In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes.

Maxim Ivanov, Mart Kals, Marina Kacevska, Andres Metspalu, Magnus Ingelman-Sundberg, Lili Milani

Nucleic acids research 2013 Apr 01

filter terms:

algorithms (1)

gene library (1)

genes (7)

human (2)

hydrogen (1)

sequence analysis (1)

sequence analysis, dna (1)

Sizes of these terms reflect their relevance to your search.

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.

Citation

Maxim Ivanov, Mart Kals, Marina Kacevska, Andres Metspalu, Magnus Ingelman-Sundberg, Lili Milani. In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes. Nucleic acids research. 2013 Apr 01;41(6):e72