New report highlights national capacity for Next Generation Sequencing

In close collaboration with the SciLifeLab Clinical Genomics platform (CG), Genomic Medicine Sweden (GMS), have compiled a national inventory of genomic analyzes on clinical samples performed in 2021. The goal was to establish an overall picture of the number of NGS (Next-Generation Sequencing-based analyzes of clinical samples) that are performed annually, in order to identify Sweden’s current capacity.

“In recent years, we have seen a large increase in how whole genome sequencing and gene panels are used in clinical practice around the country. It is gratifying that the new technologies have been able to be introduced widely and be of use for more precise diagnostics and more individualized treatment”, says Richard Rosenquist Brandell, director of Genomic Medicine Sweden in a press release.

The whole-genome sequencing for rare diseases was performed at three university hospitals in Region Stockholm, Region Skåne and Region Västra Götaland, among others.

Based on this national inventory it will be possible to predict and monitor a range of factors; including capacity, needs and actual implementation of the NGS that has been developed in a collaboration between the Clinical Genomics platform at SciLifeLab and GMS.

Over the course of 2021 more than 15,000 samples for various forms of cancer and rare diseases have been analyzed with gene panels according to the report.

“The myeloid gene panel is the first gene panel developed by GMS and the Clinical Genomics platform to be used in routine clinical practice. We are also in the final phase of introducing a broad gene panel for solid tumors and another gene panel for lymphatic malignancies”, says Richard Rosenquist Brandell.

The Clinical Genomics platform and GMS-developed gene panel for myeloid leukemia has been in clinical routine throughout 2021, with a total of 3,800 samples analyzed with the myeloid gene panel.

Results in brief:

• In 2021, the total number of patient samples analyzed with whole genome sequencing (WGS) in Sweden is 4,989 samples for rare diagnoses and 150 samples for solid tumors. During the same period, 1,953 patient samples for rare diagnoses were also analyzed with complete ex-sequencing (WES).
• In 2021, a total of 15,130 samples were analyzed with gene panels for the diagnoses; solid tumors, hematology and rare diagnoses. Of these samples, 3,803 samples were analyzed with the GMS myeloid gene panel. Since GMS started in 2017, the number of samples analyzed with gene panels has doubled (2017: 7,284 samples, 2021: 15,130 samples).
• In cancer, targeted RNA sequencing as part of gene panel analysis has been performed for 1,461 samples in solid tumors and a small number of samples in hematology.
• In microbiology and infectious diseases, 5,494 samples were analyzed with 16S / metagenomics and 2,363 samples with WGS in 2021. In addition, WGS was performed for 45,482 SARS-CoV-2 samples.