application of new dna sequencing technologies for the study of epigenetic abnormalities in breast...
TRANSCRIPT
Application of New DNA Sequencing Technologies for the Study of
EpigeneticAbnormalities in Breast Cancer
John R. [email protected]
Columbia Genome CenterJuly 25th, 2007
G - Linker -
O-Block-3’
Sequencing by SynthesisACGCTAGCGATCATGCAGCTGCATCG
TGCGATCG
Template
Primer
C
AT
Ju J, Li Z, Edwards JR, Itagaki Y. U.S. Patent (2003) 6,664,079Ju J, Li Z, Edwards JR, Itagaki Y. U.S. Patent (2003) 6,664,079
DNA Sequencing by Synthesis (SBS) on a Chip
J. Ju et al. PNAS, 2006, 103:19635-40.
Molecular Structures of 3’-O-Allyl-dNTP-Allyl-Dye Nucleotide Analogues
Fractionation Methods Show an Unbiased Coverage of the Genome
McrBC = 3073 sequences
RE = 2565 sequences
DNA Methylation in Cancer
M. Esteller (2005) Annual Review of Pharmacology and Toxicology 45:629-656.
Genomic Hypomethylation
• Genomic instability?
• Activation of proto-oncogenes?
• Loss of Imprinting?
New Tools to Probe DNA Methylation in Breast Cancer
Technology Requirements
• Whole genome approach
• Must examine state of repetitive elements
• Unbiased
• Must be useable for primary tumors
Goals
• Characterize complete methylation profile of breast cancer
• Compare normal/tumor, tumor/tumor, tumor/cell-line
• Investigate potential as biomarker
• Understand patterns of global hypomethylation and regional hypermethylation
AcknowledgementsAcknowledgements
Jingyue Ju
Timothy Bestor (Genetics and Development)Nicholas Turro (Chemistry)Victoria Haghighi (Psychiatry)
Ju LabJames J. Russo Zengmin Li Lanrong Bi Xiaoxu Li Shundi Shi Dae H. Kim
Qingleng Meng Xiaopeng Bai
Bestor Lab Rob RollinsAnne O’Donnell
National Human Genome Research Institute/NIHNSF, Packard Foundation