Evaluation of Automatic Analysis of Ultradeep Pyrosequencing Raw Data to Determine Percentages of HIV Resistance Mutations in Patients Followed-Up in Hospital

P. Bellecave, P. Recordon-Pinson, and H. Fleury. AIDS Research and Human Retroviruses. 2016, Volume 32, Number 1, pages 85-92. This email address is being protected from spambots. You need JavaScript enabled to view it.

Citation: "... This study compares the results of an analysis of UDPS raw data generated from HIV-1 clinical samples with 454 technology (Roche Diagnostics, France), by a new commercial and fully automated Web-based software provided by SmartGene ... The SmartGene NGS HIV-1 Module is based on the proprietary IDNS (Integrated Database Network System) technology of SmartGene and is accessible via a secure web interface; users can view the progress of the analysis. ...The SmartGene pipeline, a completely automated and a frame-aware alignment process, detected all mutations above the cut-off of 0.5%. A complex, proprietary homopolymer correction algorithm, which is part of the SMG pipeline, significantly reduces the problems encountered with the AVA software. The reliability of the qualitative and quantitative detection of DRMs flanked by the homopolymeric regions is of importance, since there are at least 17 protease inhibitor (PI), nucleoside reverse transcriptase inhibitor (NRTI), or NNRTI DRMs located around homopolymeric regions….In addition, the SmartGene pipeline also detects and quantifies all other mutations with regard to a reference sequence of choice (HxB2 or American Consensus B or others) for further analysis and research ...”