Sources
CNVs may either be inherited or caused by de novo mutation. A 2007 study proposed mechanism for the cause of some CNVs was fork stalling and template switching, a replication misstep. However, this model was subsequently superseded by microhomology-mediated break-induced replication (MMBIR).
CNVs can be caused by structural rearrangements of the genome such as deletions, duplications, inversions, and translocations. Low copy repeats (LCRs), which are region-specific repeat sequences, are susceptible to such genomic rearrangements resulting in CNVs. Factors such as size, orientation, percentage similarity and the distance between the copies influence the susceptibility of LCRs to genomic rearrangement. Segmental Duplications (SDs) map near ancestral duplication sites in a phenomenon called duplication shadowing which describes the observation of a ~10 fold increased probability of duplication in regions flanking duplications versus other random regions.
Read more about this topic: Copy-number Variation
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