High throughput genotyping assays have allowed the staff of the Laboratory of Genomic Diversity (LGD) to accumulate a large amount of genotypic data on subjects who are members of six large AIDS epidemiology cohorts. The bulk of the genotypes are for diallelic single nucleotide polymorphisms (SNPs) that are within or closely linked to genes that have been nominated as AIDS candidate genes on the basis of what is known about their function. The LGD has previously reported significant associations between genotypes for candidate genes and HIV infection susceptibility or progression to AIDS outcomes. This work was largely done by analyzing data one SNP and statistical test at a time. In order to efficiently analyze a large amount of accumulating data, a computer program was developed to automate the analysis. This AIDS Survival and Categorical Analysis program was written in the SAS programming language and driven by a graphical user interface based on SAS/AF software. A complete analysis of an SNP produces a 21-page report. The analyses include 1) categorical analysis of infection status by genotype, 2) categorical analysis of disease progression by genotype, and 3) survival analysis using the Kaplan-Meier and Cox proportional hazard models. The disease events analyzed include observation of CD4 cell counts of less than 200 per cubic mm, presence of disease meeting the 1993 or 1987 AIDS definitions, cytomegalovirus infection, Pneumocystis carinii pneumonia, Kaposi's sarcoma, lymphoma, mycoplasma infection, and death. In additional to the analysis program, software has been developed to extract genotypes from files produced by laboratory instruments. These include files resulting from the Taqman and single base extension assays for genotyping SNPs. Automation of AIDS Candidate Gene Analysis
| Modi, William S; Lautenberger, James; An, Ping et al. (2006) Genetic variation in the CCL18-CCL3-CCL4 chemokine gene cluster influences HIV Type 1 transmission and AIDS disease progression. Am J Hum Genet 79:120-8 |
| Nelson, George W; O'Brien, Stephen J (2006) Using mutual information to measure the impact of multiple genetic factors on AIDS. J Acquir Immune Defic Syndr 42:347-54 |
| An, Ping; Vlahov, David; Margolick, Joseph B et al. (2003) A tumor necrosis factor-alpha-inducible promoter variant of interferon-gamma accelerates CD4+ T cell depletion in human immunodeficiency virus-1-infected individuals. J Infect Dis 188:228-31 |
