In 2022, analyses of 6,700 samples with whole genome sequencing and just over 2,500 samples with whole exome sequencing were performed in clinical routine in Sweden. The majority of the analyses were performed for diagnosing patients with rare diseases. Furthermore, almost 18,000 gene panels for cancer and rare diseases were performed in the Swedish healthcare. In addition, more than 60,000 NGS-based analyses have been performed for infectious diseases, including whole genome sequencing of SARS-CoV-2.

The close collaboration between GMS and the SciLifeLab Clinical Genomics platform, together with the regional Genomic Medicine Centers (GMCs), on the development of precision diagnostics has enabled the introduction of more and new genomics-based assays in healthcare, including whole genome sequencing and gene panels.

Whole genome sequencing increases for rare diseases

Whole genome sequencing has great value in diagnosing individuals with a suspected rare disease. Since the start of GMS, and especially in the last three years, an increased use of whole genome sequencing in routine healthcare is seen in Sweden. For 2022, it is reported that more than 5,800 samples have been analyzed with whole genome sequencing for patients with rare diseases. This was carried out mainly in three of the regions with university hospital healthcare last year.

“It is crucial that we strive to offer equal care to all citizens, regardless of where they live or what medical challenges they face. By making whole genome sequencing available across Sweden, patients with a suspected rare disease can have access to the most advanced diagnostic technology and thus have a fair chance of early and accurate diagnosis,” says Anna Lindstrand, co-chair of the GMS Rare Diseases.

Other techniques are also used in the diagnosis of rare diseases, where more than 2,200 samples analyzed with gene panels and more than 2,500 samples analyzed with whole exome sequencing were reported.

Genomics-based diagnostics in cancer

For cancer, an increased use of genomics-based diagnostics is also seen. In 2022, Swedish healthcare laboratories reported that more than 15,600 samples were analyzed with gene panels for the diagnosis of solid tumours and hematological diseases. For over two years, the GMS-developed gene panel for myeloid leukemia has also been in clinical routine and in 2022, 4,256 samples were analyzed with the myeloid gene panel.

For solid tumors, a smaller number of whole genome sequencing is also reported, mainly within the pilot projects for childhood cancer and for sarcoma, a total of just over 700 samples. A small number of samples, 146, have also been analyzed with whole genome sequencing within the pilot project acute leukemias.

“This is an exciting development where gene panels and now also whole genome sequencing are increasingly used for cancer diagnostics,” says Anders Edsjö, co-chair for GMS Solid Tumours.

“We will now follow the introduction of broad gene panels. In 2022, the nationally developed GMS560 gene panel was introduced in clinical diagnostics in Region Uppsala and we are now working actively to implement it across the Sweden in 2023,” says Anders.

Microbiology and infectious diseases

In microbiology and infectious diseases, it is reported that over 6,200 samples were analyzed with 16S and over 3,400 samples with whole genome sequencing. In addition, a large number of over 53,300 SARS-CoV-2 samples have been analyzed by whole genome sequencing in healthcare laboratories.

The sequencing of the clinical samples reported has been carried out by healthcare laboratories in each healthcare region and compiled by GMS. The close collaboration between GMS and the SciLifeLab Clinical Genomics platform, together with the regional Genomic Medicine Centers (GMCs), on the development of precision diagnostics has enabled the introduction of more and new genomics-based assays in healthcare.

Read the report “Inventory of NGS-based analyses in Sweden 2022” (in Swedish only) on genomicmedicine.se.

Photo: Johan Spinnell