Computational protocol: Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene single nucleotide polymorphisms and its interaction with T2DM on pulmonary tuberculosis in Chinese Uygur population

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Protocol publication

[…] Categorical variables were presented as absolute values and percentages, and continuous variables were expressed as mean ± standard deviation (SD). Student’s t test was used to compare continuous variables, while Chi-square test was used to compare categorical variables between cases and controls. Hardy-Weinberg equilibrium (HWE) examination was used by SNPstats ( Logistic regression was performed to investigate the impact of 3 SNPs within PTPN22 gene on PTB risk, and additional stratified analysis for gene- T2DM interaction on PTB risk. Two sided test with P < 0.05 was considered statistically significant.Generalized multifactor dimensionality reduction (GMDR) [] was used to screen the best interaction combination among SNPs and T2DM., the cross-validation consistency, testing balanced accuracy and the sign test, to assess each selected interaction were calculated. The cross-validation consistency score was a measure of the degree of consistency with which the selected interaction was identified as the best model among all possibilities considered. The testing balanced accuracy was a measure of the degree to which the interaction accurately predicts case–control status with scores between 0.50 (indicating that the model predicts no better than chance) and 1.00 (indicating perfect prediction). Finally, a sign test or a permutation test (providing empirical p-values) for prediction accuracy can be used to measure the significance of an identified model. […]

Pipeline specifications

Software tools snpStats, GMDR
Application GWAS
Organisms Homo sapiens
Diseases Diabetes Mellitus, Tuberculosis, Pulmonary
Chemicals Nucleotides, Tyrosine