A statistical method to estimate DNA copy number from Illumina high-density methylation arrays

For the first time, we report here that Illumina high-density methylation arrays can also be used to estimate DNA copy number variations. We used the Illumina HM450K methylation array data to characterize the DNA copy number aberrations in the HT-29 colon cancer cell line to test our statistical model. Results were validated using an Affymetrix SNP array. Utilizing the CAMDA 2011 glioblastoma data set, we have demonstrated that our novel statistical method can potentially lower the cost and reduce the processing time of large-scale profiling studies where both DNA copy number and methylation status are of interest. Our new method, named methylCNV, is implemented in the Lumi package of Bioconductor.