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dc.contributor.authorLee, Eun-Joon
dc.contributor.authorPei, Lirong
dc.contributor.authorSrivastava, Gyan
dc.contributor.authorJoshi, Trupti
dc.contributor.authorKushwaha, Garima
dc.contributor.authorChoi, Jeong-Hyeon
dc.contributor.authorRobertson, Keith D.
dc.contributor.authorWang, Xinguo
dc.contributor.authorColbourne, John K.
dc.contributor.authorZhang, Lu
dc.contributor.authorSchroth, Gary P.
dc.contributor.authorXu, Dong
dc.contributor.authorZhang, Kun
dc.contributor.authorShi, Huidong
dc.date.accessioned2012-10-26T20:30:40Z
dc.date.available2012-10-26T20:30:40Z
dc.date.issued2011-10-23en_US
dc.identifier.citationNucleic Acids Res. 2011 Oct 23; 39(19):e127en_US
dc.identifier.issn1362-4962en_US
dc.identifier.pmid21785137en_US
dc.identifier.doi10.1093/nar/gkr598en_US
dc.identifier.urihttp://hdl.handle.net/10675.2/761
dc.description.abstractWe applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of ~1 million CpGs in more than 21â 408 CGIs and more than 15â 946 transcriptional regulatory regions. Of the CpGs analyzed, 77â 84% fell on or near capture probe sequences; 69â 75% fell within CGIs. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. Differentially methylated regions (DMRs) were identified in the 5â ²-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X-chromosome among the three breast cancer cell lines analyzed. We chose 46 candidate loci (762 CpGs) for confirmation with PCR-based bisulfite sequencing and demonstrated excellent correlation between two data sets. Targeted bisulfite sequencing of three DNA methyltransferase (DNMT) knockout cell lines and the wild-type HCT116 colon cancer cell line revealed a significant decrease in CpG methylation for the DNMT1 knockout and DNMT1, 3B double knockout cell lines, but not in DNMT3B knockout cell line. We demonstrated the targeted bisulfite sequencing approach to be a powerful method to uncover novel aberrant methylation in the cancer epigenome. Since all targets were captured and sequenced as a pool through a series of single-tube reactions, this method can be easily scaled up to deal with a large number of samples.
dc.rights© The Author(s) 2011. Published by Oxford University Press.en_US
dc.subjectMethods Onlineen_US
dc.titleTargeted bisulfite sequencing by solution hybrid selection and massively parallel sequencingen_US
dc.typeArticleen_US
dc.identifier.pmcidPMC3201883en_US
dc.contributor.corporatenameGHSU Cancer Center
dc.contributor.corporatenameDepartment of Biochemistry and Molecular Biology
dc.contributor.corporatenameDepartment of Biostatistics and Epidemiology
refterms.dateFOA2019-04-10T00:48:08Z
html.description.abstractWe applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of ~1 million CpGs in more than 21â 408 CGIs and more than 15â 946 transcriptional regulatory regions. Of the CpGs analyzed, 77â 84% fell on or near capture probe sequences; 69â 75% fell within CGIs. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. Differentially methylated regions (DMRs) were identified in the 5â ²-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X-chromosome among the three breast cancer cell lines analyzed. We chose 46 candidate loci (762 CpGs) for confirmation with PCR-based bisulfite sequencing and demonstrated excellent correlation between two data sets. Targeted bisulfite sequencing of three DNA methyltransferase (DNMT) knockout cell lines and the wild-type HCT116 colon cancer cell line revealed a significant decrease in CpG methylation for the DNMT1 knockout and DNMT1, 3B double knockout cell lines, but not in DNMT3B knockout cell line. We demonstrated the targeted bisulfite sequencing approach to be a powerful method to uncover novel aberrant methylation in the cancer epigenome. Since all targets were captured and sequenced as a pool through a series of single-tube reactions, this method can be easily scaled up to deal with a large number of samples.


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