Additional file 1 of A genome-wide association study of survival in patients with sepsis

Additional file 1. Supplementary methods, figures, and tables.The supplementary methods include a description of the GEN-SEP and MESSI study populations, genotyping and quality control, more details of the genome-wide association study of 28-day sepsis survival and the index event bias assessment, tools for the annotation of the functional effects of the sentinel variants and the gene expression of related genes, the association of polygenic risks of sepsis with the 28-day sepsis survival, the replication of genes from previous sepsis mortality GWAS, and related references. The supplementary figures include a principal component analysis, the quantile-quantile plot of the GWAS, regional plots for the genome-wide significant variants, Kaplan-Meier 28-day survival plots, a manhattan plot of sepsis 28-day survival association study results in the HLA region, a plot of expression of related genes across cell types, a boxplot of SAMD9 gene expression values in GSE54514 and GSE65682, a boxplot of SAMD9 gene expression values in GSE32707, and polygenic risk score (PRS) model fitting. The supplementary tables show the relevant demographic and clinical features of cases and controls used for the GWAS of sepsis risk and for the GEN-SEP patients, the list of previous candidate genes associated with sepsis risk, the prioritized independent SNPs, the index bias event results, the association results with 28-day mortality and the percentage of variation explained by the sentinel SNPs by separate or as part of a PRS, the association results of the sentinel variants from other sepsis mortality GWAS studies, the nominally significant results for the classical HLA alleles and amino acids, and the functional assessment of variants associated with 28-day sepsis survival