Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing

Kristen H. Taylor, Robin S. Kramer, J. Wade Davis, Juyuan Guo, Deiter J. Duff, Dong Xu, Charles W. Caldwell, Huidong Shi

Research output: Contribution to journalArticle

208 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)8511-8518
Number of pages8
JournalCancer Research
Volume67
Issue number18
DOIs
StatePublished - Sep 15 2007
Externally publishedYes

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DNA Methylation
Methylation
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Follicular Lymphoma
Genes
Mantle-Cell Lymphoma
B-Cell Chronic Lymphocytic Leukemia
Epigenomics
High-Throughput Nucleotide Sequencing
Polymerase Chain Reaction
CpG Islands
Single Nucleotide Polymorphism
Cluster Analysis
hydrogen sulfite
Neoplasms
Clone Cells
Lymphocytes
DNA

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. / Taylor, Kristen H.; Kramer, Robin S.; Davis, J. Wade; Guo, Juyuan; Duff, Deiter J.; Xu, Dong; Caldwell, Charles W.; Shi, Huidong.

In: Cancer Research, Vol. 67, No. 18, 15.09.2007, p. 8511-8518.

Research output: Contribution to journalArticle

Taylor, Kristen H. ; Kramer, Robin S. ; Davis, J. Wade ; Guo, Juyuan ; Duff, Deiter J. ; Xu, Dong ; Caldwell, Charles W. ; Shi, Huidong. / Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. In: Cancer Research. 2007 ; Vol. 67, No. 18. pp. 8511-8518.
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