Table Info

Table 1.

Table showing the gene fusions called by ADx in the 31 cases analyzed by sarcoma panel

Samples	Histology/Diagnosis*	Sarcoma panel ADx	FISH
1	Inflammatory myofibroblastic tumor^a	ETV6-NTRK3	ETV6-NTRK3
2	Myoepithelial carcinoma	EWSR1-PATZ1	EWSR1 translocated
3	EWSR1-TFCP2 rearranged sarcoma	EWSR1-TFCP2 ALK deletion (Δ2-18)	EWSR1 translocated ALK translocated
4	Extraskeletal myxoid chondrosarcoma	EWSR1-NR4A3	EWSR1-NR4A3
5	Ewing sarcoma	EWSR1-FLI1	EWSR1-FLI1
6	EWS-rearranged small round cells sarcoma	EWSR1-CREM	EWSR1 translocated
7	High grade ESS	YWHAE-NUTM2B	YWHAE translocated
8	Monophasic synovial sarcoma	SS18-SSX4^b	SS18 intragenic rearrangement
9	Biphasic synovial sarcoma	SS18-SSX1^b	SS18 not translocated
10	CIC-rearranged sarcoma	CIC-DUX4^c	CIC not translocated
11	Sclerosing epithelioid fibrosarcoma	EWSR1-CREB3L2	Not done
12	Ewing sarcoma	EWSR1-FLI1	Not done
13	Solitary fibrous tumor	NAB2-STAT6^d	Not detectable by FISH
14	Cellular congenital mesoblastic nephroma	ETV6-NTRK3	Not done
15	MPNST	No fusions	SS18, EWSR1, FUS negative
16	Composite hemangioendothelioma	No fusions	WWTR1 negative^e
17	Myoepithelial carcinoma	No fusions	SS18, BCOR, CIC negative
18	Undifferentiated sarcoma, NOS	No fusions	EWSR1, FUS negative^e
19	Embryonal rhabdomyosarcoma	No fusions	SS18 negative
20	Angiomatoid fibrous histiocytoma	No fusions	EWSR1, FUS, ATF1, CREB1 negative
21	Pleomorphic sarcoma	No fusions	Not done
22	Undifferentiated small round cell sarcoma	No fusions	EWSR1, BCOR, FUS, CIC, NCOA2 negative^e
23	Undifferentiated sarcoma, NOS	No fusions	Not done
24	Undifferentiated sarcoma, NOS	No fusions	Not done
25	Spindle cell sarcoma, NOS	No fusions	FUS negative^e
26	Meningioma	No fusions	Not done
27	Sclerosing epithelioid fibrosarcoma^f	No fusions	ALK negative
28	Malignant myopericytoma	No fusions	SS18, EWSR1, BCOR, CIC, TFE3 negative
29	Myoepithelioma	Not evaluable	PHF1, FUS, CIC, BCOR, EWSR1, NR4A3 negative
30	High grade sarcoma, NOS	Not evaluable	EWSR1, NCOA2, CIC, SS18, BCOR negative
31	Oral cavity neoplasm^g	Not evaluable	Not done

a: the ETV6-NTRK3 translocation is unusual in inflammatory myofibroblastic tumor and was found in a lung biopsy obtained from a male 67 years hold patient. b: the SS18-SSX fusions were found in samples from 2 patients that had clinical histories and immunophenotypes fitting synovial sarcoma. In one of these two cases (sample 8), FISH revealed a pattern of SS18 intragenic rearrangement suggestive of SS18 translocation. As described in the main text, SS18 cryptic fusions undetectable by FISH, are well-known events. c: the same situation described in the previous note can be drawn for CIC gene. d: NAB2- STAT6 is a translocation not detectable by FISH. e: RNAseq was performed on surgical samples while FISH was done on CNBs prior surgery. f: external diagnosis. g: final diagnosis not available. *: According to WHO classification of Soft tissue and bone tumors [17]; ESS: endometrial stromal sarcoma; MPNST: malignant peripheral nerve sheet tumor; NOS: not otherwise specified; PATZ1: POZ/BTB and AT hook containing zinc finger 1; TFCP2: transcription factor CP2; NR4A3: nuclear receptor subfamily 4 group A member 3; CREM: cAMP responsive element modulator; NUTM2B: NUT family member 2B; SSX4: SSX family member 4; DUX4: double homeobox 4; WWTR1: WW domain containing transcription regulator 1; BCOR: BCL6 corepressor; ATF1: activating transcription factor 1; CREB1: cAMP responsive element binding protein 1; PHF1: PHD finger protein 1

Supplementary materials

The supplementary materials for this article are available at: https://www.explorationpub.com/uploads/Article/file/1002102_sup_1.pdf.

Declarations

Author contributions

FB: Writing – original draft; IC, EC, AB, GD, MAT, VM, MD, CP, SD, AV, PC, and DL: Investigation; LA, PV, and AD: Software and Formal analysis; AP, IC, FB: Data curation; IC, FB, GD, FP, ET, PC, DL, AV, LA, and GP: Writing – review & editing. GP: Supervision. All the authors read and approved the submitted version.

Conflicts of interest

The authors declare that they have no conflicts of interest.

Ethical approval

This study was performed according with the Declaration of Helsinki and approved by the Ethics committee of Fondazione IRCCS Istituto Nazionale Tumori Milano (INT 277/20).

Consent to participate

Written informed consent to participate in the study was obtained from all participants.

Consent to publication

Not applicable.

Availability of data and materials

The raw data supporting the conclusions of this manuscript will be made available by the authors (luca.agnelli@istitutotumori.mi.it), without undue reservation, to any qualified researcher.

Funding

Not applicable.

Copyright

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