Detection of fusion gene in cell-free DNA of a gastric synovial sarcoma

Table 1 Overview of primers and probe sequences for all PCR methods

Primers (5’-3’)	Sequence	Product size (bp)
Reverse transcription PCR
SYT-sense	CCAGCAGAGGCCTTATGGA	118
SSX2-antisense	GCACAGCTCTTTCCCATCA
Genomic PCR
SYT1-sense	GTAGTTTGACCGGCTGCAGAA
SYT2-sense	GGTGGTCTGGTTTGTTCACC
SYT3-sense	GCAAATGTTTATTGAGCAACCA
SYT4-sense	GGGAGAAATTAAAAGGGTGGA
SYT5-sense	CACCTGTGAAACCATCAGCA
SYT6-sense	TTTTCTTTATGGATTATGCTTTTGG
SYT7-sense	GCTTACTAGGAGTTTCATTGTAATTG
SYT8-sense	CAGCCTGATAAACTGTATACC
SYT9-sense	GATTTGAATGCGTGATCACAAG
SYT10-sense	GATTGGATTCCAGACATTGTG
SYT11-sense	GCCACCTTGGAATTTGTTAATG
SYT12-sense	CTGATGATTGAAGAAACCGAG
SSX2-1-antisense	ACGGAGAATCAGGGTTCTTTGG
SSX2-2-antisense	TCAGTCTCCACACTGGCAAC
SSX2-3-antisense	TCAAGGCAACATCCGACTCC
SSX2-4-antisense	TGGTTTCCAGGGATAGAATGCT
Real-time PCR
SYT-specific-sense	CCAGCAACAGTAGTTTACTTTCTATC	106
SSX2-specific-antisense	AAACATAGGGAGGCGACAAA
SYT-SSX2-FAM probe-sense	ATA+CAA+T+C+CA+G+CAG1

¹ + C, +T, + G = LNA base.

Table 2 Results of rt-PCR analysis by the specific probe and primer sets

Types of DNA	Sample	Ct value 1	Ct value 2	Mean
Genomic	Normal tissue	Undetermined	Undetermined	Undetermined
	Tumor tissue	31.94651	31.30283	31.62467
β-actin	Tumor tissue	28.97511	30.95062	29.96287

Undetermined: No Ct detection till 40 cycles.