DeepChek®-HIV (S-12-023 (HUS)) is a flexible and customizable downstream analysis software able to handle sequencing data and intended to be used for performing HIV-1 genomic data analyses and clinical interpretations.
Compatible with Electrophoresis Capillary and Next Generation Sequencing (NGS) platforms (like MiSeq, MiniSeq, Ion Torrent, PGM, S5, 454-Junior, 454-FLX…), DeepChek®-HIV stores, organizes sequencing data in a dedicated database format and performs bio-informatics analyses and clinical interpretations of RT, PROT, INT, GP120/V3 or GP41 sequencing data. It is able to generate reports to be used either for research or for routine use.
- Supported formats: AB1, FASTA and PLAIN-TEXT for Sanger, FASTA/FASTQ (including paired sequencing), BAM/SAM for NGS covering Targeted Genes or also compatible with Whole Genome data.
- Available analyses: subtyping/high-resolution subtyping of Pure or CRFs strains, amino-acid mutations/nucleotide changes determination and validation, NGS coverage validation
- Available interpretations: drug resistance assessment (for NRTIs, NNRTIs, IIs, PIs, EIs, FIs) from genotypic of virtual-phenotypic based guidelines (including but not restricted to HIVdb/Stanford, ANRS, geno2pheno, Rega…), tropism determination, Genotypic Sensitivity Scoring (GSS)…
- Included services: updates/upgrades (quarterly releases), support, web-training, historical sequencing data import
- On-demand services: local training, integration with third-party instruments or systems, customization…
The DeepChek®-HIV software system is a secured web application which can be used through a Cloud access or locally, through pre-configured servers. It is made available with regular updates (new clinical databases, guidelines…) and quarterly upgrades (new features, modules, applications…) and can be fully integrated within the IT network of each laboratory (integration with the sequencing platform, with the Laboratory Information System – LIS, with the Hospital Information System – HIS…).
The DeepChek®-HIV software application is CE-IVD (LU/CA01/IVD/69).
Overview of the pipeline
Characteristics and performances
Compatibility with Capillary Electrophoresis (SANGER) platforms
Compatibility with Next Generation Sequencing platforms
Validated on 454 FLX/Junior, MiSeq, MiniSeq, Ion PGM, Ion S5 and others
AB1, FASTA and PLAIN-TEXT for Sanger, FASTA/FASTQ (including paired sequencing), BAM/SAM for NGS covering Targeted Genes or also compatible with Whole Genome data
From sequencing data to report in ~2 mintutes for SANGER and ~30 minutes for NGS (depending on the platform)
RT, PROT, INT, GP41, GP120/V3, Whole Genome (soon)
Subtyping, high-resolution subtyping, amino-acid mutations detection, nucleotide changes detection, NGS run quality report, tropism determination
Drug resistance through up to 7 different up-to-date genotypic-based or virtual-phenotypic-based guidelines including HIVdb/Stanford, ANRS, geno2pheno, Rega,...
Clinical genotyping report (PDF), 1-page genotyping report (soon), quality-information report on Amino-Acid changes (CSV), Quality information report on nucleotide changes (CSV)
Unlimited updates & upgrades of the software, support, training...
Secured web platform (user restriction, access monitoring...), data export, multi-sites, unlimited number of users/analyses per site
Local servers, historical data import, integration with LIS and HIS, integration with sequencers, automation of the IT workflow, customization...
Examples of reports
Quick start guide