Computational protocol: Genetic Determinants of Chronic Obstructive Pulmonary Disease in South Indian Male Smokers

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Protocol publication

[…] Descriptive statistics were calculated using SPSS v16.0 (SPSS Inc., Chicago, IL, USA). Discontinuous variables are presented with percentages. Mean and standard deviation were calculated for clinical characteristics and compared between patients and controls using unpaired Student’s t-test after adjusting for age, pack years and age - pack years interaction. Genetic analyses were carried out using PLINK software . All the SNPs were checked for deviation from Hardy-Weinberg equilibrium in controls. Allele frequency variations were compared between patients and controls using Pearson’s Chi-square test to generate odds ratio with 95% confidence limits. The contribution of each genotype to COPD susceptibility was evaluated using logistic regression under additive, dominant and recessive genetic models after adjusting for age and pack years. A linear regression model was used to study the association of SNPs with two COPD phenotypes (FEV1 and FEV1/FVC) under three genetic models with age and pack years as covariates. Haplotypes were generated using a sliding window method and their association was tested against COPD and its phenotypes using regression model after adjusting for age and pack years. The sliding window approach implemented in PLINK sequentially examines smaller sets of SNPs within the region. For example, using a 4-SNP overlapping sliding window, one would first conduct a haplotype analysis of SNPs 1–4, followed by SNPs 2–5, followed by SNPs 3–6, and so on until the last SNP in the region is reached , . A p value less than 0.05 was considered as significant throughout the analyses. The Benjamini–Hochberg False Discovery Rate method was used to correct for multiple hypothesis testing for allele and genotype association , whereas maxT permutation of 10000 steps was used to generate adjusted empirical p value for haplotype association tests . […]

Pipeline specifications

Software tools SPSS, PLINK
Applications Miscellaneous, GWAS
Organisms Nicotiana tabacum, Homo sapiens
Diseases Pulmonary Disease, Chronic Obstructive