Reading from this paper:

The remaining 9 new copy-number alterations showed altered coverage patterns on whole-genome sequencing but could not be confirmed by orthogonal methods because of their small size, low abundance, or both (Fig. 2C, Fig. S2C, and Table S5)

In the supplementary file, CNA abundance as percentage is defined as:

$$Abundance = \frac{2^{L2R} - 1}{\frac{CN}{2} - 1}*100$$

where L2R is the log$_{2}$ normalized coverage ratio vs. a panel of normals and CN is the estimated copy number for the event.

I haven't found a better definition/explanation behind "CNA abundance", is it defined elsewhere, or is it a common term in CNA analysis?


1 Answer 1


My guess by analyzing the definition is that CNA abundance is a proxy for the percentage of (tumor) cells carrying the alteration.


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