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.
Andrew
A
Feber
Paul
P
Guilhamon
Matthias
M
Lechner
Tim
T
Fenton
Gareth A
GA
Wilson
Christina
C
Thirlwell
Tiffany J
TJ
Morris
Adrienne M
AM
Flanagan
Andrew E
AE
Teschendorff
John D
JD
Kelly
Stephan
S
Beck
D000465:Algorithms; D056915:DNA Copy Number Variations / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software