gwas summary statistics for peptic ulcer disease and other ...gwas summary statistics for peptic...

GWAS summary statistics for peptic ulcer disease and other gastrointestinal disorders

16th 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 (yeda.wu@uq.edu.au) or Naomi R. Wray (naomi.wray@uq.edu.au) 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 FUT2Susceptibility toH. Pylori infection

PSCA, ABO andCDX2Response to infection related damage

H. Pylori

CCKBR and GASTStomach 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)

GenoPheno

Genetic correlation estimation

PUD, GORD, IBS and depression are genetically clustered in contrast with IBD

Peptic ulcer disease (PUD)

Gastro-oesophagealreflux 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-oesophagealreflux disease (GORD)

yeda_wu

yeda.wu@uq.edu.au