Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma

• Published in: Nature communications Vol. 13; no. 1; pp. 3406 - 15
• Main Authors: Gounder, Mrinal M., Agaram, Narasimhan P., Trabucco, Sally E., Robinson, Victoria, Ferraro, Richard A., Millis, Sherri Z., Krishnan, Anita, Lee, Jessica, Attia, Steven, Abida, Wassim, Drilon, Alexander, Chi, Ping, Angelo, Sandra P. D’, Dickson, Mark A., Keohan, Mary Lou, Kelly, Ciara M., Agulnik, Mark, Chawla, Sant P., Choy, Edwin, Chugh, Rashmi, Meyer, Christian F., Myer, Parvathi A., Moore, Jessica L., Okimoto, Ross A., Pollock, Raphael E., Ravi, Vinod, Singh, Arun S., Somaiah, Neeta, Wagner, Andrew J., Healey, John H., Frampton, Garrett M., Venstrom, Jeffrey M., Ross, Jeffrey S., Ladanyi, Marc, Singer, Samuel, Brennan, Murray F., Schwartz, Gary K., Lazar, Alexander J., Thomas, David M., Maki, Robert G., Tap, William D., Ali, Siraj M., Jin, Dexter X.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 15-06-2022; Nature Publishing Group; Nature Portfolio
• Subjects: 45/23; 631/67/1798; 631/67/1857; 631/67/2329; 631/67/69; 692/4028/67/1059/602; Biomarkers, Tumor - genetics; Bone cancer; Bone Neoplasms - genetics; Bone tumors; Cancer; Drug development; Genomics; Heterozygosity; Homologous recombination; Homology; Humanities and Social Sciences; Humans; Kinases; Loss of heterozygosity; Microsatellite instability; multidisciplinary; Mutation; Osteosarcoma; Patients; Prospective Studies; Sarcoma; Sarcoma - diagnosis; Sarcoma - genetics; Sarcoma - therapy; Science; Science (multidisciplinary); Soft tissues; Therapeutic applications; Therapeutic targets
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-30496-0

There are more than 70 distinct sarcomas, and this diversity complicates the development of precision-based therapeutics for these cancers. Prospective comprehensive genomic profiling could overcome this challenge by providing insight into sarcomas’ molecular drivers. Through targeted panel sequencing of 7494 sarcomas representing 44 histologies, we identify highly recurrent and type-specific alterations that aid in diagnosis and treatment decisions. Sequencing could lead to refinement or reassignment of 10.5% of diagnoses. Nearly one-third of patients (31.7%) harbor potentially actionable alterations, including a significant proportion (2.6%) with kinase gene rearrangements; 3.9% have a tumor mutational burden ≥10 mut/Mb. We describe low frequencies of microsatellite instability (<0.3%) and a high degree of genome-wide loss of heterozygosity (15%) across sarcomas, which are not readily explained by homologous recombination deficiency (observed in 2.5% of cases). In a clinically annotated subset of 118 patients, we validate actionable genetic events as therapeutic targets. Collectively, our findings reveal the genetic landscape of human sarcomas, which may inform future development of therapeutics and improve clinical outcomes for patients with these rare cancers.
Comprehensive molecular profiles are required to understand and treat sarcomas, which comprise more than 70 different subtypes. Here, the authors profile the genomic landscape of 7494 sarcomas across 44 histologies using targeted panel sequencing and identify potential therapeutic targets.