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

Abstract

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.

Fig. 1. Cohort characterization and diagnostic corrections of sarcoma subtypes.

a Distribution of soft tissue and bone sarcoma subtypes among the cohort of 7494 patients. b Density curves showing age distributions for common pediatric, adolescent, and young adult (P-AYA; defined as ≤30 years of age) cancers. Vertical lines represent median age for each sarcoma. c Sankey diagram illustrating diagnostic corrections for 10.5% (789/7,494) of patient samples. Left, number of cases identified for each subtype according to original submitted pathology results; right, number of corrections or refinements for each histology as determined by the presence or absence of pathognomonic genomic rearrangements or signatures. NOS not otherwise specified, W/DD well or dedifferentiated, UPS undifferentiated pleomorphic sarcoma, MFH malignant fibrous histiocytoma, MPNST malignant peripheral nerve sheath tumor, UT ESS uterine endometrial stromal sarcoma, A alveolar, GIST gastrointestinal stromal tumor, DSRCT desmoplastic small round cell tumor, E embryonal, EM extraskeletal myxoid, IMT inflammatory myofibroblastic tumor, URC/EL undifferentiated round cell/Ewing-like, LGFMS/SEF low-grade fibromyxoid sarcoma/sclerosing epithelioid fibrosarcoma, EHE epithelioid hemangioendothelioma, DFSP dermatofibrosarcoma protuberans, PEComa perivascular epithelioid cell tumor, MES mesenchymal, P pleomorphic, ES extraskeletal, RMS rhabdomyosarcoma. Source data are provided as a Source Data file.

Fig. 2. Genomic landscape of sarcomas.

a Heat map showing the frequency of recurrent short variants and copy number variants in the listed genes in each subtype of sarcoma, grouped as translocation-associated or genomically complex and other sarcomas (left), as well as the types of genomic alterations (right). b Volcano plot showing co-occurrence (odds ratio >1) and mutual exclusivity (odds ratio <1) between two genes within the same pathway. Top ten significant interactions (FDR < 0.05) are labeled. UT ESS uterine endometrial stromal sarcoma, ASPS alveolar soft part sarcoma, A alveolar, IMT inflammatory myofibroblastic tumor, LGFMS/SEF low-grade fibromyxoid sarcoma/sclerosing epithelioid fibrosarcoma, DSRCT desmoplastic small round cell tumor, URC/EL undifferentiated round cell/Ewing-like, DFSP dermatofibrosarcoma protuberans, EHE epithelioid hemangioendothelioma, UT uterine, P pleomorphic, UPS undifferentiated pleomorphic sarcoma, MFH malignant fibrous histiocytoma, ES extraskeletal, NOS not otherwise specified, PEComa perivascular epithelioid cell tumor, E embryonal, MPNST malignant peripheral nerve sheath tumor, W/DD well or dedifferentiated, GIST gastrointestinal stromal tumor. Source data are provided as a Source Data file.

Fig. 3. Gain-of-function kinase gene fusions.

a Recurrent kinase gene fusions resulting in activating oncogenes in the kinase domains of FGFR1, ALK, NTRK1, NTRK2, NTRK3, and BRAF. Arrows indicate breakpoints. b Rearrangements that result in activating fusions between TNS1 and ALK, including breakpoints in introns 18 and 16 that give rise to fusions of exons 19–29 and 17–29, respectively. These fusions were detected in 16 patients primarily in uterine and non-uterine leiomyosarcoma. Source data are provided as a Source Data file.

Fig. 4. Mutational burden and genomic loss of heterozygosity.

a Box-and-whisker plot of genomic loss of heterozygosity (gLOH) expressed as % of genome under LOH for each sarcoma histology. gLOH only evaluable n = 4619. Dashed horizontal line (19.3%) indicates 1 standard deviation above the mean gLOH. b Box-and-whisker plot of tumor mutational burden (TMB) and signatures derived from sequencing data for each sarcoma histology, grouped by age: pediatric, adolescent, and young adult (P-AYA) versus adult (>30 years). In (a, b), the lower and upper box boundaries represent 25th and 75th percentiles, lines within boxes represent medians, whiskers extend to extreme values ≤1.5 x IQR, and points beyond whiskers are outliers. Asterisk (*) indicates significant difference (with an FDR < 0.05) using a two-tailed non-parametric Mann–Whitney U test. In all cases, P-AYA harbored significantly lower TMB. c Relationship between tumor mutational burden (TMB) and genomic loss of heterozygosity (gLOH). Vertical line (10 mut/Mb) indicates distinction between “low” and “high” TMB. Dashed horizontal line (19.3%) indicates 1 standard deviation above the mean gLOH and indicates distinction between “low” and “high” gLOH. A alveolar, MES mesenchymal, DSRCT desmoplastic small round cell tumor, ASPS alveolar soft part sarcoma, URC/EL undifferentiated round cell/Ewing-like, LGFMS/SEF low-grade fibromyxoid sarcoma/ sclerosing epithelioid fibrosarcoma, DFSP dermatofibrosarcoma protuberans, OFT ossifying fibromyxoid tumor, EM extraskeletal myxoid, GIST gastrointestinal stromal tumor, E embryonal, W/DD well/dedifferentiated, EHE epithelioid hemangioendothelioma, RMS rhabdomyosarcoma, NOS not otherwise specified, UT uterine, ESS endometrial stromal sarcoma, IMT inflammatory myofibroblastic tumor, GCTB giant cell tumor of bone, PEComa perivascular epithelioid cell tumor, MPNST malignant peripheral nerve sheath tumor, P pleomorphic, ES extraskeletal, UPS undifferentiated pleomorphic sarcoma, MFH malignant fibrous histiocytoma. Source data are provided as a Source Data file.

Fig. 5. Actionability.

a Dominant mutational signatures in various sarcoma histologies. b Evidence for clinical actionability of somatic alterations across 44 sarcoma histologies. SOC, standard of care. c Flow chart of actions taken as a result of comprehensive genomic sequencing in 118 patients at MSK who underwent Foundation Medicine sequencing. OncoKB classifications were not applied retrospectively for the MSK cohort and thus reflect prevailing knowledge at time of enrollment. APOBEC, apolipoprotein B mRNA editing catalytic polypeptide-like; MMR, mismatch repair deficiency. Tobacco signifies mutational genomic signature attributable to cancers derived from tissues potentially exposed to tobacco smoke. UPS undifferentiated pleomorphic sarcoma, MFH malignant fibrous histiocytoma, MPNST malignant peripheral nerve sheath tumor, NOS not otherwise specified, PEComa perivascular epithelioid cell tumor, IMT inflammatory myofibroblastic tumor, E embryonal, DSRCT desmoplastic small round cell tumor, GIST gastrointestinal stromal tumor, ESS endometrial stromal sarcoma, W/DD well or dedifferentiated, P pleomorphic, ES extraskeletal, DFSP dermatofibrosarcoma protuberans, MES mesenchymal, LGFMS/SEF low-grade fibromyxoid sarcoma/sclerosing epithelioid fibrosarcoma, URC undifferentiated round cell, EHE epithelioid hemangioendothelioma, A alveolar, EM extraskeletal myxoid. Source data are provided as a Source Data file.

Fig. 6. Treatment outcomes of selected patients in whom sequencing identified an actionable alteration.

a Advanced, metastatic sarcoma, NOS harboring a SMARCB1 deletion with durable partial response to tazemetostat, an EZH2 inhibitor. b Metastatic, refractory sarcoma harboring BRAF^V600E with a rapid and near complete response to vemurafenib and trametinib. c Metastatic osteosarcoma with rapid progression on doxorubicin and cisplatin. After sequencing, identification of an ATM exon 57-truncating mutation, a combination of a PARP inhibitor and an investigational drug led to durable stable of >1 year. d Near complete response in metastatic, refractory undifferentiated pleomorphic sarcoma with high TMB (20 mut/Mb) treated with pembrolizumab. e Complete response in refractory malignant PEComa (TFE3 fusion-negative, TSC1 subclonal) harboring intermediate tumor mutational burden (7 mut/Mb) treated with nivolumab and ipilumumab (compassionate, off-label). f Complete response in inflammatory myofibroblastic sarcoma harboring an ETV6-NTRK3 fusion and treated with larotrectinib.