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How to understand or define some terms regarding copy number alterations?

Hi. I wanted to extract CNV signature using SigProfiler. So a input matrix for SigProfilerExtractor was generated based on ASCAT file using SigProfilerMatrixGenerator. Here are the row names of the generated matrix but I dont know what these terms mean.

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number copy cnv
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updated by Nana • Nana • written by lincaijin1994 • lincaijin1994

1 answer

Hi there.

The CNV signatures you have will be binned based on copy number and segment size. It looks like the data you have is in the format:

<Copy Number>:<Label>:<Segment Size>

  • Copy number = The number of alleles in the CNV
    • Label = Name for the copy number event:
    • Homdel = Homozygous deletion. This is CNA=0
    • LOH = Loss of heterozygousity. One of the parental alleles has been lost.
    • Het = Heterzygous. Both parental alleles are present.
  • Segment size = Size of the CNA segment.

Hope that helps!

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written by Nana • Nana

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