Table 1.

Target-specific oligonucleotide probes designed for nCounter assay.

Gene fusion probes (27 pairs)	ALK (8 variants)	ROS1 (6 variants)	RET (6 variants)	NTRK (5 variants)	BRAF (2 variants)
	EML4-ALK_V2	EZR-ROS1_E10-R34	CCDC6-RET_C1-R12	CD74-NTRK1__C7-N10	KIAA1549-BRAF_K16-B9
	EML4-ALK_V3a	GOPC-ROS1_G8-R35	KIF5B-RET_K15-R12	ETV6-NTRK3_E4-N15	KIAA1549_ex15 Fusion
	EML4-ALK_V5P	SDC43-ROS1_S2-R32	KIF5B-RET_K16-R12	ETV6-NTRK3_E5-N15
	EML4_ex13 Fusion	SDC43_ex4 Fusion	KIF5B-RET_K22-R12	MPRIP-NTRK1_M21-N12
	EML4_ex14 Fusion	SLC34A2-ROS1_S4-R32	KIF5B-RET_K23-R12	CD74_ex6 Fusion
	EML4_ex2 Fusion	TPM3-ROS1	KIF5B4_ex24 Fusion
	KIF5B-ALK_K17-A20
	TFG-ALK
Imbalance probes (37 pairs)	ALK(6 probes)	ROS1(6 probes)	RET(6 probes)	NTRK(13 probes)	BRAF(6 probes)
	ALK_ex14-18	ROS1	RET	NTRK1 _ex1-4	BRAF_ex13-14
	ALK_ex2-5	ROS1_ex18-24	RET_ex18-19	NTRK1 _ex15-16	BRAF_ex15-16
	ALK_ex22-24	ROS1_ex21-24	RET_ex19	NTRK1 _ex17	BRAF_ex18
	ALK_ex26-27	ROS1_ex39-40	RET_ex2-4	NTRK1 _ex6-8	BRAF_ex2-3
	ALK_ex29	ROS1_ex41-43	RET_ex4-5	NTRK1_ex13-14	BRAF_ex3-4
	ALK_ex8-12	ROS1_ex8-12	RET_ex6-9	NTRK1_ex4-5	BRAF_ex5-7
				NTRK2, NTRK3 _ex20
				NTRK3 _ex10-13
				NTRK3 _ex16-17
				NTRK3 _ex18-19
				NTRK3 _ex4-8, _ex8-9
Other driver genes (62 pairs)	ABCB1, ABCG2, AKT1, AKT2, AXL, BCL2, BIRC5, BRCA1,CA9, CDK4,CDK6,CDKN2A,CTAG1B,EGFR, ERBB2,ERBB3,ERBB4,ERCC1, ESR1, FGFR1,FGFR2,FKBP1A,FLT1,FLT3,FLT4,FOLH1(PSMA),GRB7,GSTP1,HSP90AA1,HSP90AB1,IL2RA,IL6,IL8,JAK1,JAK2,KDR, KIT,MAP2K1,MAP2K2,MET,MTOR,PARP1,PDGFRA,PDGFRB,PGR,PIK3CA,PIK3CB,PIK3CD,PIK3CG,POSTN,RB1, RRM1, SLC29A1, SPINK1,SPP1(OPN),SRC,TIMP1,TOP1,TOP2A,TP53, TUBB3,TYMS
Housekeeping genes	CLTC,GAPDH,GUSB,HPRT1,PGK1,TUBB (6 pairs)
Positive control	POS_A,POS_B,POS_C,POS_D,POS_E,POS_F (6 pairs)
Negative control	NEG_A,NEG_B,NEG_C,NEG_D,NEG_E,NEG_F (6 pairs)