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Serviceerklaring - Enhet for genomdiagnistikk


Scope and details of the services provided by GDx-bioinf to various units and groups at the department.


Responsible person: GDx unit leader.

Service description

The scope of the services provided by GDx-bioinf is:

  • Deliver data for ordered analyses “from sequencer to interpreter”
  • Support and maintain all operational bioinformatics systems:
    • Lab automation
    • Variant calling (including NIPT)
    • Variant annotation
    • Variant interpretation
  • Regularly update reference data sources and external software
  • Resolve incoming user issues related to operational bioinformatics systems
  • Escalate to TSD the operational issues that affect more than one user, updates via Teams channel GDx bioinformatikk - informasjon og kontaktskjema
  • Assist with routine method development, testing and validation
  • Contribute maintaining the NSC-network according to the Service agreement between "NorSeq" and "AMG-diagnostics"
  • Support project work in the department

Types of incoming issues

Typical priority is mentioned in italic, when relevant.

  • Delivery of projects
    • Priority 3,2,1 (including reanalyses)
    • New TaqMan
    • Pause delivery
    • Force delivery on demand
    • Report QC
  • For the services related to the use of TSD, GDx takes the responsibility for communication on the following:
    • Virtual machines (VM) accessibility and stability - high
    • Standalone IGV on TSD - high
    • Custom software installation - in accordance to the case-by-case agreed priority
  • Missing files (BAM files, CNV calling, coverage report, report exports, MT calls, tracks in ELLA visual, igv-load scripts) - depending on sample priority, high-to-urgent
  • NIPT issues (including hardware, infrastructure, e.g. administrator permission to copy files, sample sheet) - urgent
  • ELLA downtime (infrastructure, bugs) and performance (escalate to TSD), max one day - urgent
  • ELLA routine user support:
    • Password reset - urgent
    • User group issues - urgent
    • Delete analyses - normal
    • Import of custom analyses - according to case priority
  • Gene panel builder (GPB) support (maintain the tool, make sure it is up, export and deploy the panels) - normal
    • The doctors (ELL) are responsible for designing the panels (using GPB)
  • Issues due to bugs in release, deployment - depends on bug’s severity and impact
  • Investigate (also retrospectively) clinical impact of newly discovered software issues
  • Assistance with development of lab methods or procedures (advice on naming, adjust pipeline and system, test runs QC)
  • Questions about details of ELLA/anno/pipeline algorithms - normal (create action points to improve the documentation whenever possible)
  • Trend analyses (NA routine QC reporting with - normal to low
  • Queries of in-house databases (for given variants) – prior lab doctor’s approval - according the the priority of the case in question
  • Data export from diagnostics (patient data, research data, NIPT data for Illumina or other provider)
  • NSC-network related tasks and responsibilities are defined in the Service agreement between "NorSeq" and "AMG-diagnostics"
  • Custom software installation on non-OUS PC (example Venus software for Hamilton robot, Bionano software etc.)

Technical (maintenance) issues

  • Cleaning diagnostics workspace on NSC and TSD
  • Development infrastructure and CI
  • TSD login nodes and VMs (we can reboot ourselves), escalate to TSD when issues
  • Software updates and validation, paperwork - endringskontroll, risikovurdering
  • Bugs, releases and deployments, testing for releases
  • Training and documentation
  • Monitoring and fixing failing services