The aim of this project is to identify novel host genes and polymorphisms involved in HIV-1 infection and progression to AIDS through an examination of candidate genes along with a mapping by admixture linkage disequilibrium (MALD) genome scan. The Laboratory of Genomic Diversity (LGD) has samples from over 4,000 individuals with a history of HIV-1 exposure or infection. A high-throughput, polymerase chain reaction (PCR)-based genotyping laboratory that has assayed numerous candidate gene polymorphisms in thousands of HIV-infected and -exposed patients has been developed (See Project #Z01 BC 10270-05 LGD). The importance of the IL10-5'A polymorphism has been identified by pursuing an approach of examining over 170 candidate genes in patient cohorts to test hypotheses of susceptibility to HIV-1 and progression to AIDS. Individuals with the IL10-5'A polymorphism who have a lower level of IL-10 production in peripheral blood mononuclear cells upon stimulation progress to AIDS after about five years of infection, faster than individuals without the promoter variant. A patent application was filed on this discovery in FY00 and the work was published (Shin et al., Proc. Natl. Acad. Sci USA 97:14467-14472, 2000). Other polymorphisms around and within the IL10 gene are being examined in the laboratory to test the degree of linkage disequilibrium around this gene and the possibility that they may be involved in disease progression. For the longer term, we have been developing a novel method for disease gene identification in patient cohorts called MALD (see Project #ZO1 BC 005800-08 LGD). Candidate gene screening of polymorphisms in or near a gene depends on fine scale linkage disequilbrium that exists in human populations. Screening with the candidate genes that currently have known polymorphisms and additional loci that become available is ongoing through the identification of polymorphisms for the remaining loci. In this work, denaturing high performance liquid chromatography analysis and polymorphisms from the literature are followed by sequence analysis and conversion of these polymorphisms to PCR-formatted single-base extension assays. Several thousand DNAs of HIV-exposed and -infected individuals have been organized and aliquoted into 384-well format PCR plates for accurate and reliable high-throughput genotyping of the 13-plate Dense panel. Genotyping allows performance of survival and categorical analyses to determine relationships between genotypes and phenotypes, making possible estimates of the relative risks and hazards of genetic polymorphisms that influence HIV-1 infection and disease progression.
|Shrestha, Sadeep; Strathdee, Steffanie A; Galai, Noya et al. (2006) Behavioral risk exposure and host genetics of susceptibility to HIV-1 infection. J Infect Dis 193:16-26|
|Shrestha, Sadeep; Strathdee, Steffanie A; Broman, Karl W et al. (2006) Unknown biological mixtures evaluation using STR analytical quantification. Electrophoresis 27:409-15|
|Shrestha, Sadeep; Smith, Michael W; Beaty, Terri H et al. (2005) Theory and methodology for utilizing genes as biomarkers to determine potential biological mixtures. Ann Epidemiol 15:29-38|