Answers.Body: <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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Answers.CreationDate: 2022-02-22T19:06:24.107Z
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Body: <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>
  
Tags: <copy-number>
Title: Definition of Copy Number Abundance
ThreadText: # 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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