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Artifactual mutations in CCLE data

Hi there,

I am confused whether some of the mutations reported in some big study like CCLE are artifactual mutations. I have been asked this question many a times, but don't understand what artifactual mutations are ?

Are artifactual mutations related to:

platform related - eg. illumina, 454 etc

protocol related - eg. library preparation for rna-seq or exome-seq purposes

variant calling algorithm related - eg GATK , SAMTOOLS mpileup

or something else what I mite be missing

Please shed some light on this topic.

Thanks

Regards

ccle artifactual mutations
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updated by Ram Ram • written by monukmr98 monukmr98

All of the above, plus a number of them are germline variants which weren't identified since no non-transformed sample is available for the vast majority of cell lines

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updated by Ram Ram • written by russhh russhh

Thanks russ

In their preferred dataset, CCLE people have mentioned that the following variants were filtered out:

  • common polymorphisms
  • allelic fraction < 10%
  • putative neutral variants (missenses present in less than 2 warm-blooded vertebrates)
  • located outside of the CDS for all transcripts

It means, that germline variants have not been filtered out.

Also, I want to know whether is it possible to filter out germ line variants from cell line samples or only patient samples are eligible for that ? If yes, then what are the software or pipelines available?

Thanks

• 0 views • link
updated by Ram Ram • written by monukmr98 monukmr98

to be honest, I don't think it would be possible to predict the germline variants for cell lines that don't have a comparator. It's hard enough in tumours, where untransformed cells are present, to determine the somatic variants from the germline variants unless you have some blood DNA or somehting

• 0 views • link
written by russhh russhh

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