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types of genotypic tests
Apr 17, 2000

I understand the differences between genotypic and phenotypic tests, but aren't there several different types of genotypic tests? (Are the phenotypic tests also different?) What are the different types and in what situations is it best to use which test?

Thanks a lot!

Response from Dr. Holodniy

The genotyping tests can basically be broken down into 3 kinds: population sequencing, differential hybridization and clonal analysis. The first two are viable commercial tests, the third is research only. The first detects the predominant sequence of the entire protease gene and the first two thirds of the reverse transcriptase. Hybridization detects only a few specific drug related mutations. Some investigators think that you really only need the info on the primary drug mutations. Others think you need to interpret those in the context of the whole sequence. Phenotyping assays come in two flavors, traditional and recombinant viral assays (RVA). The traditional assay uses the patients cells with HIV negative donor cells. It is fraught with many technical limitations, takes lots of time, is not very reproducible, and is primarily research only. The RVA assay is done by two different companies and takes the protease and reverse transcriptase gene from the patients virus and inserts them into a lab strain of HIV. This recombinant assay is incubated in a cell line, in the presence of HIV drugs. It is much more reproducible. In general, phenotyping is twice the cost of genotyping. It probably comes down to who is paying the bill. The data is still emerging whether one type of assay over another provides more, or better information than the other. Many providers opt for screening with a genotype test, and leaving the phenotype test to interpret complicated genotypes in heavily treated patients. Others would go with phenotype first because it provides a real sense of how a patient's virus will grow or not grow in the presence of any of the HIV drugs. MH

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