National Sequencing Center

A number of patient groups have been selected to be offered a comprehensive genetic analysis (whole genome sequencing) via the Danish National Genome Centre. Samples are analyzed at two advanced laboratory facilities in Denmark – NGC WGS East at the Department of Genomic Medicine, The Kennedy Institute, Rigshospitalet, Copenhagen and NGC WGS West here at the Department of Molecular Medicine, Aarhus University Hospital, Aarhus.

Whole Genome Sequencing

Whole genome sequencing (WGS) is performed using DNA from blood, tissue (fresh frozen or stabilized in RNAlater®), cultured cells and bone marrow samples employing Illumina DNA PCR Free, fragmentation and sequencing on NovaSeq 6000. Germline samples are sequenced to a minimum coverage of 30x while tumor samples are sequenced to a coverage of 90x (minimum 60x). Methods and quality measures have been aligned among the two facilities. 

Selected Patient Groups

The following 17 patient groups have been selected for germline WGS
(see  patientgroups at NGC for further info )

Cancer in children and young people (up to 18 years)
Cancer in young adults (18-30 years) and hereditary cancer in adults
Endocrinologicalpatients (e.g. patients with certain metabolic diseases)
Fetal medicine (diagnosis of fetuses)
Haematological cancer (e.g. certain types of leukaemia)
Hereditary cholestatic and fibrotic liver diseases
Hereditary heart diseases
Hereditary hematological disease, incl. children and adolescents with unexplained cytopenia (patients with blood disorders)
Kidney failure
Neurogenetic patients (e.g. certain types of (hereditary) muscle diseases)
Primary immunodeficiency (e.g. patients suffering from repeated infections)
Psychiatry children and young people
Rare diseases in children and adults
Severe hereditary skin diseases
Widespread and incurable cancer

 Furthermore, for three patient groups tumor samples will also be sequenced:

 Cancer in children and young people (up to 18 years)
Haematological cancer (e.g. certain types of leukaemia)
Widespread and incurable cancer

Sequencing data are transferred to the HPC directly from the sequencing machines and the bioinformatical processing is started automatically. Upon completion the data is transferred to the relevant interpreting department and quality metrics is transferred to MOMA.  

Quality Control and Data Delivery

The WGC facility performs quality control of data to ensure sufficient coverage and data integrity and informs the interpreting departments of data delivery when data complies to quality control cutoffs. 

Interpretation of Data and Clinical Reporting of Results

Interpretation of data is performed by relevant clinical departments in the five different Danish regions. Data are primarily interpreted using VarSeq software and it is a regional responsibility to ensure reporting of results to the patients.