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I require some clarification on copy number aberrations (structural gain and loss in chromosomes). From what I understand, gain/loss per se can be divided into two types.

Consider two alleles, A and B at the same locus on homologous chromosomes.

  1. Allelic Balance: in one type of structural gain/loss, there is no resulting allelic imbalance; examples:

    • AB ==> AABB (duplication),
    • AB => -- (loss).
  2. Allelic Imbalance: in the other type of structural gain/loss, there is resulting allelic imbalance; examples:

    • AB ==> AAB (duplication of A),
    • AB => -B (deletion LOH),
    • AB ==> BB (copy-neutral LOH).

First, is what I have described above correct?

Second, if it is correct, what is the biology underpinning these copy number aberration types? Are the mechanisms responsible for bringing about allelically-imbalanced CN change distinct from the mechanisms for bringing about allelically-balanced CN change? What are these mechanisms?

NB. I'm confining this to just copy number-related allelic imbalance.

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Allelic imbalance is a pretty broad phenomenon difference in the expression of two alleles. As such you have listed would probably cause allelic imbalance, but it could be the result of methylation or even differences in RNA sequences between the alleles which say interfere with post translational splicing say.

In the case of copy number variations, if a copy number region (which is often a higly repetitive sequence in the genome and not a gene duplication) might interfere or not interfere with gene regulation. In cancer cells large segments of the genome may be copied or cut out though, so in that case the mechanism you put forth may be important.

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Regulatory effects on gene expression are obviously a v important consideration for AI. However, I suppose I'm confining myself to copy number. For e.g., for AI CN changes, the predominant mechanism may be NHEJ, whereas for allelically-balanced CN changes, the driving mechanism may be mitotic defects??? –  user1202664 Apr 11 '12 at 16:09
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