I'm concerned that there may be something wrong with my PureCN output from callAlterations(), which I ran via PureCN.R. I have 117 gastric cancer tumor samples and about 740 targeted genes. This gives about 87664 total lines of callAlterations() output from all the samples together. Of those, there are only 689 amplifications and 78 deletions. When one looks at the distribution of copy ratios in the segments, about 5% of all segments are deletions and 10% are amplifications, so I would have expected roughly the same ratio with the genes. Further, I thought I did have more gene deletions/amplifications; I'm wondering if, when I upgraded to a newer PureCN, there was a big change that drastically lowered the count? Unfortunately, I can't easily go back and rerun the old PureCN and check this, mainly due to time constraints.
At the same time, there are 24,493 genes that have been called with LOH. That's about 30% of all genes with LOH. Can that be right? And that implies that most of the LOH occurs in the absence of deletion. I would have expected most LOH to occur because one of the two alleles was deleted.
Do you agree something is wrong here? Any suggestions on where I might start looking?
My PureCN version is 1.16.0.