Varicose veins of lower extremities: Insights from the first large-scale genetic study

Fig 1. Scheme depicting the overall workflow of our study. GWAS summary statistics for VVs was obtained from the Gene ATLAS (larger sample size, less stringent filtering criteria) and the Neale Lab database (smaller sample size, more stringent filtering criteria). Search for associated loci was performed using the Neale Lab data adjusted for two potential confounders–body mass index (BMI) and deep venous thrombosis (DVT). GWAS summary statistics for these two traits were also obtained from the Neale Lab database. Since our study design did not imply a replication stage, genome-wide significance threshold was set at 5.0e-09. To be more rigorous, we filtered out those loci for which P-values in the Gene ATLAS dataset were higher than the corresponding P-values in the Neale Lab dataset (after all corrections). For the resulting 12 loci, we performed a functional annotation analysis and prioritized the most likely causal genes. Except for VEP, all in-silico analyses were conducted using the Gene ATLAS dataset since it enables to achieve the highest statistical power and is genetically equivalent to other studied VVs datasets (genetic correlation coefficient = 0.99–1.00, S1 Table).

Fig 2. Graphical summary of GWAS results after the adjustment of the Neale Lab data for DVT and BMI and the genomic control correction using LD Score regression intercept. Red line corresponds to the genome-wide significance threshold of P = 5.0e-09. Only associations with P < 1.0e-03 are presented. Points with -log10(P) >14 are depicted as points with -log10(P) = 14. Loci for which P-values in the Gene ATLAS dataset were higher than the corresponding P-values in the Neale Lab dataset are annotated in blue. These loci were not included in further analyses.

Fig 3. Pleiotropic effects of identified loci on other complex traits. Color depicts the sign and the magnitude of SMR beta coefficient. Negative sign (red) means opposed effects, and positive sign (blue) means the same direction of effect. Traits that passed both SMR and HEIDI test are marked with an asterisk. Prioritized genes in loci are shown in parentheses. Full names of traits as indicated in the Neale lab and the Gene ATLAS databases are given in S11 Table. RBC, red blood cell.

Fig 4. Matrix of genetic correlations between VVs and other complex traits. Color depicts the sign and the absolute value of genetic correlation coefficient (rg). Only the traits having |rg| ≥ 0.2 with VVs are shown. Combinations with statistically significant rg are marked with points (P < 3.1e-05). O levels of qualification correspond to the General Certificate of Education Ordinary Level/the General Certificate of Secondary Education; A or AS level correspond to Advanced or Advanced Subsidiary levels. “Qualifications: NN” means no qualification. Full names of traits as indicated in the Neale lab and the Gene ATLAS databases are given in S15 Table. For “Prospective memory result” and “Health satisfaction”, high scores correspond to poor performance. DVT, deep venous thrombosis; VTE, venous thromboembolism.

Fig 5. Volcano plot depicting the results of hypothesis-free 2SMR analysis (IVW approach). The x-axis shows 2SMR beta, and the y-axis denotes the level of statistical significance on a logarithmic scale. Grey color indicates the traits that did not pass either 2SMR, or the Steiger test, or additional robustness analysis. Small colored circles depict the traits that passed these tests, but either exhibited heterogeneity in causal effects amongst instruments after removing potential outlier SNPs or did not passed 2SMR after this procedure. Large colored circles represent the traits that both passed 2SMR and showed no heterogeneity after the outliers removal (“the most reliable traits”). 2SMR coefficients are shown as calculated before the correction for pleiotropy. “Pulmonary function” traits include different estimates of forced vital capacity and forced expiratory volume in 1-second. Further details are provided in S13 Table. MICB, MHC class I polypeptide-related sequence B.