(P 243) EVALUATION OF THE USE OF WGS IN ROUTINE DIAGNOSTICS FOR BONE AND SOFT TISSUE TUMORS

Objective: Molecular genetics may aid in the classification of soft tissue and bone tumors. Many different methods are currently in clinical practice. With technological advancement, comprehensive sequencing (WGS) has become economically feasible, but its value and role in the routine setting is yet to be determined.

We aimed to evaluate the clinical impact of introducing whole-genome sequencing (WGS) in routine diagnostics for all sarcoma cases referred to Sarcoma Center Karolinska, Sweden’s largest tertiary center for sarcomas. Primary endpoints included if WGS would change or confirm the histopathological diagnosis set clinically, and if germline analysis would detect hereditary cancer syndromes not identified by the clinicians.

Methods: In this prospective single-center study, we implemented WGS as a component of the diagnostic evaluation for patients presenting with bone or soft tissue tumors suspicious of sarcoma. We performed DNA sequencing on tumor and normal samples obtained from fresh frozen tissue and peripheral blood respectively. Sequencing was conducted once per week using the Illumina NovaSeq platform. To analyze the genomic data, we employed BALSAMIC and MIP bioinformatics tools, along with the in-house developed AutoSeq Informatics framework. Somatic single nucleotide variants, structural rearrangements, and copy number alterations were examined by clinical pathologists and geneticists. Assessment of germline variants followed the ACMG criteria, and pathogenic variants were addressed in accordance with local clinical guidelines.

Results: In this first phase of the study, 200 patients have been included. WGS altered the diagnosis in 17 patients (corresponding to 7% of high-grade sarcomas, 0% of low-grade sarcomas, 20% of benign mesenchymal tumors, 33% of non-mesenchymal tumors, and 16% of non-neoplastic lesions). Treatment prognostic targets (Tier 1-2, excluding MDM2 amplification) were identified in 27/29 GISTs, 8/95 high-grade sarcomas and 1/22 low-grade sarcomas.

The preoperative diagnosis had significant inaccuracy in 14 cases (6-14% depending on setting) when compared to the final histopathological diagnosis. If WGS had been performed on preoperative material, the genomic data could have corrected 11 of the 14 faulty diagnoses (79%). Notably, 8 cases had diagnostic pitfalls (non-subtype specific genetic variants or fusions).

In the germline analyses, 14% of the patients were found to have a theoretically clinically actionable variant, including pathogenic variants in the genes TP53, RB1, BRCA1, KCNQ1, MLH1, FH, or CHEK2. Out of those, 80% were associated with a known hereditary cancer syndrome.

Conclusion: WGS can become an important complementary tool for sarcoma diagnostics if it is used correctly. Germline analysis can preferably be added in parallel, to screen for hereditary cancer syndromes.