Effects of sequence alterations on results from genotypic tropism testing

Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology
Alejandro PirontiNico Pfeifer

Abstract

geno2pheno[coreceptor] is a bioinformatic method for genotypic tropism determination (GTD) which has been extensively validated. GTD can be affected by sequencing/base-calling variability and unreliable representation of minority populations in Sanger bulk sequencing. This study aims at quantifying the robustness of geno2pheno[coreceptor] with respect to these issues. GTD with a single amplification or in triplicate (henceforth singleton/triplicate) is considered. From a dataset containing 67,997HIV-1 V3 nucleotide sequences, two datasets simulating sequencing variability were created. Further two datasets were created to simulate unreliable representation of minority variants. After interpretation of all sequences with geno2pheno[coreceptor], probabilities of change of predicted tropism were calculated. geno2pheno[coreceptor] tends to report reduced false-positive rates (FPRs) when sequence alterations are present. Triplicate FPRs tend to be lower than singleton FPRs, resulting in a bias towards classifying viruses as X4-capable. Alterations introduced into nucleotide sequences by simulation change singleton predicted tropism with a probability ≤ 2%. Triplicate prediction lowers this probability for predicted X4 tropism, but r...Continue Reading

References

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