Computational protocol: Analysis of Social and Genetic Factors Influencing Heterosexual Transmission of HIV within Serodiscordant Couples in the Henan Cohort

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Protocol publication

[…] Strength of association, P-values, odds ratios (ORs) and 95% confidence intervals (95% CIs) for association between these genotypes and transmission status were estimated using the Fisher exact test for gender, Student’s t-test for age, viral load and frequency of sexual intercourse, and Cochran Armitage tests for ordered categorical data, such as education level and frequency of condom use. Logistic regression and generalized linear mixed models were used when assessing independence of multiple covariates. For the genetic analyses the common allele was used as the reference category. Statistical analysis was performed with R [] and the Cochran Armitage tests with the coin package []. For haplotype analysis, maximum likelihood estimates of trait associations with SNP haplotypes were measured using the method of Burkett et al. with the hapassoc package []. Linkage analysis of the CCR2-CCR5 alleles was performed with Haploview []. […]

Pipeline specifications

Software tools hapassoc, Haploview
Application GWAS
Organisms Human immunodeficiency virus 2
Diseases HIV Infections