title: Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.
abstract: 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.
authors.affiliation: Broad Institute, Cambridge, Massachusetts, USA.
authors.forename: Hongcang
authors.initials: H
authors.lastname: Gu
authors.forename: Christoph
authors.initials: C
authors.lastname: Bock
authors.forename: Tarjei S
authors.initials: TS
authors.lastname: Mikkelsen
authors.forename: Natalie
authors.initials: N
authors.lastname: Jäger
authors.forename: Zachary D
authors.initials: ZD
authors.lastname: Smith
authors.forename: Eleni
authors.initials: E
authors.lastname: Tomazou
authors.forename: Andreas
authors.initials: A
authors.lastname: Gnirke
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.forename: Alexander
authors.initials: A
authors.lastname: Meissner
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003110:Colonic Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics*; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D004273:DNA, Neoplasm; D009711:Nucleotides