RT Journal
A1 Komori, H. Kiyomi
A1 LaMere, Sarah A.
A1 Torkamani, Ali
A1 Hart, G. Traver
A1 Kotsopoulos, Steve
A1 Warner, Jason
A1 Samuels, Michael L.
A1 Olson, Jeff
A1 Head, Steven R.
A1 Ordoukhanian, Phillip
A1 Lee, Pauline L.
A1 Link, Darren R.
A1 Salomon, Daniel R.
T1 Application of microdroplet PCR for large-scale targeted bisulfite sequencing
JF Genome Research 
JO Genome Research 
YR 2011 
FD October 01 
VO 21 
IS 10 
SP 1738 
OP 1745 
DO 10.1101/gr.116863.110 
UL http://genome.cshlp.org/content/21/10/1738.abstract 
AB Cytosine methylation of DNA CpG dinucleotides in gene promoters is an epigenetic modification that regulates gene transcription. While many methods exist to interrogate methylation states, few current methods offer large-scale, targeted, single CpG resolution. We report an approach combining bisulfite treatment followed by microdroplet PCR with next-generation sequencing to assay the methylation state of 50 genes in the regions 1 kb upstream of and downstream from their transcription start sites. This method yielded 96% coverage of the targeted CpGs and demonstrated high correlation between CpG island (CGI) DNA methylation and transcriptional regulation. The method was scaled to interrogate the methylation status of 77,674 CpGs in the promoter regions of 2100 genes in primary CD4 T cells. The 2100 gene library yielded 97% coverage of all targeted CpGs and 99% of the target amplicons.