Department of Genomic Medicine

The Department of Genomic Medicine enables clinicians and researchers to investigate the entire human genome, as an intricate part of the development of personalized medicine.

About us

Department of Genomic Medicine is a part of the Diagnostic Center and comprises approximately 80 employees, including technicians, molecular biologists, doctors, bioinformaticians, engineers, medical secretaries, and others. The department works on analyzing the genome and transcriptome in both hereditary and non-hereditary conditions and consists of a laboratory section, a bioinformatics section, a clinical reporting section, and a section for research and development. The analyses are primarily based on Next-Generation Sequencing, and the department is ISO15189 accredited. The department of Genomic Medicine holds a combined high-throughput DNA/RNA sequencing and bioinformatics platform that offers a wide-range of genomic and transcriptomic analyses, including human whole-genome sequencing.

Management

Maria Rossing

Head of Department, senior chief physician

caroline.maria.rossing@regionh.dk

+45 3545 2223

Martin Skygge

Chief biomedical laboratory scientist

martin.skygge@regionh.dk

+45 2136 7897

Core and laboratory facilities

The department of Genomic Medicine (GM) utilizes advanced technologies, primarily within Next-Generation Sequencing (NGS) and Microarray analysis, that are based on comprehensive mapping of DNA and RNA from blood and tissue for the purposes of patient diagnostics and treatment.

Over the recent years, the laboratory facilities at GM have been scaled up and streamlined, and today the laboratory runs an almost fully automated workflow from sample receival, to sequencing and data processing, and variant classification and clinical reporting. Currently, GM holds one of the largest sequencing facilities in Denmark.

Whole-genome sequencing (WGS) has shown to be superior to other sequencing techniques by including information of all coding regions, regulatory sequences, and structural variations, all in one assay. In the clinical setting, WGS is now performed as standard analysis, for patients with suspected inherited disease, while smaller NGS gene panels are still routinely used to analyze individuals predisposed to cancer.

Genomic profiling for cancer patients includes fresh biopsies which are subjected to WGS analysis, transcriptome analysis (RNA sequencing) and genomic microarray analysis (SNP array). When fresh biopsies are not obtainable, archival tissue samples (FFPE) or circulating tumor DNA from plasma samples can be analyzed using a large NGS panel (TSO500).

In addition, GM performs various other analyses, including WGS of microorganisms, preimplantation genetic screening (PGS), and other specific SNP analyses (such as Dihydropyrimidine dehydrogenase (DPYD), and the hemochromatosis gene (HFE) analysis, all run on a routinely basis.

At GM we offer core facility sequencing- and microarray- services to local researchers as well as external and international collaborators.

Research

The Department of Genomic Medicine takes part in numerous collaborations with both academia and industrial partners, where most projects are focused on high-throughput sequencing with a clinical impact. The Department of Genomic Medicine currently runs research projects within areas detailed in below sections. In addition, the research and development section are focusing on implementing the latest methodologies to keep the NGS platforms at its cutting edge. Current areas of interest include new methods for whole-genome sequencing, long-reads sequencing and single-cell sequencing technologies for clinical applications.

For requests regarding research projects, including possibilities, pricing, etc., please contact:

gm-forskning.rigshospitalet@regionh.dk

Classification of genomic variants of uncertain significance

Basic and translational research is carried out to improve the classification of genomic variants of uncertain significance (VUS) discovered in patients with cancer or other genetic diseases. This is done by exploiting a wide array of established CRISPR gene editing techniques, functional assays, and fluorescence microscopy-based methods.

Genomics of bacteria and virus causing persistent infections

Long-term persistent infections from bacteria and virus cause morbidity and mortality in humans and are challenging to treat. The department uses genome sequencing in pathogen genomic investigations in long-term persistent infections to improve our understanding of the microbial pathogens and the diseases that they cause. The focus is on bacterial infections in the airways of persons with cystic fibrosis, primary ciliary disease, and chronic obstructive pulmonary disease, and infection with HIV-1, respectively. The main aspects of pathogen genomics addressed in these investigations are convergent evolution, genetic adaptation, natural selection and genetic drift, evolutionary rate, within host diversity, transmission dynamics, antibiotic resistance, and population structure.

Collaborations and partnerships

The Department of Genomic Medicine is engaged in collaborations and partnerships with multiple external institutions.

Danish National Genome Center

The primary task of the Danish National Genome Center (DNGC; https://www.ngc.dk) is to lay the foundation for the development of better diagnostics and more targeted treatments for patients using whole-genome sequencing (WGS). The Department of Genomic Medicine is one of the two national laboratory units that provide DNGC with large-scale nucleic acid sequencing, bioinformatics, and quality assessment.

Myriad Genetics

Myriad Genetics (https://myriad.com) is a company that markets the MyChoice CDx companion diagnostic test to give comprehensive clarity when making early and late-line ovarian cancer treatment decisions. The Department of Genomic Medicine serves as a partner laboratory to provide MyChoice CDx tests for patients in Scandinavia and several other European countries. This effort has already successfully enabled clinicians in both Denmark and other Nordic countries to make crucial treatment decision for ovarian cancer patients.

Biotech Research & Innovation Centre at the University of Copenhagen

The Biotech Research & Innovation Centre (BRIC) is a center in biomedical research within the University of Copenhagen with a mission to contribute to a basic understanding of how and why disease occurs, to discover new disease-related genes, and potential targets and biomarkers in order to provide more efficient treatments for patients primarily within cancer and neurological diseases (https://www.bric.ku.dk). The Department of Genomic Medicine collaborates with Professor Claus Storgaard Sørensen at BRIC on various projects involving breast cancer genomics and functional assays.

Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at the Broad Institute, Boston

The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease (CGMD) facilitates close collaborations between the Broad Institute in Boston and Danish researchers investigating the genetics and gene regulation of common complex diseases, including type 2 diabetes and obesity (https://www.broadinstitute.org/nnfc). The Department of Genomic Medicine collaborates with CGMD's Managing Director, Kasper Lage, on bringing the state-of-the-art in genomics beneficial to Danish patients.