This is a test version of Biostars. For the public version, visit https://www.biostars.org.
fusion detection for DNA Sequencing data

Hi all,

We have designed IDT probe to enrich the target region for tumor samples, including intron regions of known fusion genes.

We have tried several fusion detection tools, such as delly, manta, genefuse to determine the fusion status, however, we found delly and manta were sometimes lack of sensitivity, especially for ctDNA based data. While genefuse was too sensitive, which always gave noise/false fusion results. And genefuse can not determine structure variants such as exon deletion (MET EXON14 SKIP).

Can anyone help?

Thanks, Junfeng

fusion ngs dna
• 3,662 views • link
updated by bounlu bounlu • written by J.F.Jiang J.F.Jiang

2 answers

Hello again Junfeng,

I have previously used SViCT - it was designed specifically for ctDNA. I recommend that you try it:

Kevin

• 0 views • link
written by Kevin Blighe Kevin Blighe

will have a try, and response if have any question

• 0 views • link
written by J.F.Jiang J.F.Jiang

Hi Kevin,

Any suggestions for the input bam? Since unproper mapped reads might be removed during alignment, what kind of bam file should I used?

I tried raw data mapped file or markdup one, without any result, while delly or manta can give out.

• 0 views • link
written by J.F.Jiang J.F.Jiang

Inless you've got a weird aligner, or using non-default settings, unmapped reads will still be in the BAM file - they'll just be marked as unmapped.

• 0 views • link
written by d-cameron d-cameron

I've had success with using GRIDSS on WGS as well as cancer panels with tiled introns. Haven't tried it on ctDNA.

AFAIK, GRIDSS2/PURPLE/LINX (https://www.biorxiv.org/content/10.1101/781013v1) is the only toolset that will do compound (multi-breakpoint) fusion prediction from DNA-seq data, but it's designed for WGS, not panel data.

• 0 views • link
written by d-cameron d-cameron

Now LINX also supports panel data through WiGiTS, but only TSO-500 is supported by default, reference data must be prepared by the user for custom panels.

• 0 views • link
written by bounlu bounlu

Log in to answer this question.

More posts like this