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Title: Abnormal Dosage of Ultraconserved Elements Is Highly Disfavored in Healthy Cells but Not Cancer Cells
Authors: McCole, Ruth B.;Fonseka, Chamith Y.;Koren, Amnon;Wu, C.-ting
subject: Biology and Life Sciences;Computational Biology;Genome Complexity;Genome Evolution;Evolutionary Biology;Genetics;Genomics
Year: 2014
Publisher: Public Library of Science
Description: Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian cell. Here we address the process by which CNVs become depleted of UCEs. We begin by showing that depletion for UCEs characterizes the most recent large-scale human CNV datasets and then find that even newly formed de novo CNVs, which have passed through meiosis at most once, are significantly depleted for UCEs. In striking contrast, CNVs arising specifically in cancer cells are, as a rule, not depleted for UCEs and can even become significantly enriched. This observation raises the possibility that CNVs that arise somatically and are relatively newly formed are less likely to have established a CNV profile that is depleted for UCEs. Alternatively, lack of depletion for UCEs from cancer CNVs may reflect the diseased state. In support of this latter explanation, somatic CNVs that are not associated with disease are depleted for UCEs. Finally, we show that it is possible to observe the CNVs of induced pluripotent stem (iPS) cells become depleted of UCEs over time, suggesting that depletion may be established through selection against UCE-disrupting CNVs without the requirement for meiotic divisions.
Standard no: McCole, Ruth B., Chamith Y. Fonseka, Amnon Koren, and C.-ting Wu. 2014. “Abnormal Dosage of Ultraconserved Elements Is Highly Disfavored in Healthy Cells but Not Cancer Cells.” PLoS Genetics 10 (10): e1004646. doi:10.1371/journal.pgen.1004646.
Appears in Collections:HMS Scholarly Articles

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