Epicopy, a Statistical Method to Identify Genomic Copy Number Variation (CNV) using High-density DNA Methylation Arrays

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Genetic and epigenetic alterations have been implicated in carcinogenesis and integrated analyses of these have provided new insights into the mechanisms of cancer development. We developed Epicopy, a statistical method to identify copy number variation (CNV) using high-density Illumina 450K methylation arrays. Using Epicopy, we studied the instances where CNV information can be reliably measured and provided guidelines to confidently identify CNVs. Using paired SNP and methylation arrays from TCGA, we showed that Epicopy provides a robust method to obtain both copy number and methylation information from a single chip. Epicopy is available on Bioconductor.
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Mitchell Harris
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