Volume 143, Issue 5, Pages 1244-1252.e12 (November 2012) Genome-Wide Association Study Identifies Variants Associated With Progression of Liver Fibrosis From HCV Infection  Etienne Patin, Zoltán Kutalik, Julien Guergnon, Stéphanie Bibert, Bertrand Nalpas, Emmanuelle Jouanguy, Mona Munteanu, Laurence Bousquet, Laurent Argiro, Philippe Halfon, Anne Boland, Beat Müllhaupt, David Semela, Jean–François Dufour, Markus H. Heim, Darius Moradpour, Andreas Cerny, Raffaele Malinverni, Hans Hirsch, Gladys Martinetti, Vijayaprakash Suppiah, Graeme Stewart, David R. Booth, Jacob George, Jean–Laurent Casanova, Christian Bréchot, Charles M. Rice, Andrew H. Talal, Ira M. Jacobson, Marc Bourlière, Ioannis Theodorou, Thierry Poynard, Francesco Negro, Stanislas Pol, Pierre–Yves Bochud, Laurent Abel  Gastroenterology  Volume 143, Issue 5, Pages 1244-1252.e12 (November 2012) DOI: 10.1053/j.gastro.2012.07.097 Copyright © 2012 AGA Institute Terms and Conditions

Figure 1 Manhattan plots of genome-wide analyses of liver fibrosis using (A) the binary F0–1/F3–4 phenotype (949 F0–1/F3–4 patients), (B) the duration F0–1/F3–4 phenotype (872 F0–1/F3–4 patients with available duration of infection), and (C) the QTF phenotype (1064 patients with available duration of infection). Larger points correspond to SNPs producing a P value <10−6. All the analyses were performed on 780,650 genotyped or imputed SNPs (Patients and Methods). Gastroenterology 2012 143, 1244-1252.e12DOI: (10.1053/j.gastro.2012.07.097) Copyright © 2012 AGA Institute Terms and Conditions

Figure 2 Genotype/phenotype relationships for the 4 SNPs most associated with liver fibrosis in the final combined cohort. (A) SMUs (Patients and Methods) for the 3 genotypes of SNP rs16851720 (located within RNF7), identified using the QTF phenotype. Bars represent standard errors (SEM) of each mean SMU. Genotype AA was used as the reference (SMU = 0). (B) Survival curves for SNP rs4374383 (located within MERTK) identified using the duration F0–1/F3–4 phenotype in the subsample of transfused patients. (C) Proportions of all HCV-infected patients with METAVIR scores of F0 and F4, by genotype at rs2629751 (located within GLT8D2), a replicated SNP identified using the binary F0/F4 phenotype. (D) Survival curves for SNP rs9380516 (located near TULP1), a replicated SNP identified using the duration F0–1/F3–4 phenotype stratified in male patients. Gastroenterology 2012 143, 1244-1252.e12DOI: (10.1053/j.gastro.2012.07.097) Copyright © 2012 AGA Institute Terms and Conditions

Supplementary Figure 1 Quantile-quantile plots of GWA of liver fibrosis using the binary F0–1/F3–4 phenotype. This analysis includes 949 patients genotyped or imputed for 780,650 SNPs using an additive genetic model. (A) P values using logistic regression and (B) P values using logistic regression adjusted on the first 4 principal components of the principal component analysis (Supplementary Figure 2). No significant deviations from expectations were observed. The genomic inflation factor λ was equal to 1.013. Gastroenterology 2012 143, 1244-1252.e12DOI: (10.1053/j.gastro.2012.07.097) Copyright © 2012 AGA Institute Terms and Conditions

Supplementary Figure 2 Principal component (PC) analysis of the 2 primary cohorts analyzed in this study. Stratification was assessed using EIGENSOFT v3.0,1 selecting only SNPs that were present in both BeadChips and that were in linkage equilibrium (r2 < 0.1). Ancestry outliers were removed by EIGENSOFT default removal procedure. After outlier removal, none of the 10 first principal components produced a significant difference in ancestry between cases and controls. Of note, a slight difference between the French and Swiss cohorts was observed on PC2. Gastroenterology 2012 143, 1244-1252.e12DOI: (10.1053/j.gastro.2012.07.097) Copyright © 2012 AGA Institute Terms and Conditions

Supplementary Figure 3 Manhattan plots of genome-wide analyses of liver fibrosis using (A) the binary F0/F4 phenotype (309 F0/F4 patients) and (B) the duration F0/F4 phenotype (268 F0/F4 patients with available duration of infection). Larger points correspond to SNPs producing a P value <10−6. All the analyses included 780,650 genotyped or imputed SNPs. Additive, dominant, and recessive genetic models were tested for each SNP, and the P value for the best model is reported. Gastroenterology 2012 143, 1244-1252.e12DOI: (10.1053/j.gastro.2012.07.097) Copyright © 2012 AGA Institute Terms and Conditions

Supplementary Figure 4 Regional plots for (A) rs16851720 (located within RNF7) and (B) rs4374383 (located within MERTK), the 2 SNPs that provided genome-wide significant evidence for association with liver fibrosis progression in the combined cohort. The 2 most associated SNPs are represented by purple dots. Colors of the other SNPs are scaled by r2 value with the 2 most associated SNPs. The blue line represents variation in recombination rate. Plots were generated by LocusZoom.9 Gastroenterology 2012 143, 1244-1252.e12DOI: (10.1053/j.gastro.2012.07.097) Copyright © 2012 AGA Institute Terms and Conditions

Supplementary Figure 5 Association analysis strategy. The table reports genome-wide analyses of HCV-induced liver fibrosis that were conducted using different phenotype definitions and genetic models (in columns), subsamples (in rows), and number of SNPs (in colors). Analyses colored in dark gray and black were conducted on all SNPs, while analyses colored in light gray were conducted on a restricted set of 75,000 SNPs. Gastroenterology 2012 143, 1244-1252.e12DOI: (10.1053/j.gastro.2012.07.097) Copyright © 2012 AGA Institute Terms and Conditions