HIV Genotyping / Sequencing (GART)
- Genotypic assays fall into two categories; DNA sequencing assays and point mutation assays.
- DNA sequencing assays give you the complete nucleotide sequence by means of cycle sequencing (dideoxy chain termination) or gene chip sequencing (hybridization of ologonucleotide probe assays).
- In the early 2000's, two companies gained FDA approval for their DNA sequencing assays. The HIV ViroSeq genotyping assay TM developed by Applied Biosystems/Celera diagnostics (Foster City , CA) and the TruGene TM assay developed by Bayer (Emeryville , CA).
- Both of these assays are approved for use in clinical laboratories for patient care.
- The point mutation assays are classified as specific PCR or differential hybridization assays.
- This methodology is not commonly used for genotypic testing for clinical patients as it does not provide the complete nucleotide sequence. It only detects changes in the sequence for which there are known probes available.
- Ultimately the purpose of a genotypic assay is to detect changes in the nucleotide sequence of HIV.
- These changes are often interpreted by various programs to predict a pattern of drug resistance for each individual genotype. It is an indirect prediction of the phenotypic resistance pattern.
- Today, phenotypic predictions generated from a genotype go even further through the use of databases that match various genotypes to stored phenotypes and report out a predicted phenotype based on these data.
- This is referred to as a VirtualPhenotypeTM (Virco).
- In our lab at Stanford University Medical Center , the department of Diagnostic Virology has been offering to physicians HIV-1 Genotyping since 1997.
- We use an in-house DNA sequencing methodology that was first developed at the Center for AIDS Research at Stanford in the mid-1990's.
- Over the past several years the assay has been streamlined for clinical use, the report has been revised to clarify and present the interpretation of the genotype in a manner that is useful to the ordering physicians, and as more drugs gain FDA approval and new mutations associated with drug resistance are discovered the interpretation of the genotype will be updated to reflect these changes.
- Today, phenotypic predictions generated from a genotype go even further through the use of databases that match various genotypes to stored phenotypes and report out a predicted phenotype based on these data.
- This is referred to as a VirtualPhenotypeTM (Virco).
