Computational protocol: Drug Metabolizing Enzyme and Transporter Gene Variation, Nicotine Metabolism, Prospective Abstinence, and Cigarette Consumption

Similar protocols

Protocol publication

[…] We used: SAS (Cary, NC) for data curation and HWE testing; plink [] to evaluate Mendelian transmission; GCTA [] to estimate principal components; STATA (StataCorp, College Station, TX) to perform HLM, imputation and other regression analyses; P ACT [] and meta-P ACT [] to adjust for multiple testing; Haploview to calculate linkage disequlibrium []; SNAP [] to identify proxy SNPs; Quanto [] for power analyses; and dbSNP [] and Affymetrix resources for SNP annotation. Chromosome coordinates are from the NCBI36/hg18 assembly []. SNP models were additive, tests were two-sided, and all alphas were 0.05. […]

Pipeline specifications

Software tools PLINK, GCTA, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Lung Neoplasms
Chemicals Cotinine, Nicotine, Nucleotides