A systematic evaluation of whole genome amplification of bisulfite-modified DNA

Using a sufficient amount of bisulfite-modified DNA for WGA was critical for downstream application. The considerable deviations from original bisulfite-modified DNA were found in the middle range of DNA methylation levels. Distribution of hyper- and hypomethylation were equal, which suggested that the deviation at each CpG site occurred randomly. Averaging the data from independently amplified WGA products dramatically improved the overall quality.WGA of bisulfite-modified DNA could be a valuable tool for epigenetic research, but careful experimental design and data interpretation are required.In mammals, DNA methylation is mainly observed at the cytosine residues of CpG dinucleotides. The methyl group is transferred to the fifth position of cytosine by DNA methyltransferases. This modification plays important roles in the regulation of gene expression [1]. In the promoter region, where a CpG-rich region known as the CpG island is often situated, DNA methylation is generally involved in gene silencing. In the intragenic regions, where most of the methylcytosine is enriched, DNA methylation is associated with highly expressed genes and alternative splicing, although its precise role remains unclear [2-5].DNA methylation is involved in genomic imprinting, X chromosome inactivation, and tissue-specific gene expression. Alteration of the DNA methylation results in developmental deficits and diseases [1,6]. Studies have shown that, in addition to cancer, various kinds of diseases, such as autoimmune diseases, diabetes, and neuropsychiatric diseases, are associated with altered DNA methylation [6-8]. Detailed qualitative and quantitative analyses of DNA methylation profiles should be the first step of epigenetic research in clinical medicine.Sodium bisulfite modification of genomic DNA, which converts non-methyl cytosine to uracil, has been the gold standard method for DNA methylation analysis for decades. However, this method causes the degradation of genomic DNA, resul