Table 3.

Identification of expressed chimeric transcripts in five micropapillary breast carcinomas

Sample ID	Gene 5′	Gene 3′	Mapping 5′	Mapping 3′	Total reads	Spanning reads	In frame	Validated	Copy number 5′	Copy number 3′
MPC10	ELMO2	RAE1	chr20:45014762	chr20:55943760	25	14	No	Y	Gain	Amp
MPC10	BCAS4	AURKA	chr20:49411466	chr20:54944444	24	1	Yes	Y	Gain	Amp
MPC10	SLC2A1	FAF1	chr1:43424304	chr1:50906934	12	5	Yes	Y	Amp	Gain
MPC10	TSEN54	UNC84A	chr17:73512608	chr7:934970	7	0	No	N	Gain	Gain
MPC10	CD46	USH2A	chr1:207925401	chr1:215796235	6	1	No	Y	Amp	Gain
MPC71	LASP1	CDK12	chr17:37026111	chr17:37646809	5	4	No	Y	Amp	Amp
MPC10	DENND1C	SURF1	chr19:6470305	chr9:136218665	4	0	Yes	N	No change	No change
MPC10	UBE2V1	SULF2	chr20:48713208	chr20:46286150	4	1	No	Y	Amp	Amp
MPC08	BC018860	CDK5RAP3	chr1:566461	chr17:46052524	3	1	No	N	No change	No change
MPC10	LRRC6	HPRG1	chr8:133584447	chr8:133572744	3	0	No	N	Amp	Amp
MPC08	PDLIM5	TCEB1	chr4:95373037	chr8:74858633	3	3	No	N	No change	Amp
MPC08	TSPAN14	DYDC2	chr10:82214037	chr10:82126443	3	1	No	N	Amp	No change
MPC10	IFI44L	IFI44	chr1:79086087	chr1:79115476	2	0	No	N	Loss	Loss
MPC10	MRPL21	BX640963	chr11:68660870	chr2:69686413	2	0	No	N	No change	No change
MPC10	SYNGAP1	RALY	chr6:33387846	chr20:32664833	2	0	No	N	Gain	Gain
MPC72	MUC1	C1orf86	chr1:155161501	chr1:2115916	2	0	No	N	Gain	Loss
MPC71	CYB5B	CALB2	chr16:69458497	chr16:71416621	2	2	No	Y	No change	No change
MPC71	NSF	C17orf57	chr17:44668037	chr17:45438743	2	2	No	Y	Amp	No change

5′, 5′ partner gene; 3′, 3′ partner gene; total reads, total number of reads supporting the nominated fusion; spanning reads, number of reads spanning the fusion junction.

Copy number derived from smoothed cbs ratios of aCGH data; loss, copy number loss; no change, no copy number change; gain, copy number gain, amp, amplification.