 th ).
Figure 57: Regional association plot for index SNP rs2365286 (7:156258179_G/A) using conditional eGFR association analysis (conditioned on secondary signal, tertiary signal, signal of 4 th , signal of 5 th , signal of 6 th ).

Figure 58:
Colocalization of the known index SNPs using unconditional eGFR association analysis. Figure 59: Colocalization of the known index SNPs using conditional eGFR association analysis.

Figure 61:
Colocalization results for index SNP rs807624 and tertiary signal rs807574 on chromosome 2. Plot A: conditional eGFR association analysis adjusted for secondary signal (rs4441471) and tertiary signal (rs807574). Plot B: conditional eGFR association analysis adjusted for index SNP (rs807624) and secondary signal (rs4441471).

Figure 62:
Colocalization results for index SNP rs1397764 and secondary signal rs147877018 on chromosome 3. Plot A: conditional eGFR association analysis adjusted for secondary signal (rs147877018). Plot B: conditional eGFR association anaylsis adjusted for index SNP (rs1397764).

Figure 64:
Colocalization results for index SNP rs6921580 and secondary signal rs3904600 on chromosome 6. Plot A: conditional eGFR association analysis adjusted for secondary signal (rs3904600). Plot B: conditional eGFR association analysis adjusted for index SNP (rs6921580).

Figure 67:
Colocalization results for index SNP rs3757387 and tertiary signal rs13227214 on chromosome 7. Plot A: conditional eGFR association analysis adjusted for secondary signal (rs62491533) and tertiary signal (rs13227214). Plot B: conditional eGFR association analysis adjusted for index SNP (rs3757387) and secondary signal (rs62491533).

Figure 69:
Colocalization results for index SNP rs2039424 and signal of 4 th rs4745268 on chromosome 9. Plot A: conditional GWAS adjusted for secondary signal (rs7019089) and signal of 4 th (rs4745268). Plot B: conditional GWAS adjusted for index SNP (rs2039424) and secondary signal (rs7019089).

Figure 70:
Colocalization results for index SNP rs11227260 and tertiary signal rs1193692 on chromosome 11. Plot A: conditional eGFR association analysis adjusted for secondary signal (rs34400381) and tertiary signal (rs1193692). Plot B: conditional eGFR association analysis adjusted for index SNP (rs11227260) and secondary signal (rs34400381).

Figure 74:
Colocalization results for index SNP rs1153855 and tertiary signal rs4775830 on chromosome 15. Plot A: conditional eGFR association analysis adjusted for secondary signal (rs68087211) and tertiary signal (rs4775830). Plot B: conditional eGFR association analysis adjusted for index SNP (rs1153855) and secondary signal (rs68087211).