Ultradeep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454 Sequencing Export

@article{citeulike:1675503, abstract = {We developed a novel approach for conducting multisample, multigene, ultradeep bisulfite sequencing analysis of DNA methylation patterns in clinical samples. A massively parallel sequencing-by-synthesis method (454 sequencing) was used to directly sequence >100 bisulfite PCR products in a single sequencing run without subcloning. We showed the utility, robustness, and superiority of this approach by analyzing methylation in 25 gene-related CpG rich regions from >40 cases of primary cells, including normal peripheral blood lymphocytes, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), follicular lymphoma (FL), and mantle cell lymphoma (MCL). A total of 294,631 sequences was generated with an average read length of 131 bp. On average, >1,600 individual sequences were generated for each PCR amplicon far beyond the few clones (<20) typically analyzed by traditional bisulfite sequencing. Comprehensive analysis of CpG methylation patterns at a single DNA molecule level using clustering algorithms revealed differential methylation patterns between diseases. A significant increase in methylation was detected in ALL and FL samples compared with CLL and MCL. Furthermore, a progressive spreading of methylation was detected from the periphery toward the center of select CpG islands in the ALL and FL samples. The ultradeep sequencing also allowed simultaneous analysis of genetic and epigenetic data and revealed an association between a single nucleotide polymorphism and the methylation present in the LRP1B promoter. This new generation of methylome sequencing will provide digital profiles of aberrant DNA methylation for individual human cancers and offers a robust method for the epigenetic classification of tumor subtypes. [Cancer Res 2007;67(18):85118] 10.1158/0008-5472.CAN-07-1016}, author = {Taylor, Kristen H. and Kramer, Robin S. and Davis, Wade J. and Guo, Juyuan and Duff, Deiter J. and Xu, Dong and Caldwell, Charles W. and Shi, Huidong}, citeulike-article-id = {1675503}, citeulike-linkout-0 = {http://dx.doi.org/10.1158/0008-5472.CAN-07-1016}, citeulike-linkout-1 = {http://cancerres.aacrjournals.org/cgi/content/abstract/67/18/8511}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17875690}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17875690}, day = {15}, doi = {10.1158/0008-5472.CAN-07-1016}, journal = {Cancer Res}, keywords = {epigenetics, methods, methylation, pyrosequencing}, month = {September}, number = {18}, pages = {8511--8518}, posted-at = {2007-09-19 11:14:08}, priority = {5}, title = {Ultradeep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454 Sequencing}, url = {http://dx.doi.org/10.1158/0008-5472.CAN-07-1016}, volume = {67}, year = {2007} }

TY - JOUR ID - citeulike:1675503 L3 - citeulike-article-id:1675503 N2 - We developed a novel approach for conducting multisample, multigene, ultradeep bisulfite sequencing analysis of DNA methylation patterns in clinical samples. A massively parallel sequencing-by-synthesis method (454 sequencing) was used to directly sequence >100 bisulfite PCR products in a single sequencing run without subcloning. We showed the utility, robustness, and superiority of this approach by analyzing methylation in 25 gene-related CpG rich regions from >40 cases of primary cells, including normal peripheral blood lymphocytes, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), follicular lymphoma (FL), and mantle cell lymphoma (MCL). A total of 294,631 sequences was generated with an average read length of 131 bp. On average, >1,600 individual sequences were generated for each PCR amplicon far beyond the few clones (<20) typically analyzed by traditional bisulfite sequencing. Comprehensive analysis of CpG methylation patterns at a single DNA molecule level using clustering algorithms revealed differential methylation patterns between diseases. A significant increase in methylation was detected in ALL and FL samples compared with CLL and MCL. Furthermore, a progressive spreading of methylation was detected from the periphery toward the center of select CpG islands in the ALL and FL samples. The ultradeep sequencing also allowed simultaneous analysis of genetic and epigenetic data and revealed an association between a single nucleotide polymorphism and the methylation present in the LRP1B promoter. This new generation of methylome sequencing will provide digital profiles of aberrant DNA methylation for individual human cancers and offers a robust method for the epigenetic classification of tumor subtypes. [Cancer Res 2007;67(18):85118] 10.1158/0008-5472.CAN-07-1016 IS - 18 JF - Cancer Res EP - 8518 TI - Ultradeep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454 Sequencing VL - 67 SP - 8511 KW - epigenetics KW - methods KW - methylation KW - pyrosequencing AU - Taylor, Kristen AU - Kramer, Robin AU - Davis, Wade AU - Guo, Juyuan AU - Duff, Deiter AU - Xu, Dong AU - Caldwell, Charles AU - Shi, Huidong PY - 2007/09/15/ UR - http://dx.doi.org/10.1158/0008-5472.CAN-07-1016 ER -