Use of biological knowledge to inform the analysis of gene-gene interactions involved in modulating virologic failure with efavirenz-containing treatment regimens in ART-naïve ACTG clinical trials participants.

TitleUse of biological knowledge to inform the analysis of gene-gene interactions involved in modulating virologic failure with efavirenz-containing treatment regimens in ART-naïve ACTG clinical trials participants.
Publication TypeJournal Article
Year of Publication2011
AuthorsGrady BJ, Torstenson ES, McLaren PJ, DE Bakker PIW, Haas DW, Robbins GK, Gulick RM, Haubrich R, Ribaudo H, Ritchie MD
JournalPac Symp Biocomput
Pagination253-64
Date Published2011
ISSN2335-6936
KeywordsAnti-HIV Agents, ATP-Binding Cassette Transporters, Benzoxazines, Computational Biology, Double-Blind Method, Drug Resistance, Viral, Epistasis, Genetic, Genome-Wide Association Study, HIV Infections, HIV-1, Humans, Polymorphism, Single Nucleotide, Potassium Channels, Inwardly Rectifying, Receptors, Drug, Risk Factors, Software, Sulfonylurea Receptors, Treatment Failure
Abstract

Personalized medicine is a high priority for the future of health care. The idea of tailoring an individual's wellness plan to their unique genetic code is one which we hope to realize through the use of pharmacogenomics. There have been examples of tremendous success in pharmacogenomic associations however there are many such examples in which only a small proportion of trait variance has been explained by the genetic variation. Although the increased use of GWAS could help explain more of this variation, it is likely that a significant proportion of the genetic architecture of these pharmacogenomic traits are due to complex genetic effects such as epistasis, also known as gene-gene interactions, as well as gene-drug interactions. In this study, we utilize the Biofilter software package to look for candidate epistasis contributing to risk for virologic failure with efavirenz-containing antiretroviral therapy (ART) regimens in treatment-naïve participants of AIDS Clinical Trials Group (ACTG) randomized clinical trials. A total of 904 individuals from three ACTG trials with data on efavirenz treatment are analyzed after race-stratification into white, black, and Hispanic ethnic groups. Biofilter was run considering 245 candidate ADME (absorption, distribution, metabolism, and excretion) genes and using database knowledge of gene and protein interaction networks to produce approximately 2 million SNP-SNP interaction models within each ethnic group. These models were evaluated within the PLATO software package using pair wise logistic regression models. Although no interaction model remained significant after correction for multiple comparisons, an interaction between SNPs in the TAP1 and ABCC9 genes was one of the top models before correction. The TAP1 protein is responsible for intracellular transport of antigen to MHC class I molecules, while ABCC9 codes for a transporter which is part of the subfamily of ABC transporters associated with multi-drug resistance. This study demonstrates the utility of the Biofilter method to prioritize the search for gene-gene interactions in large-scale genomic datasets, although replication in a larger cohort is required to confirm the validity of this particular TAP1-ABCC9 finding.

Alternate JournalPac Symp Biocomput
PubMed ID21121053
PubMed Central IDPMC3094912
Grant ListAI062435 / AI / NIAID NIH HHS / United States
AI069439 / AI / NIAID NIH HHS / United States
AI069472 / AI / NIAID NIH HHS / United States
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