Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2006-12-05
2006-12-05
Goldberg, Jeanine A. (Department: 1634)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091200, C435S287200, C536S023100
Reexamination Certificate
active
07144701
ABSTRACT:
The present invention provides a method of hybridization, differential methylation hybridization (DMH) for high throughput methylation analysis of multiple CpG island loci. DMH utilizes nucleic acid probes prepared from a cell sample to screen numerous CpG dinucleotide rich fragments affixed on a screening array. Positive hybridization signals indicate the presence of methylated sites. Methods of preparing the hybridization probes and screening array are also provided.
REFERENCES:
patent: 4682195 (1987-07-01), Yilmaz
patent: 4683202 (1987-07-01), Mullis
patent: 4800159 (1989-01-01), Mullis et al.
patent: 5589339 (1996-12-01), Hampson et al.
patent: 5591575 (1997-01-01), Hampson et al.
patent: 5786146 (1998-07-01), Herman et al.
patent: 5871917 (1999-02-01), Duffy
patent: 6027894 (2000-02-01), Sapolsky et al.
patent: 6605432 (2003-08-01), Huang
Cross et al. “Purification of CpG islands using a methylated DNA binding column.” Nature Genetics, vol. 6, pp. 236-244, Marych 1994.
Donini et al. “AFLP fingerprinting reveals pattern differences between template DNA extracted from different plant organs.” Genome. vol. 40, pp. 521-526, 1997.
Akopyants et al., “PCR-based Subtractive Hybridization and Differences in Gene Content Among Strains ofHelicobacter pylori”, Proc. Natl. Acad. Sci. USA, vol. 95, pp. 13108-13113, 1998.
Antequera, F., et al., “High Levels of De Novo Methylation and Altered Chromatin Structure at CpG Islands in Cell Lines”, Cell, vol. 2, pp. 503-514, 1990.
Baylin et al., “Alterations in DNA Methylation: A Fundamental Aspect of Neoplasia”, Advances in Cancer Research, pp. 140-196, 1998.
Baylin, Stephen B., “Tying it all Together. Epigenetics, Genetics, Cell Cycle, and Cancer”, Science, vol. 277, pp. 1948-1949, 1997.
Belinsky et al., “Aberrant Methylation ofp16INK4ais an Early Event in Lung Cancer and a Potential Biomarker for Early Diagnosis”, Proc. Natl. Acad. Sci. USA, vol. 95, pp. 11891-11896, 1998.
Belinsky et al., “Increased Cytosine DNA-methyltransferase Activity is Target-cell-specific and an Early Event in Lung Cancer”, Proc. Natl. Acad. Sci. USA, vol. 93, pp. 4045-4050, 1996.
Bloom, H.J.G. and Richardson, W.W., “Histological Grading and Prognosis in Breast Cancer”, British Journal of Cancer, vol. 11, pp. 359-377, 1957.
Brandeis, M. et al., “Sp1 Elements Protect a CpG Island fromde novoMethylation”, Nature, vol. 371, pp. 435-438, 1994.
Carotti et al., “Influence of Pre-existing Methylation on the de Novo Activity of Eukaryotic DNA Methyltransferase”, Biochem. J., vol. 37, pp. 1101-1108, 1998.
Christman et al., “5-Methyl-2′-deoxycytidine in single-stranded DNA can act in cis to Signalde novoDNA Methylation”, Proc. Natl. Acad. Sci., USA, vol. 92, pp. 7347-7351, 1995.
Chuang et al., “Human DNA-(Cytosine-5) Methyltransferase-PCNA Complex as a Target forp21WAF1”, Science, vol. 277, pp. 1996-2000, 1997.
Craig et al., “Removal of Repetitive Sequences from FISH Probes Using PCR-Assisted Affinity Chromatography”, Hum. Genet., vol. 100, pp. 472-476, 1997.
Frommer, M. et al., “A Genomic Sequencing Protocol that Yields a Positive Display of 5-Methylcytosine Residues in Individual DNA strands”, Proc. Natl. Acad. Sci. USA, vol. 89, pp. 1827-1931, 1992.
Graff et al., “Mapping Patterns of CpG Island Methylation in Normal and Neoplastic Cells Implicates Both Upstream and Downstream Regions inde novoMethylation”, J. Biol. Chem., vol. 272, No. 35, pp. 22322-22329, 1997.
Herman et al., “Methylation-specific PCR: A Novel PCR Assay for Methylation Status of CpG Islands”, Proc. Natl. Acad. Sci. USA, vol. 93, pp. 9821-9826, 1996.
Huang, T.H., et al., “Methylation Profiling of CpG Islands in Human Breast Cancer Cells”, Human Molecular Genetics, vol. 8, No. 3, pp. 459-470, 1999.
Jones, P.A., “DNA Methylation Errors and Cancer”, Cancer Res., vol. 56, pp. 2463-2467, 1996.
Laird et al., “DNA Methylation and Cancer”, Hum. Mol. Genet., vol. 3, pp. 1487-1495, 1994.
Lee J.H. and Welch D.R., “Identification of Highly Expressed Genes in Metastasis-Suppressed Chromosome 6/Human Malignant Melanoma Hybrid Cells Using Subtractive Hybridization and Differential Display”, Int. J. Cancer, vol. 71, pp. 1035-1044, 1997.
Li et al., “Role for DNA Methylation in Genomic Imprinting”, Nature, vol. 366, pp. 362-365, 1993.
Mummaneni, P., et al., “Epigenetic Gene Inactivation Induced by a Cis-acting Methylation Center”, J. Biol. Chem., vol. 270, No. 2, pp. 788-792, 1995.
Pfeifer, G.P., et al., “Polymerase Chain Reaction-Aided Genomic Sequencing of an X Chromosome-linked CpG Island: Methylation Patterns Suggest Clonal Inheritance, CpG Site Autonomy, and an Explanation of Activity State Stability”, Proc. Natl. Acad. Sci. USA, vol. 87, pp. 8252-8256, 1990.
Saiki et al., “Primer-Directed Enzymatic Amplification of DNA with a Thermostable DNA Polymerase”, Science, vol. 239, pp. 487-491, 1988.
Schena et al., “Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray”, Science, vol. 270, pp. 467-470, 1995.
Singer-Sam, J. and Riggs, A..D., “X-Chromosone Inactivation and DNA Methylation”, DNA Methylation: Molecular Biology and Biological Significance, pp. 358-384, 1993.
Vertino et al., “De Novo Methylation of CpG Island Sequences in Human Fibroblasts Overexpressing DNA (Cytosine-5)—Methyltransferase”, Mol. Cell Biol., vol. 16, pp. 4555-4565, 1996.
Wu et al., “Expression of ProkaryoticHhalDNA Methyltransferase is Transforming and Lethal to NIH 3T3 Cells”, Cancer Res., vol. 56, pp. 616-622, 1996.
Davis Wright Tremaine
Davison Barry L.
Goldberg Jeanine A.
The Curators of the University of Missouri
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