Making sense from complexity


  • Up-to-date resistance interpretation with multiple algorithms and viral gene targets
  • Automated longitudinal resistance reporting and mutation history
  • Searchable sequence archive facilitates patient follow-up and clinical studies
  • NGS pipeline provides quantitation of viral sub-populations and quasi-species

Challenges and opportunities in HIV patient care

Multi-drug resistance, therapy failures, and the need to select combination treatments which consider resistance, efficacy, and tolerability are persistent challenges in HIV medicine. Sequencing a patient’s virus and using expert rules to infer resistance phenotypes from the viral genotype is the standard of care in HIV medicine and reveals opportunities to optimize patient care. Now, deep sequencing technologies enable the identification of viral sub-populations and quasi-species whose patterns of mutations may be harbingers of emerging resistance to anti-retroviral therapies in the patient’s future.

SmartGene provides Web-based applications for Sanger and NGS which manage and interpret HIV sequence data to identify precisely the mutations in a patient’s virus, to interpret those mutations for drug resistance using multiple up-to-date rule sets, and to provide the results for Protease, Reverse Transcriptase, and Integrase genes on a single report for the physician and patient. Furthermore, the SmartGene HIV NGS Pipeline provides sensitive detection and relative quantitation of viral sub-populations elucidating minor populations of the virus which express amino acid mutations at resistance-relevant positions in the viral genome.

Each sample’s nucleotide sequences, associated information, and results are archived together facilitating easy, multi-parameter searches. SmartGene HIV provides retrospective comparisons of results, reinterpretation of archived sequences with current algorithms, ad-hoc and automated longitudinal reporting of patient cases, a query tool for specialized mutation searches, and generating statistics plus secure networking.

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