I needed help with the interpretation of these copy number to scatter plots from 2 patients. I'm interested in copy number changes in the CCR4 gene on chr3. The data is derived from a custom target panel. I realize from the plots that both patients have copy number losses in CCR4. However, I need help understanding
1) why patient C has 2 orange segments in the CCR4 region (would each indicate a different allele?)
2) whether we can comment on the bi-allelic or mono-allelic nature of the losses in each patient
I am assuming that this is from sequencing-based approach. PatientB has a very strong signal for a deletion segment spanning ~30thMb to 60th Mb region, which includes your gene.
PatientC appears to have a deletion signal but which appears to be focal around CCR4 only.
The orange line is the 'segmentation' outcome which takes into account how many probes/markers in surrounding area were different to, say the base trend i.e. copy ratio '0' (no change in copy number).
Because the deletion signal in patientB is much large (~30thMb to 60th Mb), the 'segmentation' process binned that part of the region into a separate segment (i.e. a region which is in a different copy number state), and hence the separate orange line at copy ratio '-1'.
In patientC, the deletion signal is not widespread and hence the 'segmentation' process hasn't created a separate 'segment' (orange line).
In terms of the fig. and whats available from the plot, it could be said that pat.B has mono-allelic loss (as the separate orange line is at '-1').
You could say the same for pat.C as well, albeit with somewhat lower confidence.
Hope this helps.