1. Ultradeep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454 Sequencing
- Author
-
Juyuan Guo, Kristen H. Taylor, Dong Xu, Robin Kramer, Huidong Shi, Deiter J. Duff, Charles W. Caldwell, and J. Wade Davis
- Subjects
Cancer Research ,Genome, Human ,Lymphoma, Non-Hodgkin ,Bisulfite sequencing ,Sequence Analysis, DNA ,Methylation ,DNA Methylation ,Precursor Cell Lymphoblastic Leukemia-Lymphoma ,Biology ,Leukemia, Lymphocytic, Chronic, B-Cell ,Polymorphism, Single Nucleotide ,Molecular biology ,Bisulfite ,Oncology ,DNA methylation ,Humans ,Sulfites ,Illumina Methylation Assay ,CpG Islands ,Epigenetics ,Methylated DNA immunoprecipitation ,Promoter Regions, Genetic ,Exome sequencing - 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 (
- Published
- 2007