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Copy Number Variants and Segmental Duplications Show Different Formation Signature | | Philip M. Kim
; Jan O. Korbel
; Xueying Chen
; Mark B. Gerstein
; | | Date: |
26 Sep 2007 | | Abstract: | In addition to variation in terms of single nucleotide polymorphisms (SNPs),
whole regions ranging from several kilobases up to a megabase in length differ
in copy number among individuals. These differences are referred to as Copy
Number Variants (CNVs) and extensive mapping of these is underway. Recent
studies have highlighted their great prevalence in the human genome. Segmental
Duplications (SDs) are long (>1kb) stretches of duplicated DNA with high
sequence identity. First, we analyzed the co-localization of SDs and find that
SDs are significantly co-localized with each other, resulting in a power-law
distribution, which suggests a preferential attachment mechanism, i.e. existing
SDs are likely to be involved in creating new ones nearby. Second, we look at
the relationship of CNVs/SDs with various types of repeats. We we find that the
previously recognized association of SDs with Alu elements is significantly
stronger for older SDs and is sharply decreasing for younger ones. While it
might be expected that the patterns should be similar for SDs and CNVs, we
find, surprisingly, no association of CNVs with Alu elements. This trend is
consistent with the decreasing correlation between Alu elements and younger
SDs, the activity of Alu elements has been decreasing and by now it they seem
no longer active. Furthermore, we find a striking association of SDs with
processed pseudogenes suggesting that they may also have mediated SD formation.
Moreover, find strong association with microsatellites for both SDs and CNVs
that suggests a role for satellites in the formation of both. | | Source: | arXiv, 0709.4200 | | Services: | Forum | Review | PDF | Favorites | |
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