tumor heterogeneity target capture
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7.5 years ago
cristinam09 ▴ 20

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.

sequencing heterogeneity tumor target-capture • 1.5k views
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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.

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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.  

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