A summary of the precision diagnostic analyses performed in routine healthcare in Sweden in 2023 shows that more than 90,800 clinical samples were analyzed. In addition to SARS-CoV-2, which continues to represent a significant proportion, many analyses were performed using whole genome and whole exome sequencing for rare diseases and gene panels for cancer in healthcare. Overall, there is an increase in both the number of samples and precision diagnostic methods used.
“In 2020, we estimated that the number of analyses based on next-generation sequencing (NGS) would increase significantly in the coming years. Our annual inventory of NGS analyses performed in healthcare in 2023 confirms that we are increasingly using both whole genome sequencing and gene panels, but also other omics technologies,” says Richard Rosenquist Brandell, Director of Genomic Medicine Sweden.
The development of precision diagnostics and the introduction of an increasing number of technologies into routine healthcare has been made possible by the close collaboration between Genomic Medicine Sweden (GMS) and the SciLifeLab Clinical Genomics platform, together with the regional Genomic Medicine Centers (GMCs) and healthcare laboratories.
Whole genome sequencing for rare diseases
A genetic diagnosis of a person with a rare disease has a direct impact on treatment, care, family planning and support for the individual and the whole family. Whole genome sequencing can play a crucial role in providing a diagnosis. In 2023, more than 8,100 samples for individuals with suspected rare diseases were analyzed using whole genome sequencing.
“The demand for broad genetic diagnostics has steadily increased in recent years. At our laboratory, more than twice as many patients had access to whole genome sequencing in 2023 compared to the previous year,” says Hans Ehrencrona, co-chair of GMS Rare diseases working group and Head of section for Clinical genetics in Lund.
“It is gratifying to be able to contribute to significantly shortening the diagnostic odyssey that many patients with rare diseases and their families have previously experienced. At the same time, it is important to note that more than half of the patients analyzed still do not receive a genetic diagnosis. Here, the GMS’s work with technology development and knowledge sharing is an important component in improving diagnostic outcomes and offering equal diagnosis and care across the country,” concludes Hans Ehrencrona.
Other techniques are also increasingly used in the diagnosis of rare diseases, with more than 4,700 samples analyzed by gene panels and more than 3,700 samples analyzed by whole exome sequencing reported.
Gene panel analysis in cancer
For cancer, there is a steady increase in precision medicine analysis using NGS, allowing for improved diagnosis, prognosis assessment and targeted treatment. In 2023, approximately 10,500 samples for solid tumors were analyzed with gene panels. Of these, about 500 samples have been analyzed with the GMS560 gene panel, which is being implemented in healthcare in region after region. For solid tumors, there is also an increased use of whole genome sequencing and other methods such as whole transcriptome sequencing and targeted RNA sequencing.
Also for blood cancers, gene panels are increasingly used for prognosis and disease monitoring. In 2023, more than 7,200 samples were analyzed. Of these, 63 percent were performed with GMS’s gene panel for myeloid leukemias. Whole genome sequencing is also being evaluated in a separate pilot project for acute leukemias.
“Gene panels will continue to be important diagnostic tools in cancer. In addition, whole genome sequencing is being introduced for certain cancer diagnoses, both for children with cancer and acute leukemias. The results so far show that we find the same alterations as current diagnostic methods, but also gain additional clinically relevant information,” says Richard Rosenquist Brandell.
Microbiology
For microbial analyses, it is reported that more than 9,500 samples were analyzed with 16S sequencing for the identification of bacterial infections and 4,900 samples were analyzed with whole genome sequencing, an increase of 53 and 42 percent, respectively, from 2022. In addition, a large number of SARS-CoV-2 analyses, more than 26,000 samples, continued to be analyzed with whole genome sequencing in healthcare laboratories.
“The increased sequencing we are now seeing in the field of infectious diseases, together with the introduction of the latest generation sequencing technologies for rapid analysis of bacteria and viruses, will shorten response times and promote our national precision diagnostics across the country,” says Paula Mölling, co-chair of GMS Microbiology and researcher at the Laboratory Medicine Clinic at Örebro University Hospital and the Department of Medical Sciences at Örebro University.
About the inventory
The sequencing of the clinical samples has been performed by the healthcare laboratories within each healthcare region. The collection of statistics for the number of NGS-based analyses performed in Sweden in 2023 has been done by the respective GMCs in Lund, Gothenburg, Linköping, Örebro, Stockholm, Uppsala and Umeå in collaboration with the hospitals’ university laboratories, universities and SciLifeLab Clinical Genomics and compiled by GMS in a report.
Read the report (in Swedish)
Photo: Samuel Avraham, SciLifeLab