Frame number in Oncofuse output

Question

[henryvuong]

Hi,

I applied Oncofuse to annotate fusion genes from DNA-seq and would like to determine if the fusion is in-frame or not. Oncofuse provided 5_FRAME (frame of translated 5'FPG), 3_FRAME (frame of translated 3'FPG) and FPG_FRAME_DIFFERENCE (difference in 5' and 3' FPG frames). Their values are 0, 1 and 2. May I ask what these values mean? How do I interpret the FPG_FRAME_DIFFERENCE? Thanks.

Answer 1

[mikhail.shugay]

Hello!

The 5'FRAME is the frame of 5' fusion partner gene sequence at the breakpoint, same for 3'FRAME. FPG_FRAME_DIFFERENCE is the frameshift once fusion partner genes are joined.

FPG_FRAME_DIFFERENCE = (5'FRAME + 3'FRAME) % 3

If the sum of 5'FRAME and 3'FRAME is a multiple of 3, then the frame difference is 0 and fusion is considered in-frame, other situations mean out-of-frame.

PS. Just in case, here is the main thread for questions related to Oncofuse: Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data