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

Feber, A; Guilhamon, P; Lechner, M; Fenton, T; Wilson, GA; Thirlwell, C; Morris, TJ; ... Beck, S; + view all (2014) Using high-density DNA methylation arrays to profile copy number alterations. Genome Biol , 15 (2) , Article R30. 10.1186/gb-2014-15-2-r30. Green open access

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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.

Type: Article
Title: Using high-density DNA methylation arrays to profile copy number alterations.
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/gb-2014-15-2-r30
Publisher version: http://dx.doi.org/10.1186/gb-2014-15-2-r30
Language: English
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.
Keywords: Algorithms, DNA Copy Number Variations, DNA Methylation, Genome, Human, Humans, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Software
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Oncology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Pathology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Surgery and Interventional Sci
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Surgery and Interventional Sci > Department of Targeted Intervention
URI: https://discovery.ucl.ac.uk/id/eprint/1422708
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