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

Question

[lincaijin1994]

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.

Answer 1

[Nana]

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!