title: Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors.
abstract: Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rho = 0.96) and to pyrosequencing (rho = 0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into "hepitypes" and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer.
authors.affiliation: Institute of Internal Medicine I, Christian-Albrechts University, Kiel, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Herrmann
authors.forename: Andrea
authors.initials: A
authors.lastname: Haake
authors.forename: Ole
authors.initials: O
authors.lastname: Ammerpohl
authors.forename: Idoia
authors.initials: I
authors.lastname: Martin-Guerrero
authors.forename: Karol
authors.initials: K
authors.lastname: Szafranski
authors.forename: Kathryn
authors.initials: K
authors.lastname: Stemshorn
authors.forename: Michael
authors.initials: M
authors.lastname: Nothnagel
authors.forename: Steve K
authors.initials: SK
authors.lastname: Kotsopoulos
authors.forename: Julia
authors.initials: J
authors.lastname: Richter
authors.forename: Jason
authors.initials: J
authors.lastname: Warner
authors.forename: Jeff
authors.initials: J
authors.lastname: Olson
authors.forename: Darren R
authors.initials: DR
authors.lastname: Link
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
authors.forename: Michael
authors.initials: M
authors.lastname: Krawczak
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.forename: Peter
authors.initials: P
authors.lastname: Nürnberg
authors.forename: Reiner
authors.initials: R
authors.lastname: Siebert
authors.forename: Jochen
authors.initials: J
authors.lastname: Hampe
mesh_terms: D000368:Aged; D003110:Colonic Neoplasms / Q000235:genetics; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000737:chemistry / Q000235:genetics*; D005260:Female; D051522:Fibroblast Growth Factor 6 / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000145:classification / Q000235:genetics; D015894:Genome, Human / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods; D006239:Haplotypes; D006801:Humans; D008224:Lymphoma, Follicular / Q000235:genetics; D008297:Male; D008875:Middle Aged; D009369:Neoplasms / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites / Q000737:chemistry; D015238:Sulfotransferases / Q000235:genetics; D055517:snRNP Core Proteins / Q000235:genetics
chemical_list: D004273:DNA, Neoplasm; C496452:FGF6 protein, human; D051522:Fibroblast Growth Factor 6; C526417:SNRPN protein, human; D013447:Sulfites; D055517:snRNP Core Proteins; D015238:Sulfotransferases; C021350:heparitin sulfotransferase; C009279:sodium bisulfite