A program named AIDS Restriction Gene (ARG) Tracks has been developed for the analysis of associations of genotypes from diallelic loci with HIV/AIDS-related clinical outcomes. The statistical computations performed include: 1) categorical analysis of infection status; 2) tests for Hardy-Weinberg equilibrium in defined groups; 3) estimation of relative hazards using the Cox proportional hazards model; 4) estimation of survival functions by the Kaplan-Meier product-limit method; 5) categorical analysis of disease progression; and 6) categorical analysis of specific AIDS-defining conditions (sequelae). The program can be invoked by selecting a Windows icon and execution can be controlled through a graphical user interface (GUI). The program makes extensive use of relational database technology implemented through the SAS Institute Structured Query Language (SAS SQL) procedure. This allows combining separate tables containing genotypic data, clinical data, and genetic map data. For each statistical test, P-values are computed as an indicator of the significance of the association and, when possible, odds ratios or relative hazards are computed as measures of the strength of the association. Computed values are placed in a table that can be viewed directly or read by other programs. For categorical analyses, the table includes observed cell counts and frequencies, cell counts expected under the hypothesis of no association, and the contributions of individual cells to chi-square goodness of fit statistics. For Cox regression, the table includes the number of subjects and the number of failure events that were observed for each genotypic class. For each marker, analysis results can be displayed as a six-page report in the form of a PDF file. While the program presently is dedicated to the analysis of HIV/AIDS-related outcomes, many of the procedures can be easily applied to the analysis of other dichotomous clinical traits or to survival data. The program can be applied to multiallelic loci or haplotype systems if new markers are defined that indicate the presence or absence of the alleles or haplotypes of interest.
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