title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes.
abstract: DNA methylation is one of the most important epigenetic alterations involved in the control of gene expression. Bisulfite sequencing of genomic DNA is currently the only method to study DNA methylation patterns at single-nucleotide resolution. Hence, next-generation sequencing of bisulfite-converted DNA is the method of choice to investigate DNA methylation profiles at the genome-wide scale. Nevertheless, whole genome sequencing for analysis of human methylomes is expensive, and a method for targeted gene analysis would provide a good alternative in many cases where the primary interest is restricted to a set of genes. Here, we report the successful use of a custom Agilent SureSelect Target Enrichment system for the hybrid capture of bisulfite-converted DNA. We prepared bisulfite-converted next-generation sequencing libraries, which are enriched for the coding and regulatory regions of 174 ADME genes (i.e. genes involved in the metabolism and distribution of drugs). Sequencing of these libraries on Illumina's HiSeq2000 revealed that the method allows a reliable quantification of methylation levels of CpG sites in the selected genes, and validation of the method using pyrosequencing and the Illumina 450K methylation BeadChips revealed good concordance.
authors: Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm 17177, Sweden.
authors: Maxim
authors: M
authors: Ivanov
authors: Mart
authors: M
authors: Kals
authors: Marina
authors: M
authors: Kacevska
authors: Andres
authors: A
authors: Metspalu
authors: Magnus
authors: M
authors: Ingelman-Sundberg
authors: Lili
authors: L
authors: Milani
mesh_terms: D000465:Algorithms; D019175:DNA Methylation; D004798:Enzymes / Q000235:genetics; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D004364:Pharmaceutical Preparations / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013447:Sulfites
chemical_list: D004798:Enzymes; D004364:Pharmaceutical Preparations; D013447:Sulfites; C042345:hydrogen sulfite