Question: Why are there too many mutations in controls, but not in tumour?
1
gravatar for MAPK
4.3 years ago by
MAPK1.5k
MAPK1.5k wrote:

I have been studying different cancer samples and comparing them with the germline controls for driver mutations. As a result I have found quite of few somatic mutations that are exclusive to tumour samples. However, I have also found some mutations that are present in controls, but not in any of the tumour samples. Can someone please put some light on the reason behind this?

cancer somatics mutation • 1.2k views
ADD COMMENTlink modified 4.3 years ago by Lemire590 • written 4.3 years ago by MAPK1.5k
1

Are the samples matched? (i.e. control and tumour from a single individual) How are you defining mutation? Excluding known SNPs? Only in coding regions?

ADD REPLYlink written 4.3 years ago by jotan1.2k

To add to these questions - what's the coverage like? If you look at these regions in IGV, are there lots of ambiguously mapped reads that might indicate misalignments?

ADD REPLYlink written 4.3 years ago by Chris Miller21k

Also, what kind of somatic mutation caller are you using that reports these sites? Most of the ones I'm aware of clearly label such sites as LOH or Germline mutations, if they report them at all.

ADD REPLYlink written 4.3 years ago by Chris Miller21k
1
gravatar for Lemire
4.3 years ago by
Lemire590
Canada
Lemire590 wrote:

That's probably loss of heterozygosity, not somatic substitutions. Caused by chromosomal regions where one parental copy was loss in the tumor (i.e. deleted). Check if they tend to cluster in regions.

ADD COMMENTlink written 4.3 years ago by Lemire590
0
gravatar for WouterDeCoster
4.3 years ago by
Belgium
WouterDeCoster44k wrote:

Are you sure these positions are references calls or simply unsequenced/absent from the data?

ADD COMMENTlink written 4.3 years ago by WouterDeCoster44k
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