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Genomic DNA is digested using HpaII and MspI isoschizomers (DNA methylation sensitive and insensitive, respectively), ligated to a synthetic adaptor, and Alu elements are specifically amplified by qPCR in two separated reactions. The ratio between the two reactions gives the percentage of unmethylated Alu elements (PUMA). DNA normalization is performed by parallel amplification of L1PA.
