Question: fusion detection for DNA Sequencing data
0
gravatar for J.F.Jiang
6 months ago by
J.F.Jiang850
China
J.F.Jiang850 wrote:

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

dna ngs fusion • 276 views
ADD COMMENTlink modified 6 months ago by d-cameron2.2k • written 6 months ago by J.F.Jiang850
0
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe66k
Kevin Blighe66k wrote:

Hello again Junfeng,

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

Kevin

ADD COMMENTlink written 6 months ago by Kevin Blighe66k
1

will have a try, and response if have any question

ADD REPLYlink written 6 months ago by J.F.Jiang850

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.

ADD REPLYlink written 6 months ago by J.F.Jiang850

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.

ADD REPLYlink written 6 months ago by d-cameron2.2k
0
gravatar for d-cameron
6 months ago by
d-cameron2.2k
Australia
d-cameron2.2k wrote:

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.

ADD COMMENTlink written 6 months ago by d-cameron2.2k
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