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 Infi...

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Detalles Bibliográficos
Autores principales: Feber, Andrew, Guilhamon, Paul, Lechner, Matthias, Fenton, Tim, Wilson, Gareth A, Thirlwell, Christina, Morris, Tiffany J, Flanagan, Adrienne M, Teschendorff, Andrew E, Kelly, John D, Beck, Stephan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054098/
https://www.ncbi.nlm.nih.gov/pubmed/24490765
http://dx.doi.org/10.1186/gb-2014-15-2-r30
Descripción
Sumario: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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