Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.

Gu H, Bock C, Mikkelsen TS, J├Ąger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A.

Nat Methods. 2010 Feb;7(2):133-6. PMCID: PMC2860480

Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical samples: here we outline how restriction digestion targets bisulfite sequencing to hotspots of epigenetic regulation and describe a statistical method for assessing significance of altered DNA methylation patterns. Thirty nanograms of DNA was sufficient for genome-scale analysis and our protocol worked well on formalin-fixed, paraffin-embedded samples.
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