PureCN

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Hi, I would like to know why arbitrary thresholds of 6/7 were selected to label amplifications - was an internal comparison performed to define these thresholds? Is it safe to consider copy numbers > 3 as gains

Thanks

Hi, they are arbitrary and I’m open to improving them, i.e. open to suggestions. In some cases like Her2 you could optimize based on FISH concordance. In others that are almost always focal you can look at their copy number distributions. Others might have a strong dosing effect, where a copy number of 4 is already pathogenic.

I would define round(ploidy)+1 as gain I guess.