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Somatic copy-number alteration identification software tools | DNA methylation microarray data analysis

The 450k platform is based on similar biochemical reaction principle and technology as the Infinium SNP arrays, making it possible to use the 450k platform to detect copy number variants (CNVs) as a zero-cost byproduct of methylation studies (Feber et al., 2014). CN calling consists of the following principal steps: normalization of probe intensities, calculation of the Log R Ratios (LRRs), segmentation and determination of copy number status for each segment based on a chosen cutoff level or a P-value threshold.

References:
(Feber et al., 2014) Using high-density DNA methylation arrays to profile copy number alterations. Genome Biol.

Source text:
(Marzouka et al., 2016) CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array. Bioinformatics.

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