Making sense from complexity
Benefits
- 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
- Dedicated NGS pipeline for Provirus analysis, filtering out reads from non-replicative genomes
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.
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 multiple gene targets including Gag-p24, Protease, Reverse Transcriptase, Integrase, and Glycoproteins (gp120 and gp41) on a single report for the physician and patient. Furthermore, the SmartGene HIV Apps for NGS provide 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 the possibility to generate statistics all in a secure, networking environment.
Details of the SmartGene HIV Provirus NGS pipeline
Individuals infected with HIV-1 are nowadays treated with highly effective anti-retroviral therapy (ART) rendering the potentially deadly virus undetectable in the blood. Lifelong treatment suppresses viral replication, enabling a good quality of life for many patients. However, HIV remains integrated in the genomes of the patients' cells, and can reemerge when a particular treatment is no longer sufficient.
For HIV-infected individuals with longevity, there is an increasing need for other treatments to address age-dependent diseases. Some of these treatments may not be compatible with the ongoing ART, and thus an adaptation of the drug treatment therapy may be required. In order to guide such adaptation of therapy, a resistance assessment of the patient's HIV is needed. This is challenging since there is not enough circulating virus in the blood. Laboratories, therefore, turn to HIV "provirus" instead, which analyzes the DNA of HIV incorporated into the cellular genomes. This viral DNA, however, naturally contains many errors (mutations, reading frame changes, insertions/deletions, APOBEC mutations) which give rise to defective (non-replicative) virions, which are not harmful and termed non-functional.
After filtering out and discounting the reads derived for non-functional HIV, the remaining reads of functional virus provide a better and more realistic assessment of the viral resistance with regard to current therapy. Accurate resistance interpretation of HIV Provirus is thus of medical importance; clinicians want their patients to maintain a low or undetectable viral load. HIV Provirus analysis can indicate when an adjustment to the current therapy is needed. Demand for HIV Provirus analysis continues to increase with the success of ART.
The SmartGene HIV Provirus pipeline enables the use of all current sequencing technologies to produce reads for an integrated view of a patient's HIV status incorporating HIV Provirus data. SmartGene's Next Generation Sequencing technologies offer an enhancement when compared to dideoxy sequencing due to the number of reads produced as opposed to a single consensus signal.