What absolute copy number would you call an Amplification?

Question

[senowinski]

I have absolute copy number data for a diploid organism. I would like to distinguish between a Gain and an Amplification. I am currently using the term Gain to define any chromosomal copy number increase from the norm - in this case 2. I would like to know if anyone has an arbitrary absolute copy number cut-off to distinguish between a Gain and and Amplification. For example, would you consider it to be a copy number greater than say copy number 4?

Answer 1

[Devon Ryan]

Well, it's amplified versus something (presumably a "normal" state/sample/etc.), so any value larger than that would be amplified. So for single-copy genes in a diploid organism, an absolute copy of 3 would be amplified. This, of course, is assuming there's no heterogeneity in whatever sample you're looking at.

[senowinski]

So by your definition you can't distinguish between a gain and an amplification (in a diploid organism) - both refer to any copy number aberration greater than 2. Let's say then for those cases where copy number is 12 you would class in the same manner you would a copy number of 3, and call both an amplification despite any implications this may have biologically?

[Devon Ryan]

Part of the problem is that "gene amplification" is an ambiguous term and only has a particular meaning in the context of cancer biology (and even there only recently). There, I've seen suggestions that a copy number of 10 or more is needed to term something an amplification. Realistically speaking, you'd need to ensure that there's a concomitant expression change to really term something that, since even a 100x increase could result in no expression difference (though that'd be unlikely).

Outside of cancer biology, a copy number gain is an amplification (not that you'd normally term it as such).

Answer 2

[felipebatalini]

I have seen gain to be used when the copies are up to 9x, and from 10x and above, it would be called amplification. Seems a little arbitrary to me but that is what I've seen.