Clinical Genomics Stockholm

Infrastructure unit

Contact

Valtteri Wirta, Head of Unit and Platform Scientific Director

valtteri.wirta@scilifelab.se

Anna Gellerbring, Project Coordinator

anna.gellerbring@scilifelab.se

Anna Lyander, Head of Unit Laboratory

anna.lyander@scilifelab.se

Henrik Stranneheim, Head of Unit Bioinformatics & IT

henrik.stranneheim@scilifelab.se

Recent user publications

The publications in this database are the result of research conducted at the units of SciLifeLab – both in user projects and technology development.

Clinical Genomics Stockholm

The Clinical Genomics Stockholm unit is a research infrastructure at Science for Life Laboratory (SciLifeLab) for large-scale, genomics-based analyses using next generation sequencing technologies. The unit assists in translational research projects, in the translation of genomics-based tools to routine clinical care and also aims to improve the capability for national microbial surveillance and for pandemic preparedness.

Enheten Clinical Genomics Stockholm är en forskningsinfrastruktur vid Science for Life Laboratory (SciLifeLab) för storskaliga, genomik-baserade analyser med hjälp av storskalig DNA sekvenseringsteknik. Enheten bistår i translationell forskning, faciliterar införandet av genomikbaserade analyser till rutinvård och strävar också efter att förbättra förmågan för nationell mikrobiell övervakning samt förberedelser inför pandemier.

Applications

We provide expertise, method development and end-to-end service to translational research and precision diagnostics for the development of tomorrow’s diagnostics. Our current disease focus areas are:

  • Cancers (including solid tumors and hematological malignancies)
  • Rare inherited disease
  • Microbial diseases and surveillance

Services

Our national services within NGS and other molecular technologies include development of methods for clinical implementation or translational research with strong clinical utility. These include, but are not restricted to:

  • Consultation (Project design, Target capture design)
  • Sample management (Resistance typing)
  • QC of samples for various analyses (Sequencing data)
  • Sequencing:
    • DNA sequencing (WGS, WES, Panels, microbial genomes, metagenomics)
    • RNA sequencing (total RNA, mRNA)
  • Other molecular technologies (Optical genome mapping)
  • User access service (Fragmentation of DNA and chromatin, DNA/RNA concentration measurements, Sequencing)
  • Bioinformatics (Bioinformatic analysis (data generated at CG or elsewhere))

Fees and principles for prioritisation

The fee structure of the unit is set so that the entire or parts of the RI’s costs are covered. The estimated analysis fees vary depending on whether the user is a government agency, healthcare or a private company. A committee makes prioritizing decisions following a technical feasibility assessment, after which samples are processed according to date of reception.

Avgifter och principer för prioritering

Avgiften sätts så att hela eller delar av forskningsinfrastrukturens kostnader täcks. Beräknad analyskostnad varierar beroende på om användaren är en statlig myndighet, sjukvården eller ett privat företag. En nämnd gör prioriteringsbeslut efter en teknisk genomförbarhetsbedömning, varefter prover behandlas i enlighet med mottagningsdatum.

Equipment

Our node has access to specialized equipment that enable us to factilitate the translation of new high-throuput techniques into clinical use. These include, but are not restricted to:

  • Various automatic robotic systems (BRAVO NGS Workstation, Hamilton NGS Star)
  • Various systems for QC, quantification and fragment analyses (TapeStation, Quantification using fluorescent assay (Qubit, Quantit))
  • Instrumentation for real time PCR and ddPCR (BioRad qPCR)
  • Instrumentation for Multispectral imaging (Saphyr optical mapper)
  • Sequencing platforms:
    • Illumina (NovaSeq 6000, NovaSeq 6000 Dx, NovaSeq X)
    • Nanopore (PromethION “access via NGI”)
    • PacBio (Revio)

Accessing the Local Unit

For more information about our services, please visit our websites:

Clinical Genomics 

If you do not find the service or technology you require, contact us directly or visit another Clinical Genomics node.


Last updated: 2024-01-15

Content Responsible: admin(website@scilifelab.se)