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Using high-density DNA methylation arrays to profile copy number alterations.

Feber, A, Guilhamon, P, Lechner, M, Fenton, TR, Wilson, GA, Thirlwell, C, Morris, TJ, Flanagan, AM, Teschendorff, AE, Kelly, JD, and others. (2014) Using high-density DNA methylation arrays to profile copy number alterations. Genome Biology, 15 (2). ISSN 1474-760X. (doi:10.1186/gb-2014-15-2-r30)

Abstract

The integration of genomic and epigenomic data is an increasingly popular approach for studying the complex mechanisms driving cancer development. We have developed a method for evaluating both methylation and copy number from high-density DNA methylation arrays. Comparing copy number data from Infinium HumanMethylation450 BeadChips and SNP arrays, we demonstrate that Infinium arrays detect copy number alterations with the sensitivity of SNP platforms. These results show that high-density methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. Our method is available in the ChAMP Bioconductor package: http://www.bioconductor.org/packages/2.13/bioc/html/ChAMP.html.

Item Type: Article
DOI/Identification number: 10.1186/gb-2014-15-2-r30
Additional information: © 2014 Feber et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Uncontrolled keywords: Algorithms, DNA Copy Number Variations, DNA Methylation, Genome, Human, Humans, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Software
Divisions: Faculties > Sciences > School of Biosciences
Depositing User: Tim Fenton
Date Deposited: 25 Apr 2017 07:34 UTC
Last Modified: 29 May 2019 18:59 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/61509 (The current URI for this page, for reference purposes)
Fenton, TR: https://orcid.org/0000-0002-4737-8233
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