During Phase II of this program, the plan is to continue efforts to develop a rapid and efficient method for detecting mutations associated with drug resistance in the reverse transcriptase (RT) and protease (PR) genes of the human immunodeficiency virus type 1 (HIV-1). In Phase II of this research, the feasibility of monitoring the PR and RT genes of HIV-1 will be tested by: designing and synthesizing a single RT/PR chip that contains both overlapping and specialized probe arrays that monitor codons 1-99 of the PR gene and codons 1-241 of the RT gene (1040 nucleotides); demonstrating the capability of the RT/PR chip to discriminate HIV-1 sequences at each of approximately 35 codons in both genes that correlate with a decreased drug sensitivity; measuring the performance of the RT/PR chip versus standard dideoxynucleotide sequencing using previously characterized clones; examining the capability of the RT/PR chip to detect the presence of mixtures of HIV-1 genotypes. Completion of these Phase II goals will provide performance data in detecting mutations that confer resistance to both approved and pre-approval therapeutics, as well as potentially detecting resistant viruses when present as a minority population. In Phase III, the RT/PR chip will be redesigned and tested in a clinical laboratory setting in both retrospective and prospective studies.
| Kozal, M J; Shah, N; Shen, N et al. (1996) Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat Med 2:753-9 |
