Question: CNV analysis for tumor panel
0
gravatar for J.F.Jiang
14 months ago by
J.F.Jiang830
China
J.F.Jiang830 wrote:

Hi all,

In order to evaluate the drug response of patient, we want to analyze the CNV status of target region.

The panel was developed and synthetized by IDT.

I am wondering if there is any tool to define the CNV status of the target region, such as MET/EGFR/HER2, beside GATK, FREEC, XHMM, since we find the accuracy problem while calling process.

Thanks

Junfeng

cnv • 449 views
ADD COMMENTlink modified 14 months ago by Eric T.2.6k • written 14 months ago by J.F.Jiang830

There are many dozens of copy number calling programs. FREEC and XHMM are actually regarded as among the best. What, exactly, is your input data? - genome sequencing, exome / targeted sequencing, microarray, or PCR?

ADD REPLYlink written 14 months ago by Kevin Blighe65k

the input data is target sequencing using IDT Capture probe.

ADD REPLYlink written 14 months ago by J.F.Jiang830

Okay, I have had success using FREEC for Exome-seq, which can be regarded as 'genome-wide' target capture. Did you configure FREEC properly? - there are many parameters. Here is an example config file that I used for an Exome-seq sample (Mus musculus):

[general]
BedGraphOutput=TRUE
bedtools=/Programs/bedtools2/bin/bedtools
breakPointThreshold=0.8
breakPointType=2
chrFiles=mm10/chromosomes/
chrLenFile=mm10/mm10.fasta.fai
SNPfile=mm10/mm10_dbSNP137.ucsc.freec.txt
coefficientOfVariation=0.06
contamination=0
contaminationAdjustment=TRUE
degree=3
forceGCcontentNormalization=1
#gemMappabilityFile=mm10/GRCm38_68_mm10.gem
#minMappabilityPerWindow=0.85
intercept=1
minCNAlength=3
minExpectedGC=0.35
maxExpectedGC=0.55
minimalSubclonePresence=0.3
maxThreads=3
numberOfProcesses=2
noisyData=TRUE
outputDir=Out/FREEC/
ploidy=2
printNA=TRUE
readCountThreshold=10
samtools=/Programs/samtools-1.9/samtools
sex=XY
step=10000
telocentromeric=50000
#uniqueMatch=TRUE
window=50000

[sample]
inputFormat=BAM
mateFile=Aligned_Sorted_PCRDuped_FiltMAPQ.bam
mateOrientation=FR
ADD REPLYlink written 14 months ago by Kevin Blighe65k
1

Thanks,

I tried both FREEC and CNVKit. Both work well, but sometimes came with some bugs, especially depth calculation of FREEC.

ADD REPLYlink written 5 months ago by J.F.Jiang830
1
gravatar for Eric T.
14 months ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

CNVkit tends to work well on tumor panels and is easy to use.

ADD COMMENTlink written 14 months ago by Eric T.2.6k
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