von Mehren M, Randall RL, Benjamin RS, et al (2018) Soft tissue sarcoma, Version 2.2018, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw16:536–563

Sbaraglia M, Bellan E, Dei Tos AP (2021) The 2020 WHO classification of soft tissue tumours: news and perspectives. Pathologica 113:70–84

Article  PubMed  Google Scholar 

Demetri GD, Baker LH, Beech D et al (2005) Soft tissue sarcoma clinical practice guidelines in oncology. J Natl Compr Canc Netw 3:158–194

PubMed  PubMed Central  Google Scholar 

Szurian K, Kashofer K, Liegl-Atzwanger B (2017) Role of next-generation sequencing as a diagnostic tool for the evaluation of bone and soft-tissue tumors. Pathobiology 84:323–338

Article  PubMed  Google Scholar 

de Alava E (2017) Ewing sarcoma, an update on molecular pathology with therapeutic implications. Surg Pathol Clin 10:575–585

Article  PubMed  Google Scholar 

Arnold MA, Barr FG (2017) Molecular diagnostics in the management of rhabdomyosarcoma. Expert Rev Mol Diagn 17:189–194

Article  PubMed  PubMed Central  Google Scholar 

ESMO/European Sarcoma Network Working Group. Soft tissue and visceral sarcomas: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol 2014;25:iii102–12

Tian Z, Yao W (2023) Chemotherapeutic drugs for soft tissue sarcomas: a review. Front Pharmacol 14:1199292

Article  PubMed  PubMed Central  Google Scholar 

Kyriazoglou A, Gkaralea LE, Kotsantis I et al (2022) Tyrosine kinase inhibitors in sarcoma treatment. Oncol Lett 23:183

Article  PubMed  PubMed Central  Google Scholar 

Tang F, Tie Y, Wei YQ et al (2021) Targeted and immuno-based therapies in sarcoma: mechanisms and advances in clinical trials. Biochim Biophys Acta Rev Cancer 1876:188606

Article  PubMed  Google Scholar 

Nakano K, Takahashi S (2020) Precision medicine in soft tissue sarcoma treatment. Cancers (Basel) 12:221

Article  PubMed  Google Scholar 

Gounder MM, Agaram NP, Trabucco SE et al (2022) Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma. Nat Commun 13:3406

Article  PubMed  PubMed Central  Google Scholar 

Chen S, Zhou Y, Chen Y et al (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890

Article  PubMed  PubMed Central  Google Scholar 

Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

Article  PubMed  PubMed Central  Google Scholar 

Lai Z, Markovets A, Ahdesmaki M et al (2016) VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Res 44:e108

Article  PubMed  PubMed Central  Google Scholar 

Li Q, Wang K (2017) InterVar: clinical interpretation of genetic variants by the 2015 ACMG-AMP Guidelines. Am J Hum Genet 100:267–280

Article  PubMed  PubMed Central  Google Scholar 

Talevich E, Shain AH, Botton T et al (2016) CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing. PLoS Comput Biol 12:e1004873

Article  PubMed  PubMed Central  Google Scholar 

Newman AM, Bratman SV, Stehr H et al (2014) FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution. Bioinformatics 30:3390–3393

Article  PubMed  PubMed Central  Google Scholar 

FDA Recognition of Public Human Genetic Variant Databases. (Official FDA website, 2024) or MSK's Precision Oncology Knowledge Base

Drilon A, Laetsch TW, Kummar S et al (2018) Efficacy of larotrectinib in TRK fusion-positive cancers in adults and children. N Engl J Med 378:731–739

Article  PubMed  PubMed Central  Google Scholar 

Hasegawa N, Hayashi T, Niizuma H et al (2024) Detection of novel tyrosine kinase fusion genes as potential therapeutic targets in bone and soft tissue sarcomas using DNA/RNA-based clinical sequencing. Clin Orthop Relat Res 482(3):549–563

Article  PubMed  Google Scholar 

Jin G, Wang C, Jia D et al (2021) Next generation sequencing reveals pathogenic and actionable genetic alterations of soft tissue sarcoma in Chinese patients: a single center experience. Technol Cancer Res Treat 20:15330338211068964

Article  PubMed  PubMed Central  Google Scholar 

Gan M, Zhang C, Qiu L et al (2022) Molecular landscape and therapeutic alterations in Asian soft-tissue sarcoma patients. Cancer Med 11:4070–4078

Article  PubMed  PubMed Central  Google Scholar 

Zhang Q, Yang Y, You X et al (2023) Comprehensive genomic analysis of primary bone sarcomas reveals different genetic patterns compared with soft tissue sarcomas. Front Oncol 13:1173275

Article  PubMed  PubMed Central  Google Scholar 

Sharpless NE (2005) INK4a/ARF: a multifunctional tumor suppressor locus. Mutat Res 576:22–38

Article  PubMed  Google Scholar 

Nakano K, Takahashi S (2020) Precision medicine in soft tissue sarcoma treatment. Cancers (Basel) 12:221

Article  PubMed  Google Scholar 

Delattre O, Zucman J, Melot T et al (1994) The Ewing family of tumors–a subgroup of small-round-cell tumors defined by specific chimeric transcripts. N Engl J Med 331:294–299

Article  PubMed  Google Scholar 

Riggi N, Cironi L, Suvà ML, et al (2007) Sarcomas: genetics, signalling, and cellular origins. Part 1: The fellowship of TET. J Pathol 213:4–20

Riggi N, Cironi L, Provero P et al (2005) Development of Ewing’s sarcoma from primary bone marrow-derived mesenchymal progenitor cells. Cancer Res 65:11459–11468

Article  PubMed  Google Scholar 

Riggi N, Suvà ML, Suvà D et al (2008) EWS-FLI-1 expression triggers a Ewing’s sarcoma initiation program in primary human mesenchymal stem cells. Cancer Res 68:2176–2185

Article  PubMed  Google Scholar 

Ladanyi M, Antonescu CR, Leung DH et al (2002) Impact of SYT-SSX fusion type on the clinical behavior of synovial sarcoma: a multi-institutional retrospective study of 243 patients. Cancer Res 62:135–140

PubMed  Google Scholar 

McBride MJ, Pulice JL, Beird HC et al (2018) The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma. Cancer Cell 33:1128-1141.e7

Article  PubMed  PubMed Central  Google Scholar 

Nielsen TO, Poulin NM, Ladanyi M (2015) Synovial sarcoma: recent discoveries as a roadmap to new avenues for therapy. Cancer Discov 5:124–134

Article  PubMed  PubMed Central  Google Scholar 

Koboldt DC (2020) Best practices for variant calling in clinical sequencing. Genome Med 12(1):91

Article  PubMed  PubMed Central  Google Scholar 

van Belzen IAEM, Schönhuth A, Kemmeren P, Hehir-Kwa JY (2021) Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology. NPJ Precis Oncol 5(1):15

Article  PubMed  PubMed Central  Google Scholar 

Liu Z, Roberts R, Mercer TR, Xu J, Sedlazeck FJ, Tong W (2022) Towards accurate and reliable resolution of structural variants for clinical diagnosis [published correction appears in Genome Biol 23(1):198.

Benayed R, Offin M, Mullaney K et al (2019) High yield of RNA sequencing for targetable kinase fusions in lung adenocarcinomas with no mitogenic driver alteration detected by DNA sequencing and low tumor mutation burden. Clin Cancer Res 25(15):4712–4722

Article  PubMed  PubMed Central  Google Scholar 

Cohen D, Hondelink LM, Solleveld-Westerink N et al (2020) Optimizing mutation and fusion detection in NSCLC by sequential DNA and RNA sequencing. J Thorac Oncol 15(6):1000–1014

Article  PubMed