Web Table 1

Information on molecular validation of synovial sarcoma cases

			Confirmation of Diagnosis*
Case #	diagnosis	subtype	Cytogenetics	RTPCR-frozen	RTPCR-FFPE	SYT FISH	expression profile	biphasic
1	SynSarc	monophasic	+
2	SynSarc	monophasic					+
3	SynSarc	biphasic			+			+
4	SynSarc	monophasic			+
5	SynSarc	monophasic			+
6	SynSarc	monophasic		+ (SSX2)
7	SynSarc	biphasic					+	+
8	SynSarc	monophasic			+
9	SynSarc	monophasic	+	+ (SSX1)
10	SynSarc	monophasic	+		+
11	SynSarc	monophasic	+
12	SynSarc	monophasic	+
13	SynSarc	biphasic			+			+
14	SynSarc	monophasic	+	+ (SSX1)			+
15	SynSarc	monophasic	+	+ (SSX1)	+
16	SynSarc	monophasic			+
17	SynSarc	monophasic			+
18	SynSarc	monophasic	+
19	SynSarc	biphasic	+					+
20	SynSarc	monophasic	+	+ (SSX1)
21	SynSarc	monophasic			+
22	SynSarc	biphasic	+	+ (SSX1)				+
23	SynSarc	monophasic			+
24	SynSarc	monophasic			+
25	SynSarc	monophasic	+
26	SynSarc	monophasic	+
27	SynSarc	monophasic			+
(28)	(kidney)	(murine)
29	SynSarc	monophasic			+	+
30	SynSarc	monophasic			+	+
31	SynSarc	monophasic
32	SynSarc	monophasic
33	SynSarc	monophasic				+
34	SynSarc	monophasic			+	+
35	SynSarc	biphasic			+	+		+
36	SynSarc	biphasic				+		+
37	SynSarc	monophasic			+
38	SynSarc	monophasic			+
39	SynSarc	monophasic			+	+
40	SynSarc	biphasic				+		+
41	SynSarc	monophasic				+
42	SynSarc	biphasic			+	+		+
43	SynSarc	monophasic			+	+
44	SynSarc	monophasic				+
45	SynSarc	biphasic	+	+ (SSX2)		+		+
46	SynSarc	monophasic			+	+
47	SynSarc	biphasic				+		+

* Definition of confirmation of diagnosis

Cytogenetics = t(X;18) by classical cytogenetic karyotyping
RTPCR-frozen = reverse transcriptase PCR on frozen tumor tissue or cell pellet, first using primers bracketing the SYT-SSX fusion site, and then with SSX subtype specific primers
RTPCR-FFPE = reverse transcriptase PCR on formalin-fixed, paraffin-embedded tissue using primers bracketing the SYT-SSX fusion site; product confirmed by Southern blot
SYT FISH = confirmation by fluorescent in situ hybridization analysis, using interphase nuclei in the archival tissue microarray cores, that the SYT gene has been split
expression profile = cDNA microarray analysis, on arrays with 22k or 42k spots, of mRNA from frozen tumor gives profile which clusters tightly with other synovial sarcomas
biphasic = classical biphasic histology present on some of the original whole sections