Computational protocol: HBV/HIV co-infection and APOBEC3G polymorphisms in a population from Burkina Faso

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Protocol publication

[…] SPSS version 20.0 was used for data analysis. Power-Marker software version 3.25 was used for the determination of the Hardy-Weinberg equilibrium and the calculation of allele and genotype frequencies. Changes were considered statistically significant at p ≤ 0.05, using the Fisher Exact test. Odds ratio (OR) and confidence intervals (CI) at 95 % were calculated to estimate the associations of HIV-1/HBV co-infection with the rs6001417, H186R, and rs35228531 polymorphisms using Epi Info 7. Logistic regression was performed on all SNPs with statistically significant allele or genotype tests, associating additive, dominant and recessive models with minor allele as the risk allele.Linkage disequilibrium (LD) was characterized and haplotype frequencies were computed using Power-marker [], Haploview [], and SNPStats [] statistical softwares. Descriptive summary statistics were calculated using Haploview []. Power Marker, Haploview and SNPStats use the Expectation Maximization (EM) algorithm to determine haplotype frequency distributions in cases of unknown phase. Only haplotypes with a minimum frequency of 10 % were considered in the analysis. […]

Pipeline specifications

Software tools Haploview, snpStats
Application GWAS
Organisms Hepatitis B virus, Human immunodeficiency virus 1, Homo sapiens, Martes pennanti
Diseases Hepatitis B, Infection, HIV Infections