Table 2.

Summary of candidate gene fusions identified by paired end RNA-Seq

Sample	PEFS >0	PEFS >= 5	PEFS >= 5 plus junction spanning reads
SUM149PT	1	1	1
SUM1315O2	20	2	0
HCC3153	8	1	1
T92	13	0	0
T50	1090	2	1
T160	437	4	1
HCC2337	14	2	0
MCF10A	10	0	0

In order to prioritize gene fusion candidates with the most read support, we selected candidates with a minimum PEFS of 5 for further investigation. A total of 12 gene fusion candidates with a PEFS >= 5 were identified based on discordantly aligned paired reads. Of these, four candidates (33%) were further found to have supporting reads spanning the exon-exon fusion junction.