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It is almost common sense that local amplification of gene increase the its mRNA expression . I recently heard that large scale SCNA (such as arm-level amplification) does not increase the mRNA expression level of gene within the region. I did some analysis (SCNA is determined by SNP array and NGS, mRNA expression is measured by RNA-Seq) and found that this is indeed the case. I further did some research and did not found any explanations. it seems like a common acknowledgement. Is there any technical bias or biological explanation that I am missing here? Or is it something that has not have a answer yet?

I have no clue about this at all. Can you recommend this papers on this?

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Answer from @devon-ryan, converted from comments:

The common presumption in such cases is that there's a feedback loop on most genes to control their expression level. It doesn't have to be specific to arm-level expression.

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