Additional file 1 of Trans-ancestral rare variant association study with machine learning-based phenotyping for metabolic dysfunction-associated steatotic liver disease

Additional file 1. Supplementary tables. Table S1: Characteristics of different participant cohorts analyzed in this study. Table S2: Genome-wide significant common variant associations in PNPLA3 with true MASLD and PDFF. Table S3: Definitions of exclusionary diagnoses, Elixhauser comorbidities, MASLD outcomes, and MASLD risk factors. Table S4: Exome-wide significant rare and ultra-rare variant associations with true MASLD and PDFF. Table S5: Single variant allele frequencies in gnomAD v4.1.0. Table S6: Bonferroni-significant gene-level associations with true MASLD and PDFF. Table S7: Previously reported rare variants associated with MASLD. Table S8: Nominally significant rare coding variant associations with true MASLD and PDFF in GCKR, ATG7, MTTP, and PNPLA3. Table S9: Nominally significant associations of identified variants with laboratory and physical measurements. Table S10: Nominally significant associations of identified genes with laboratory and physical measurements. Table S11: Features included in the machine learning model to predict PDFF. Table S12: Performance metrics for PDFF prediction models among participants with different time gaps. Table S13: Performance metrics for identifying steatosisat different thresholds of predicted PDFF. Table S14: Most important features for the PDFF prediction model. Table S15: Power estimates for true and predicted phenotypes. Table S16: Heritability of and genetic correlation between MASLD and PDFF phenotypes in the UK Biobank. Table S17: Replication of 40 previously reported MASLD-associated variants. Table S18: Replication of 40 previously reported MASLD-associated variants in sex-stratified analyses. Table S19: Exome-wide significant rare and ultra-rare variant associations with predicted MASLD and PDFF. Table S20: Bonferroni-significant gene-level associations with predicted MASLD and PDFF. Table S21: Ancestry-stratified single variant and gene-level associations with predicted MASLD and PDFF. Table S22: Sex-stratified single variant and gene-level associations with predicted MASLD and PDFF. Table S23: Functional and clinical annotations for single variants identified in this study.