Reasonable number of mutations in a human cancer cell exome

Question

[kshaffman]

Hi,

I am doing some variant calling on my NGS data. I have the sequenced exome of a cancer cell line I am working on that I mapped using BWA-MEM to hg38. When I did my variant calling I got ~170k and ~220k mutations of my evolved cancer cell line and original cancer cell line. This seems like too many mutations, but I have no experience with bioinformatics so I don't know if this is a reasonable number of variants to find, or if I did something wrong in my workflow.

A collaborator of my lab also did variant calling on this data set and got ~28k and ~48k respectively for the evolved and original.

Please let me know which, if any, of these values is reasonable.

ALSO if anyone has a good tutorial or would give me advice on how to take the raw NGS data (Fastq format) to variant calling and analysis I would be very grateful. I have been using galaxy for my workflow since I don't have coding experience. I used the following tutorial starting with the "Map with BWA-MEM" step.

Thanks for the help,

Kevin

Answer 1

[LauferVA]

This can't be accurately answered without further knowledge.

Different mechanisms of carcinogenesis behave differently. A good example for the current question is PolE as the basis of a given cancer. If present, this singular risk factor, over time, will give rise to a mutation rate orders of magnitude higher than other cancers.

Could these results in fact be due to issues with QC or processing some how? 100% yes, definitely. But how many variants should you have? This question cant be answered without knowing a lot more about the samples as well as the QC process.