Cross-GWAS coherence test at the gene and pathway level

Abstract

Proximal genetic variants are frequently correlated, implying that the corresponding effect sizes detected by genome-wide association studies (GWAS) are also not independent. Methods already exist to account for this when aggregating effects from a single GWAS across genes or pathways. Here we present a rigorous yet fast method for detecting genes with coherent association signals for two traits, facilitating cross-GWAS analyses. To this end, we devised a new significance test for the covariance of datapoints not drawn independently but with a known inter-sample covariance structure. We show that the distribution of its test statistic is a linear combination of χ2 distributions with positive and negative coefficients. The corresponding cumulative distribution function can be efficiently calculated with Davies’ algorithm at high precision. We apply this general framework to test for dependence between SNP-wise effect sizes of two GWAS at the gene level. We extend this test to detect also gene-wise causal links. We demonstrate the utility of our method by uncovering potential shared genetic links between the severity of COVID-19 and (1) being prescribed class M05B medication (drugs affecting bone structure and mineralization), (2) rheumatoid arthritis, (3) vitamin D (25OHD), and (4) serum calcium concentrations. Our method detects a potential role played by chemokine receptor genes linked to TH1 versus TH2 immune response, a gene related to integrin beta-1 cell surface expression, and other genes potentially impacting the severity of COVID-19. Our approach will be useful for similar analyses involving datapoints with known auto-correlation structures.

Phenotypic and Genetic Characteristics of Retinal Vascular Parameters and their Association with Diseases

“…To identify the genes modulating specific vascular IDPs, we employed our PascalX analysis tool [53, 54]. This tool aggregates SNP-wise association signals within gene windows and generates gene scores.…”

“…SNP-wise heritabilities and genetic correlations between IDPs were derived using LDSR [52]. Gene and pathway scores were computed using PascalX [54, 74]. Both protein-coding genes and lincRNAs were scored using the novel, approximate “saddle” method, taking into account all SNPs within a 50kb window around each gene.…”

“…To identify the genes modulating specific vascular IDPs, we employed our PascalX analysis tool [53,54].…”

“…Finally, to identify the genes modulating specific vascular IDPs in the replication cohort (RS), we employed our PascalX analysis tool [53,54]. We applied the Benjamini-Hochberg procedure [59] for the genes.…”

“…SNP-wise heritabilities and genetic correlations between IDPs were derived using LDSR [52]. Gene and pathway scores were computed using PascalX [54,74].…”