Regional Cancer Centres in Sweden fund development of long-read sequencing for cancer diagnostics

2024-05-24

The Regional Cancer Centres in Sweden recently conducted a call for projects aiming to improve cancer care. Clinical Genomics (CG) Uppsala will play a major role in a project focusing on implementation of long-read sequencing for diagnostics of leukemias and inherited cancer.

Photo: Ida Höijer

Advanced genetic characterization is important for cancer diagnostics. The increasing availability of personalized treatments demands rapid and high-quality diagnostics to determine which patients that would benefit from the targeted treatment. While current genetic diagnostics is mainly performed using short-read sequencing, long-read sequencing can offer both faster and more accurate genetic profiling.

With short-read sequencing technologies, it is difficult to analyze repeated regions in the genome, where pathogenic copy number variations, structural variants, and expansions occur frequently. Rapid technology development in recent years has resulted in high-quality and relatively cost-effective methods for long-read sequencing that are suitable for clinical applications, says Ida Höijer, expert in long-read sequencing technologies at CG Uppsala and the National Genomics Infrastructure.

The granted project has two major aims:

Shorten the turnaround time for genetic investigation of leukemias from the current 4-6 weeks to 1-3 weeks.
Improve the diagnostics of hereditary cancer to identify more individuals carrying congenital mutations.

Faster diagnostics of leukemias will lead to more effective treatments, which will hopefully prolong survival. In hereditary cancer, we will be able to detect or exclude genetic variants that were previously unidentifiable. This will allow for family investigations, screening, and in the long run early detection of cancer in families that previously could not be given that opportunity, says Panagiotis Baliakas, senior consultant in hematology and clinical genetics and PI for the project.

CG Uppsala will also contribute to a project aiming to implement molecular classification of endometrial cancer using the GMS560 gene panel developed by Genomic Medicine Sweden and the national CG platform, led by Patrick Micke, that was funded in the same call.