BCL2 fusion not catched?

[asaki1986]

Hi all,

I am using JAFFA-2.4 to discover the BCL2 fusions in FFPE target RNA sequencing data.

While this sample had been verified positive using FISH, with partener gene IGHJ, which had been verified based on DNA sequencing data.

However, we did not find BCL2-IGHJ fusion in the jaffa_results.csv.

I carefully examined the raw files in the analysis folder.

And I indeed found lots of evidence in SAMPLE.txt file as follows,

E150003903L1C001R0023300833/1/1 98 105 BCL2:IGHJ6 150 hg19_wgEncodeGencodeBasicV19_ENST00000398117.1__range=chr18:60790579-60987361__5'pad=0__3'pad=0__strand=-__repeatMasking=none 4513 hg19_wgEncodeGencodeBasicV19_ENST00000390560.2__range=chr14:106329408-106329468__5'pad=0__3'pad=0__strand=-__repeatMasking=none 16 99 104 plus

There are 920 lines supporting this kind of fusion, however it seems these reads were not considered in the final results. Can you please explain the detailed column names for this file?

And I am wondering whether these lines are preliminary results, and what parameters/cutoff were set to filter these results?

Thanks,

Junfeng