The Clinical Genomics facility

The Clinical Genomics facility

www.scilifelab.se

Clinical Genomics facility in Stockholm was established in 2013 as a spin out from the NGI facility due to the increased demand of services from the health care setting and the need to establish at SciLifeLab a service profile specifically addressing the needs of translational research and the health care setting. MTC/Karolinska Institutet is the host department for Clinical Genomics since 2014.

Lars Engstrand is Director for this facility and overall responsible for the activities at the facility, communications within SciLifeLab and KI (including the Board and Director), communication and outreach activities and strategic discussions with clinical collaborators.

The activities within the Clinical Genomics facility are centered around applying and validating high-throughput genomic technologies for future implementation into clinical diagnostics within the health-care system. In detail, we cover the following three types of projects: i) direct transfer of high-throughput technology into routine diagnostics, ii) development of a high-throughput analysis with an expected utility in routine diagnostics, and iii) high profile translational research with a future potential application in clinical diagnostics.

Clinical Genomics in Stockholm has during the first year of operations focused on establishing the infrastructure for operations and a quality assurance system following the ISO/IEC 17025 standard, as well as setting up experimental and analytical capability for inherited diseases and microbial genomics. On the experimental side we are now delivering exomes at a pace and quality required for this type of translational and diagnostic sequencing (>99.5% coverage, turn-around time in 3-4 days if needed), and we are preparing for a switch to whole genome sequencing. On the analytical side we have developed an in-house data processing capability starting with the raw data from the sequence run and processing the data all the way to ranked variants ready for clinical interpretation and decision making. A key challenge has been the development of an analytical pipeline that provides results quickly enough, also for whole genome data. Current estimates indicate that it will be possible to reduce the processing time to ca 6 hours for exome level data, and 24-30 hours for whole genome data. We have also developed a set of support tools for clinical decision making, enabling clinical collaborators to view the results without requirement of in-depth bioinformatic knowledge. Further, we have established the principle of acute setting whole genome sequencing providing clinical answers starting at 15 hours after sample has been received. This provides a foundation for a new strategy for diagnostics and treatment choices for acute setting metabolic medicine.   

We have also established a basic capability for microbial diversity characterisation and monitoring of transmission and outbreak routes in epidemiological and hospital settings.

The facility is currently also engaged in several cancer projects and aiming for identification of personalised treatment and prognosis strategies. These projects are expected to be carried out during 2015 and focus on five different cancers; breast, colon, lung, pancreas and pediatric neuroblastoma. Finally, the facility will also start providing non-invasive prenatal testing together with Klinisk Genetik at Karolinska university hospital.

Further development of the technology used by the facility is a central aspect of the work carried out. There are numerous ways how this is done.

  1. We carry out internal development to both establish new assays and to further develop the quality of the existing assays.
  2. We are also continuously testing new technologies available at other SciLifeLab facilities for different types of applications within our platform.
  3. We work together with the other SciLifeLab facilities and make a joint effort to develop technology and adapt this for diagnostic testing. Collaborative work has been carried out with all three NGI facilities in Stockholm and Uppsala.
  4. We also carry out development work in joint collaborative projects with researches at other research organisations.
  5. We work with commercial entities (both global leaders in their respective fields and small-scale startups) to test in early access mode and possibly implement new products. Examples of such activities include work carried out with Illumina, Agilent technologies, Genalice and others. We are also in active dialogue regarding software and analysis based collaborations with several leading analysis solution providers such as Molecular Health, IBM and others.

Clinical Genomics members

Head of unit

Valtteri Wirta

Phone: +46-(0)8-524 815 45
Organizational unit: Clinical Genomics Facility
E-mail: valtteri.wirta@ki.se

Bioinformatician

Robin Andeer

Organizational unit: Clinical Genomics Facility
E-mail: robin.andeer@ki.se

Bioinformatician

Emma Sernstad

Organizational unit: Clinical Genomics Facility
E-mail: emma.sernstad@ki.se

Research engineer

Cecilia Svensson

Organizational unit: Clinical Genomics Facility
E-mail: cecilia.svensson@ki.se

Research engineer

Anna Zetterlund

Organizational unit: Clinical Genomics Facility
E-mail: anna.zetterlund@ki.se

Research engineer

Daniel Backman

Organizational unit: Clinical Genomics Facility
E-mail: daniel.backman@ki.se

Research engineer

Keyvan Elhami

Organizational unit: Clinical Genomics Facility
E-mail: keyvan.elhami@ki.se

Bioinformatician

Kenny Billiau

Organizational unit: Clinical Genomics Facility
E-mail: kenny.billiau@ki.se

 

Genomics