Digitag2 assay

Details of the prediction model based on a logistic regression model in which the backward elimination (P < 0.05) method was applied after including age, sex, weight, Child-Pugh classi cation, platelet, %PT, albumin, AST, ALT, total bilirubin, BUN, Cre, Na, etiology (HBV, HCV, alcohol, and NASH). Receiver operating characteristics (ROC) analysis was used to assess the prediction ability of the model. All analyses were carried out using SPSS for Windows version 25.0 (IBM, Armonk, NY, USA).
In the GWAS (including genome-wide imputation data) and replication study, the chi-square test was applied to a 2-by-2 contingency table in the allele frequency model. The odds ratio (OR) and the con dence interval (CI) were calculated using the major alleles as references. We considered P < 5 x 10 - 8 as the threshold for genome-wide signi cance in the combined analysis.
In the replication stage, we selected 134 SNPs with P values < 10 - 5 and linkage disequilibrium (LD) < 0.9 from the results of the chi-square test in the GWAS using genome-wide imputed data. We additionally selected 49 SNPs located on the functionally interested genes. DigiTag2 assay and TaqMan SNP genotyping assay (Applied Biosystems, Foster City, CA, USA) were used to con rm the genotypes at each SNP. We genotyped 80 cases and 333 controls to validate the GWAS results and for the replication study.

DigiTag2 assay or TaqMan SNP genotyping assays (Applied Biosystems, Foster City, CA, USA) were used to genotype the candidate SNPs identified in the GWAS discovery set in the Japanese population. For the replication study, we selected SNPs with info score 1.000 and genotyped by the Affymetrix Axiom Japonica array and in linkage disequilibrium (r 2 >0.7) with SNPs having a suggestive evidence of association ( p-value<3×10 -6 ). For the replicated chromosomal region, additional SNPs with expression quantitative trait locus (eQTL) evidence in RegulomeDB v 1.1 (category 1) and moderately suggestive association ( p-value<5×10 -3 ) were further validated to detect primary association in the locus [22] . In total, six candidate SNPs were genotyped successfully with a call rate of >99% in 591 MAC cases and 718 healthy controls.