Computational protocol: Body mass index change in gastrointestinal cancer and chronic obstructive pulmonary disease is associated with Dedicator of Cytokinesis 1

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Protocol publication

[…] Genotyping quality control procedures were used to ensure high‐quality data for association testing. The Affymetrix 500 k and 50 k data were cleaned separately and then combined prior to association testing. Briefly, DNA samples were excluded if missing more than 3% of genotypes, if reported familial relationships did not agree with those estimated from the genotypes, exhibited excess heterozygosity or homozygosity, or were outliers by using principal components analysis to detect population substructure. Single‐nucleotide polymorphisms (SNPs) that failed genotyping in more than 5% of the samples or with Hardy–Weinberg equilibrium P‐values less than 1 × 10−7 were removed. SNP analyses were restricted to autosomal variants with minor allele frequencies greater than 5%. A total of 4 GWAS (within COPD, all cancer, lung cancer, and GI cancer subjects) were performed by using generalized estimating equations accounting for family structure in FHS to test for association between 418 365 SNPs and ΔBMI by using the R library GWAF. All GWAS findings were further adjusted by using genomic control to control for population substructure. Meta‐analyses were performed between independent samples from FHS cancer cases and FHS COPD cases without cancer, assuming a fixed effects model by using metal software. Meta‐analysis results with P heterozygosity < 0.1 were excluded. Regional association plots were generated by using LocusZoom. HaploReg v4.1 was used to assess the relationship between significant GWAS SNPs and epigenomic annotations in cell types from the Roadmap Epigenomics and ENCODE projects. The results with P < 5 × 10−8 were considered statistically/genome‐wide significant (GWS) accounting both for the number of variants tested and the linkage disequilibrium (LD) structure of the genome., […]

Pipeline specifications

Software tools LocusZoom, HaploReg
Databases Roadmap Epigenomics Project
Application GWAS
Organisms Homo sapiens
Diseases Gastrointestinal Neoplasms, Lung Neoplasms, Neoplasms, Pulmonary Disease, Chronic Obstructive
Chemicals Nucleotides