Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors.

Authors:
Alexander Herrmann, Andrea Haake, Ole Ammerpohl, Idoia Martin-Guerrero, Karol Szafranski, Kathryn Stemshorn, Michael Nothnagel, Steve K Kotsopoulos, Julia Richter, Jason Warner, Jeff Olson, Darren R Link, Stefan Schreiber, Michael Krawczak, Matthias Platzer, Peter Nürnberg, Reiner Siebert, Jochen Hampe
Year of publication:
2011
Volume:
6
Issue:
7
Issn:
1932-6203
Journal title abbreviated:
PLoS ONE
Journal title long:
PloS one
Impact factor:
2.806
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.