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Test ID: GHIVR    
HIV-1 Genotypic Drug Resistance Mutation Analysis, with Reflex to Phenotypic Drug Resistance Prediction, Plasma

Method Description Describes how the test is performed and provides a method-specific reference

Genotyping drug resistance:

Trugene HIV-1 Genotyping assay, developed by Siemens Healthcare Diagnostics, Inc., determines the nucleotide bases by simultaneous bidirectional sequencing (1.9 kb total) of the viral reverse transcriptase (1,600 nucleotide) and protease (300 nucleotide) genes of HIV-1 in a blood sample and identifies any mutations. An automated DNA sequencing system (OpenGene computer software) compares the sample genotype to the known resistance mutations and generates a list of the mutations present and the antiviral drugs to which the mutations confer resistance.(Package insert: Trugene HIV-1 Genotyping Kit, Siemens Healthcare Diagnostics, Inc., Tarrytown, NY)

 

Phenotyping drug resistance:

HIV-1 target genomic sequence obtained from the genotyping test is analyzed by a proprietary software application with a large correlative database of approximately 30,000 matching clinical HIV-1 genotypes and phenotypes at Virco Lab Inc. USA (Bridgewater, NJ). The analysis identifies all the mutations that can affect resistance to each drug and then interrogates the database for phenotypic drug resistance patterns from previous clinical samples that match these patterns of genotypic mutations.

 

When all matches have been identified, the software further analyzes the data for all the matches using the Virtual Phenotype-LM linear regression modeling application, which takes into account the weighted contribution of individual mutations and mutation pairs to make fold change (FC) predictions for each drug. This predicted FC in IC50 for each drug is typically based on data from thousands of real phenotypes with the same patterns of genotypic mutations. Clinically relevant interpretation of predicted FC is based on comparison between the FC in IC50 and the clinical cutoff (CCO) values for the given drug. The CCO values are derived from a clinical outcomes database containing clinical data from more than 17,000 patients, including treatment history, current treatment, and changes in viral load and CD4 count after modifying treatment based on drug resistance testing results. When CCO values for a given drug are not available from the database, biological cutoff (BCO) value derived from in vitro susceptibility testing is used for comparison.(www.vircolab.com)

Day(s) and Time(s) Test Performed Outlines the days and times the test is performed. This field reflects the day and time the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time required before the test is performed. Some tests are listed as continuously performed, which means assays are performed several times during the day.

Varies; test will be performed in batches of 4

Analytic Time Defines the amount of time it takes the laboratory to setup and perform the test. This is defined in number of days. The shortest interval of time expressed is "same day/1 day," which means the results may be available the same day that the sample is received in the testing laboratory. One day means results are available 1 day after the sample is received in the laboratory.

2-3 days

Maximum Laboratory Time Defines the maximum time from specimen receipt at Mayo Medical Laboratories until the release of the test result

10 days

Specimen Retention Time Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

2 months

Performing Laboratory Location The location of the laboratory that performs the test

Rochester