tumor heterogeneity target capture
I would like to use target NGS data, covering about 150 genes at ~500X, to estimate tumor heterogeneity using tools like sciClone. I know people usually use WGS or WES data. Does anybody knows if sequencing of a smaller panel pose any issue? I would not think so but I am interested to hear what are the thoughts of this community. Thank you for your comments.
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Won't how well this works depend entirely on the genes that you intend to look at? I imagine it'd be difficult to predict how well this'll work without knowing that.
You'll need to have enough variants to capture the heterogeneity. With 150 genes, I suspect that you will not unless your experimental system is quite unusual.