Epi meets genomics: Technologies for finding and reading the 5th base

Tim Hui Ming Huang, Christoph Plass, Gangning Liang, Peter W. Laird

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations


This chapter presents several high-throughput scanning techniques for the exploration and exploitation of the epigenome. It is now known that the methylation state of multiple 5th bases is susceptible to changes in disease conditions, such as cancer. The described techniques, including restriction landmark genomic scanning (RLGS), methylation-sensitive arbitrarily-primed polymerase chain reaction (MS APPCR), and differential methylation hybridization (DMH), generate unique methylation profiles of multiple DNA molecules. Another technique, MethyLight, analyzes methylation patterns of linked CpGs within individual DNA molecules in the genome. The techniques complement one another in the discovery and utilization of this rich resource of epigenome information. RLGS and MS AP-PCR analyses can result in the identification of multiple differentially methylated molecules in disease cells. This large number of candidate sites can further be evaluated by DMH. MethyLight, which is amenable to automated setup and analysis, utilizes the validated 5th-base markers for routine clinical diagnosis.

Original languageEnglish (US)
Title of host publicationThe Epigenome
Subtitle of host publicationMolecular Hide and Seek
Number of pages26
ISBN (Electronic)9783527601516
ISBN (Print)3527304940, 9783527304943
StatePublished - Mar 16 2005
Externally publishedYes


  • 5th base
  • Arbitrarily primed PCR
  • DNA-cutting enzymes
  • Differential methylation hybridization
  • Epigenome
  • Genomic ponds
  • Genomic shadows
  • MethyLight
  • Restriction landmark genomic scanning

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology


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