Table 1.

Characteristics of rearrangement junctions identified in patient, reference, and cell line samples

Patient Junctions

APatient Bank #	BJunctions	CGene 1	DGene 2	EOrientation	FIntron	GReading Frame	HFISH	IERG Stain	JReads	KJunction Reads	LSequence Flanking Breakpoint
4	TMPRSS2-ERG	chr21:41794326	chr21:38753597	s/s	1–3	IF	D	+	2	1
10	TMPRSS2-ERG	chr21:41792775	chr21:38792757	s/s	1–3	IF	n/a	n/a	6	1
70	TMPRSS2-MPRL12	chr21:41783383	chr17:77283404	s/a		ND	n/a	n/a	6	3
	HAP1*-TMPRSS2	chr17:37144837	chr21:41779769	a/s		ND			19	5
	TMPRSS2-HAP1*	chr21:41794230	chr17:37149531	s/s		ND			12	4
	TMPRSS2-SWI5	chr21:41779767	chr9:130085490	s/s		ND			5	2
82	EIF3K–TMPRSS2	chr19:43815389	chr21:41788584	a/s		ND	n/a	n/a	5	2
	NF1-TMPRSS2	chr17:26590306	chr21:41774186	a/s		ND			13	4
134	TMPRSS2-ERG	chr21:41795069	chr21:38803391	s/s	1–3	IF	n/a	n/a	8	2
	ACPP-TMPRSS2	chr3:133565489	chr21:41795096	a/s		ND			6	2
144	TMPRSS2-ERG	chr21:41779065	chr21:38796877	s/s	5–3	ND	n/a	n/a	7	5
	TMPRSS2-TMPRSS2	chr21:41789960	chr21:41781176	s/s		ND			5	0
199	TMPRSS2-ERG	chr21:41786586	chr21:38748712	s/a	3–3	ND	n/a	n/a	6	3
206	TMPRSS2-ERG	chr21:41793812	chr21:38763138	s/s	1–3	IF	n/a	n/a	9	0
214	TMPRSS2-ERG	chr21:41797467	chr21:38749676	s/s	1–3	IF	n/a	n/a	3	1
341	TMPRSS2-ERG	chr21:41785537	chr21:38798302	s/s	3–3	ND	n/a	n/a	4	1
353	TMPRSS2-ERG	chr21:41789358	chr21:38799621	s/s	2–3	IF	n/a	n/a	1	1
357	TMPRSS2-ERG	chr21:41794131	chr21:38797829	s/s	1–3	IF	n/a	n/a	4	2
372	TMPRSS2-ERG	chr21:41797622	chr21:38784847	s/s	1–3	IF	−	−	1	0
	S LC 45A 3-ERG	chr1:203908669	chr21:38798718	s/s		IF			1	1
535	TMPRSS2-ERG	chr21:41790462	chr21:38748584	s/s	2–3	IF	D	+	1	1
558	TDRD7*-TMPRSS2	chr9:99213679	chr21:41794880	s/s		ND	n/a	n/a	2	0
	TMPRSS2-TMPRSS2	chr21:41771407	chr21:41780399	s/s		ND			7	1
	MX1-TMPRSS2	chr21:41752881	chr21:41775109	s/s		ND			6	3
580	MX1-TMPRSS2	chr21:41752819	chr21:41775553	s/s		ND	n/a	n/a	2	1
652	TMPRSS2-ERG	chr21:41792424	chr21:38775810	s/s	1–3	IF	T	+	4	1
	ERG-ERG	chr21:38830023	chr21:38872708	s/s		ND			2	1
675	TMPRSS2-ERG	chr21:41798800	chr21:38789416	s/s	1–3	IF	D	+	13	0
682	TMPRSS2-ERG	chr21:41796887	chr21:38791968	s/s	1–3	IF	D	+	6	1
733	TMPRSS2-ERG	chr21:41794661	chr21:38816717	s/s	1–3	IF	n/a	n/a	7	3
738	THSD7A–TMPRSS2	chr7:11743984	chr21:41788390	s/s		ND	n/a	−	4	2
780	TMPRSS2-ERG	chr21:41792243	chr21:38787029	s/s	1–3	IF	n/a	n/a	1	0
808	TMPRSS2-ERG	chr21:41790468	chr21:38780232	s/s	2–3	IF	T	+	38	13
	TMPRSS2-ERG	chr21:41783369	chr21:38805184	a/a	Exon4-Intron3	ND			10	5
	SPATA5L1*-TMPRSS2	chr15:43481074	chr21:41771055	a/s		ND			9	1
814	TMPRSS2-ERG	chr21:41792783	chr21:38784111	a/s	1–3	ND	T+		9	0
	MORC3-TMPRSS2	chr21:36673099	chr21:41762272	s/a		ND			12	0
816	TMPRSS2-ERG	chr21:41791718	chr21:38797360	s/s	2–3	IF	T	+	10	4
	C1qTNF1-TMPRSS2	chr17:74540999	chr21:41791286	s/s		ND			6	2
	C1qTNF1-TMPRSS2	chr17:74540985	chr21:41764084	a/s		ND			9	2
	TMPRSS2-TMPRSS2	chr21:41764044	chr21:41796946	s/a		ND			13	3
981	TMPRSS2-ERG	chr21:41795091	chr21:38796469	s/s	1–3	IF	D	+	15	3
989	FAM177A1-ERG	chr14:34584342	chr21:38756847	a/s		ND	D	+	5	1
995	TMPRSS2-ERG	chr21:41780434	chr21:38793491	a/a	5–3	ND	T+		5	0
	TMPRSS2-TMPRSS2	chr21:41762098	chr21:41773713	a/s		ND			12	3
	TMPRSS2-TMPRSS2	chr21:41780464	chr21:41790293	s/a		ND			10	3
	TMPRSS2-TMPRSS2	chr21:41786495	chr21:41773659	s/s		ND			2	1
	ERG-ERG	chr21:38793472	chr21:38793604	a/s		ND			5	0
1164	TMPRSS2-TV5	chr21:41797113	chr3:187278460	s/s	1–7	IF	T, TMPRSS2	+ for ETV5	11	1
1273	ELK4-RG	chr1:203858916	chr21:38746745	a/s		ND	T,ERG	−	7	0
1355	TMPRSS2-RG	chr21:41788584	chr21:38799738	s/s	2–3	IF	n/a	+	1	0
1422	TMPRSS2-RG	chr21:41795553	chr21:38788443	a/s	1–3	IF	n/a	+	7	2
1538	TMPRSS2-TV4	chr21:41795742	chr17:38978855	s/s	1–3	IF	T,TMPRSS2	+ for ETV4	17	0
1665	TMPRSS2-RG	chr21:41791298	chr21:38729732	s/s	2–4	IF	n/a	n/a	1	0
1863	TMPRSS2-MPRSS2	chr21:41761944	chr21:41777674	a/s		ND	n/a	n/a	5	0
VCAP Cell Line Junctions
VCAP	TMPRSS2-RG	chr21:41779893	chr21:38798223	a/s	5–3	ND	T+		28	4
	TMPRSS2-MPRSS2	chr21:41793823	chr21:41779387	s/a		ND			19	7
Reference Case Junctions
Case 45	TMPRSS2-ERG	chr21:41800806	chr21:38776561	s/s	1–3	IF	n/a	+	18	5
Case 66	TMPRSS2-ERG	chr21:41795687	chr21:38804491	s/s	1–3	IF	n/a	+	24	11
Case 77	TMPRSS2-ERG	chr21:41799367	chr21:38790118	s/s	1–3	IF	n/a	+	21	12

^APatient Bank # indicates the subject identification number used for each patient specimen.

^BGenes involved in rearrangements with 5' rearrangement partner listed first.

^cGenomic position of the rearrangement breakpoint for the 5' partner.

^DGenomic position of the rearrangement breakpoint for the 3' partner.

^ERefers to the strand orientation of Gene1/Gene2 in the rearrangement; s = sense and a = antisense.

^FIndicates the introns involved in a TMPRSS2-ETS gene rearrangement.

^GReading frame denoted as being In-Frame (IF) or Non-determinable (ND)

^HRearrangement status by FISH; Rearrangement with Deletion (D) or with Translocation (T)

^IERG staining status by IHC; additional ETS rearrangement staining by CISH

^JNumber of paired-end reads flanking or directly overlapping the rearrangement junction.

^KNumber of reads directly overlapping the rearrangement junction.

^LConfirmed nucleotide resolution of rearrangemnt junctions with relevant architecture; and are shown with and at or near the junction. Microhomologies were defined as being one or more ambiguously assignable nucleotides at the junction and three or more nucleotides in sequences flanking the junction that had identity in both partner sequences.

^*Indicates nearest gene when rearrangement occurs in intergenic space