true translocation or not with 3to3 CT tag

[asaki1986]

Hi all,

We recently found a EGFR-CTNNA2 fusion in a sarcoma FFPE sample, both in DNA and RNA samples.

For DNA, we used delly, while STAR-Fusion for RNA data.

In DNA, CT tag was labelled as 3to3, indicating a "join chrA_left with chrB_left (3to3)" event, which was displayed in IGV shot as below. 7 55241923 EGFR_NM_005228:intron18 + 2 80724906 CTNNA2_NM_001282597:intron9 + 3to3

While in RNA data, STAR-Fusion reported similar SV as below, EGFR--CTNNA2 1091 36 1091.00 36.00 ONLY_REF_SPLICE EGFR^ENSG00000146648.11 chr7:55241736:+ CTNNA2^ENSG00000066032.14 chr2:80772107:+ YES_LDAS 27.684 GT 1.8892 AG 1.9329 ["INTERCHROMOSOMAL[chr7--chr2]"]

Since EGFR is located on p-arm with + strand, and CTNNA2 is also on p-arm with + strand, how could this derivate chromosome appear without centromere?

Best, Junfeng