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

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2022-02-22T19:06:24.107Z
2022-02-22T19:06:24.107Z
gc5
<p>Reading from <a href="https://www.nejm.org/doi/full/10.1056/NEJMoa2024534" rel="nofollow noreferrer">this paper</a>:</p>
<blockquote>
<p>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, <strong>low abundance</strong>, or both (Fig. 2C, Fig. S2C, and Table S5)</p>
</blockquote>
<p>In the supplementary file, CNA abundance as percentage is defined as:</p>
<p><span class="math-container">$$Abundance = \frac{2^{L2R} - 1}{\frac{CN}{2} - 1}*100$$</span></p>
<p>where L2R is the log<span class="math-container">$_{2}$</span> normalized coverage ratio vs. a panel of normals and CN is the estimated copy number for the event.</p>
<p>I haven't found a better definition/explanation behind &quot;CNA abundance&quot;, is it defined elsewhere, or is it a common term in CNA analysis?</p>

<copy-number>
Definition of Copy Number Abundance
# Definition of Copy Number Abundance

(Asked by: username_0 on 2021-12-01)

Reading from [this paper](https://www.nejm.org/doi/full/10.1056/NEJMoa2024534):

> 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?

**Tags:** copy-number

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## 1 answers

### Answer by username_0 on 2022-02-22. Score: 0 | Accepted answer

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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