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Geneticist Assistant

This new tool is a unique package designed to allow users of all next-gen sequencing systems to check QC, make pathogenicity predictions and search and archive patient runs. The database can take alignments in from any pipeline but has a tool to auto detect new runs analysed by the NextGENe software, making for a simplified analysis pathway.

The software can be run either locally, from a server or accessed via the web and so a single licence can flexibly serve a number of users or sites. The software is as easy to use as all SoftGenetics products and allows users to set up databases of commonly found variants, patient information and quality metrics.

The software once set up will then allow clinical users to rapidly check QC on whole runs, screen for commonly found variants and also make pathogenicity predictions for newly discovered mutations. Over time labs can build up databases by panel and also per patient or family and these can be used with the powerful search functions to quickly screen new data sets.

  • Whole run Quality control-automatically order samples for re-run or Sanger sequencing
  • Databases of variants by disease panel.
  • Archive patient mutation report data
  • Determine pathogenicity of new variants

Geneticist Assistant NGS Interpretative Workbench

Developed in collaboration with the Laboratory Medicine, Information Technology and Health Science Research departments of Mayo Clinic, Rochester MN.

Read Genome News Bioinform article about SoftGenetics and Mayo Clinic

Geneticist Assistant NGS Interpretative Workbench, is a web-based tool for the control, visualization, interpretation and historical knowledge base of next generation sequencing data targeted at specific genes for the purpose of identifying potentially pathogenic variants associated with specific conditions such as hereditary colon cancer. Geneticist Assistant is compatible with data processed from all leading next generation sequencing platforms such as those from Ion Torrent, Illumina and Roche.  The program accepts standardized BAM and VCF files, includes prediction information from SIFT, Polyphen2, LRT and Mutation Taster, as well as three conservation scores from PhyloP, GERP++ and SiPh.  Additionally data from proprietary custom databases and information from the COSMIC database of somatic mutations are easily imported into the workbench.

Geneticist Assistant Workflow
Geneticist Assistant is designed to integrate multiple data sources into an efficient workflow for laboratories utilizing Next Generation Sequencing technology.  The workbench comes with an array of tools to speed NGS workflows from quality control through laboratory reporting with accessibility either through encrypted internet protocol by multiple collaborating institutions or a local institutional network or through a local computer.

Geneticist Assistant NGS Interpretative Workbench

Geneticist Assistant Features:

User Control Functionality:  Geneticist Assistant Workbench includes a user control feature which limits accessibility by password, logs all sign in and sign-out of users, recording user activities for recall.

Quality Control:  The GA Workbench first ascertains and identifies sequence or regions not meeting user specified quality control parameters. Prepares Action Lists of samples or regions requiring re- sequencing.

Variant Identification: logs all identified variants by individual, sample and disease panel, includes interactive “pile up” review, complete annotation by transcript, as well as coverage depth and other metrics.

Pathogenicity Prediction:  provides scores from multiple databases; links to confirmatory articles such as PubMed, dbSNP and other resources while building a historical knowledge base by gene, test panel. Includes the ability to easily import custom proprietary pathogenicity databases or others such as COSMIC.  Color codes variants as to determined prediction, while creating action lists of newly found variants for pathogen confirmation.

Reporting:  Geneticist Assistant workbench provides custom laboratory reports in pdf form or the ability to export information to LIMS systems.

Accessibility:  Geneticist Assistant workbench affords several methods of accessibility allowing for a paperless system through-out your institution if so desired.  Multiple collaborating facilities can access the workbench through encrypted internet profile, single institutions can utilize local internet, or single labs may run off a local computer.

Minimum Hardware Requirements:

Client:
Windows or Linux
64 bit Operating System
2 core processor
4gb ram
Server:
Windows or Linux
64 bit Operating System
2 core processor
4gb ram

Other products from SoftGenetics available from BioGene Ltd


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