P-A10 Improving Sanger and Next Generation Sequencing (NGS) HIV Data Management Using New Downstream Analysis Systems Tailored for Clinical Diagnostics and Research Applications

Abstract

Next Generation Sequencing (NGS) and Sanger-based technologies are used for HIV drug resistance genotyping. Here we describe DeepChek®-HIV (DC) and ViroScore-HIV (VS), the first CE-IVD marked medical devices for NGS and Sanger, respectively. DC and VS perform automated analysis and HIV resistance interpretation of both Sanger and NGS sequences in a matter of minutes. DC accepts raw sequences (FASTQ) or alignment files (BAM, FASTA) from any type of sequencing platform (MiSeq, 454…) and includes several clinical guidelines for drug resistance assessments. Specific bioinformatics pipelines were developed to address major issues influencing treatment decision (insertions, deletions and homopolymer corrections). Both DC and VS are secured applications following good practices for software development and were validated for safety and efficacy in several research and diagnostic laboratories. We analyzed in 6 months more than 3300 samples from various cohorts worldwide with both DC and VS. On average, DC identified over 40% new variants missed by Sanger sequencing while also detecting the majority (94%) of the substitutions identified by Sanger. Usually, additional mutations found by Sanger corresponded to artefact information coming from chromatogram interpretations. The variant calling component of the algorithm demonstrated both accurate classification of low-frequency variants and the efficient handling of homopolymer sequencing errors. In a specific panel of 170 samples, DC identified new insertions (prevalence ≥1%), in 7% of the samples all of which missed by alternative technologies. DeepChek-HIV and ViroScore-HIV are downstream analysis platforms for HIV genotyping and drug resistance testing. It optimally managed the end to end analysis and comparison of NGS and Sanger data. It should provide additional reliable guidance to ARV treatment choices for research and clinical uses.