Using high-density DNA methylation arrays to profile copy number alterations.
Using high-density DNA methylation arrays to profile copy number alterations.
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.
Algorithms, DNA Copy Number Variations, DNA Methylation, Genome, Human, Humans, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Software
Feber, A
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Guilhamon, P
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Lechner, M
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Fenton, TR
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Wilson, GA
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Thirlwell, C
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Morris, TJ
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Flanagan, AM
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Teschendorff, AE
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Kelly, JD
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Beck, S
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1 February 2014
Feber, A
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Guilhamon, P
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Lechner, M
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Fenton, TR
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Wilson, GA
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Thirlwell, C
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Morris, TJ
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Flanagan, AM
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Teschendorff, AE
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Kelly, JD
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Beck, S
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Feber, A, Guilhamon, P, Lechner, M, Fenton, TR, Wilson, GA, Thirlwell, C, Morris, TJ, Flanagan, AM, Teschendorff, AE, Kelly, JD and Beck, S
(2014)
Using high-density DNA methylation arrays to profile copy number alterations.
Genome Biology, 15 (2).
(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.
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gb-2014-15-2-r30
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Published date: 1 February 2014
Additional Information:
copyright 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
Identifiers
Local EPrints ID: 453908
URI: http://eprints.soton.ac.uk/id/eprint/453908
ISSN: 1465-6906
PURE UUID: b70659a3-f9e3-449d-a7b5-cea0c40c0ca9
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Date deposited: 25 Jan 2022 17:51
Last modified: 17 Mar 2024 04:11
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Author:
A Feber
Author:
P Guilhamon
Author:
M Lechner
Author:
GA Wilson
Author:
C Thirlwell
Author:
TJ Morris
Author:
AM Flanagan
Author:
AE Teschendorff
Author:
JD Kelly
Author:
S Beck
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