How to Differentiate Amplification on eccDNA vs. Linear Genome?

[talhamufeed]

I have a question regarding the differentiation between amplifications occurring on eccDNA and those on the linear genome. So if a gene "A" present on an eccDNA is shown by AC to have x copy number. Is this copy number specific for the eccDNA. And if yes how can I find the copy number of gene "A" on linear genome/chromosome.
Regards.
Talha

[jluebeck]

Hi Talha,

Unfortunately our method does not distinguish the copy number on ecDNA specifically versus the remaining copies still on the chromosome - it only reports the total copy number. If it is important to estimate the exact number of copies on ecDNA, you could examine the copy number profile of the surrounding native chromosome (say the flanking regions have CN=x) and make an estimate that there are "x" or "x-1" copies still remaining on chromosomal DNA (x-1 if you assume that the break was not repaired by homologous recombination after the ecDNA was not formed).

Jens