Queries on applying ONCOCNV on Exome Seq Data

[vyomeshj209]

Hello Sir/Ma'am,

1] Trying to apply oncocnv for exome data i.e. without reference to amplicon id. What should be modification required in bed file for applying it on Exome data.

Standard bed file:
track name="4477685_CCP_Designed" description="Amplicon_Insert_4477685_CCP" type=bedDetail
chr1 2488068 2488201 AMPL242431688 0 TNFRSF14

Bed file used for Exome data:
track name="Covered" description="Illumina Exon - Genomic regions covered by probes" db=hg19
chr1 14694 14814 AMPL1354 0 WASH7P

Above bed file used, contains random amplicon id in 3rd column and 0 in 5th column, is it right strategy to use for Exon seq data?

2] While applying ONCOCNV for EXON data what precautions or prerequisite should be taken care of?

Kindly Guide.

Regards,
Vyomesh

[valeu]

Dear Vyomesh,
yes, your bed file should work. Two important considerations: Amplicon IDs should be unique, and Gene names should be provided to allow prioritizing breakpoints in intergenic regions.

Otherwise, it looks good to me.
Of note, OncoCNV can take some time to run on exome-seq as it was designed for amplicon-seq with fewer regions.
Also, OncoCNV will not take into account BAF info from SNPs. If you wish to do so, you can try the ControlFREEC method (C++) also developed by my team for whole genome and whole exome sequencing data.

[vyomeshj209]

Hi Valentina Boeva,

We are currently using ControlFREEC method & reproduce the same results in ONCOCNV. But we are finding difference in outcome.

Test Sample (Output from ControlFEEEC):
19 66376 5610130 8 gain STK11

Test Sample (Output from ONCOCNV):
chr19 1206907 1207207 STK11 AMPL224571 0.669761037
chr19 1218389 1218509 STK11 AMPL224572 -0.475328357
chr19 1219292 1219412 STK11 AMPL224573 0.052617935
chr19 1220372 1220522 STK11 AMPL224574 -0.253691951
chr19 1220573 1220723 STK11 AMPL224575 -0.179748549
chr19 1221199 1221332 STK11 AMPL224576 0.493683735
chr19 1221901 1222021 STK11 AMPL224577 -0.111910189
chr19 1222975 1223181 STK11 AMPL224578 -0.059582191
chr19 1223609 1223760 STK11 AMPL224579 NA
chr19 1226445 1226656 STK11 AMPL224580 -0.255746161

Can you help in understanding why there is difference?

Thanks,
Vyomesh

[valeu]

Dear Vyomesh, do you have .png images with the output of FREEC and ONCOCNV for this gene?
When you run FREEC, do you provide the .bed file with exon coordinates?

[vyomeshj209]

Hi Valentina Boeva,

Apologies for late response.
Yes, using bed file with exon coordinates for running FREEC tool.

For FREEC, I do not have image but for ONCOCNV the image attached below:

[valeu]

I am lost.. I thought you had WES data.. But then why do you have so few regions in the OncoCNV output figure?

[valeu]

For FREEC, you can generate the .png using an R script in the scripts folder

[vyomeshj209]

Yes working on WES but have restricted gene list to approx. 1200 gene. Will try the R script for FREEC tool and share the details