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GWAS summary statistics for peptic ulcer disease and other gastrointestinal disorders 16 th Feb 2021 Published in Wu et al. GWAS of peptic ulcer disease implicates Helicobacter pylori infection, other gastrointestinal disorders and depression. Nature Communications, 2021. Below is a description of the five summary statistics for the peptic ulcer disease (PUD), gastro-oesophageal reflux disease (GORD), irritable bowel syndrome (IBS), inflammatory bowel diseases (IBD) and combinations of PUD, GORD and their medications (PG+M). The summary statistics were generated for individuals of European ancestry from the UK Biobank sample. Please refer to the original study above for detailed phenotype information. 1. PUD_summary: peptic ulcer disease (PUD) 2. GORD_summary: gastro-oesophageal reflux disease (GORD) 3. PGM_summary: combinations of PUD, GORD and their medications (PG+M) 4. IBS_summary: irritable bowel syndrome (IBS) 5. IBD_summary: inflammatory bowel diseases (IBD) The summary statistics are in COJO format: 1. SNP: rsID or positional SNP identifier. 2. A1: Effect allele. 3. A2: Other allele. 4. freq: Allele frequency of A1. 5. b: Effect size for A1, 6. se: standard error for A1. 7. p: P-value from infinitesimal mixed model association test p-value. 8. n: Number of individuals for the trait. For refer any query to Yeda Wu ([email protected]) or Naomi R. Wray ([email protected]) Below is part of the results from the study above created by Yeda Wu for your pleasure: Biological interpretation Loci within genes with known mechanistic involvement and drug target for PUD Epithelial cell Protective mucus MUC1, MUC6 and FUT2 Susceptibility to H. Pylori infection PSCA, ABO and CDX2 Response to infection related damage H. Pylori CCKBR and GAST Stomach motility and acid secretion H. pylori - relevant PUD Non H. pylori - relevant PUD GWAS discoveries 4 phenotypes (PUD, GORD, PG+M and IBS) 456,327 participants in total Single nucleotide polymorphism (SNP) 2. Gastro-oesophageal reflux disease (GORD) 1. Peptic ulcer disease (PUD) 3. PUD, GORD and corresponding medications (PG+M) 4. Irritable bowel syndrome (IBS) Geno Pheno Genetic correlation estimation PUD, GORD, IBS and depression are genetically clustered in contrast with IBD Peptic ulcer disease (PUD) Gastro-oesophageal reflux disease (GORD) Irritable bowel syndrome (IBS) Inflammatory bowel diseases (IBD) Depression Disease relevant tissue PG+M GWAS is enriched in brain BA9 region, multiple explanations including brain-gut links. FOXP1 Causal effect exploration Genetically predicted major depression are associated with risk of PUD, GORD and IBS + + + + + Major depression Peptic ulcer disease (PUD) Irritable bowel syndrome (IBS) Gastro-oesophageal reflux disease (GORD) yeda_wu [email protected]
