High-throughput methods for detecting DNA methylation

Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C435S091100, C435S091200, C536S023100, C536S024300

Reexamination Certificate

active

07807358

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
patent: 5143854 (1992-09-01), Pirrung et al.
patent: 5589339 (1996-12-01), Hampson
patent: 5591575 (1997-01-01), Hampson
patent: 5786146 (1998-07-01), Herman
patent: 5858659 (1999-01-01), Sapolsky et al.
patent: 5871917 (1999-02-01), Duffy
patent: 6027894 (2000-02-01), Sapolsky
patent: 6045994 (2000-04-01), Zabeau et al.
patent: 6300071 (2001-10-01), Vuylsteke
patent: 6605432 (2003-08-01), Huang
patent: 7144701 (2006-12-01), Huang
patent: WO 97/25426 (1997-07-01), None
patent: WO 99/06426 (1999-02-01), None
Donini et al. “AFLP fingerprinting reveals pattern differences between template DNA extracted form different plant organs” Genome, 1997 40: 521-526.
Adams et al., “Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence,” Nature, 1995, pp. 3-174, vol. 377.
Ahuja et al., “Association between CpG Island Methylation and Microsatellite Instability in Colorectal Cancer,” Cancer Research, 1997, pp. 3370-3374, vol. 57.
U.S. Appl. No. 60/120,592, filed Feb. 18, 1999, Huang.
U.S. Appl. No. 60/118,760, filed Feb. 5, 1999, Huang.
Akopyants et al., “PCR-based Subtractive Hybridization and Differences in Gene Content Among Strains ofHelicobacter pylori,” The Proceedings of the National Academy of Sciences, 1998, pp. 13108-13113, vol. 95.
Altschul et al., “Basic Local Alignment Search Tool,” Journal of Molecular Biology, 1990, pp. 403-410, vol. 215.
Antequera et al., “High Levels of De Novo Methylation and Altered Chromatin Structure at CpG Islands in Cell Lines,” Cell, 1990, pp. 503-514, vol. 2.
Antequera et al., “Number of CpG islands and genes in human and mouse,” The Proceedings of the National Academy of Sciences, 1993, pp. 11995-11999, vol. 90.
Baylin et al., “Alterations in DNA Methylation: A Fundamental Aspect of Neoplasia,”Advances in Cancer Research, 1998, Vande Woude (editor), pp. 140-196.
Baylin, “Tying it all Together: Epigenetics, Genetics, Cell Cycle, and Cancer,” Science, 1997, pp. 1948-1949, vol. 277.
Belinsky et al., “Aberrant methylation of p16INK4ais an early event in lung cancer and a potential biomarker for early diagnosis,” The Proceedings of the National Academy of Sciences, 1998, pp. 11891-11896, vol. 95.
Belinsky et al., “Increased Cytosine DNA-methyltransferase Activity is Target-cell-specific and an Early Event in Lung Cancer,” The Proceedings of the National Academy of Sciences, 1996, pp. 4045-4050, vol. 93.
Bloom et al., “Histological Grading and Prognosis in Breast Cancer,” British Journal of Cancer, 1957, pp. 359-377, vol. 11.
Brandeis et al., “Sp1 Elements Protect a CpG Island fromde novoMethylation,” Nature, 1994, pp. 435-438, vol. 371.
Brock et al., “Mosaic methylation of the repeat unit of the human ribosomal RNA genes,” Human Molecular Genetics, 1997, pp. 451-456, vol. 6.
Carotti et al., “Influence of Pre-existing Methylation on the de Novo Activity of Eukaryotic DNA Methyltransferase,” The Biochemical Journal, 1998, pp. 1101-1108, vol. 37.
Chiang et al., “S-Adenosylmethionine and methylation,” The FASEB Journal, 1996, pp. 471-480, vol. 10.
Christman et al., “5-Methyl-2'-deoxycytidine in single-stranded DNA can act in cis to Signalde novoDNA Methylation,” The Proceedings of the National Academy of Sciences, 1995, pp. 7347-7351, vol. 92.
Chuang et al., “Human DNA-(Cytosine-5) Methyltransferase-PCNA Complex as a Target forp21WAF1,” Science, 1997, pp. 1996-2000, vol. 277.
Craig et al., “Removal of Repetitive Sequences from FISH Probes Using PCR-Assisted Affinity Chromatography,” Human Genetics, 1997, pp. 472-476, vol. 100.
Cross et al., “Purification of CpG Islands Using a Methylated DNA Binding Column,” Nature Genetics, 1994, pp. 236-244, vol. 6.
Database, Adams et al., GeneCore, EST, clone AA313068, Nature, 1995, 377(6547, Supplement):3-174.
Database, Cross et al., GeneCore, GenEmbl, clone HS13F7R, Nature Genetics, 1994, 6(3):236-244.
Database, Frudakis et al., GenCore, Geneseq, clone V 49815, WO 97/25426, published Jul. 17, 1997.
Database, Frudakis et al., GenCore, Geneseq, clone VX83369, WO 97/25426, Published Jul. 17, 1997.
Database, Lanfranchi et al., GenCore, EST, clone F16311, Genome Research, 1996, 6(1):35-42.
Database, Pan, GenCore, Genseq, done X22302, WO 99/06426, published Feb. 11, 1999.
Database, Tubby, GeneCore, Geneseq, clone HS29K1, Dec. 18, 1997.
Derisi et al “Use of a cDNA microarray to analyse gene expression patterns in human cancer,” Nature Genetics, 1996, pp. 457-460, vol. 14.
Donini et al., “AFLP fingerprinting reveals pattern differences between template DNA extracted from different plant organs,” Genome, 1997, pp. 521-526, vol. 40.
Engelman et al., “Sequence and detailed organization of the human caveolin-1 and -2 genes located near the D7S522 locus (7q31.1),” FEBS Letters, 1999, pp. 221-230, vol. 448.
Esteller et al., “Detection of Aberrant Promoter Hypermethylation of Tumor Suppressor Genes in Serum DNA from Non-Small Cell Lung Cancer Patients,” Cancer Research, 1999, pp. 67-70, vol. 59.
Frommer et al., “A Genomic Sequencing Protocol that Yields a Positive Display of 5-Methylcytosine Residues in Individual DNA strands,” The Proceedings of the National Academy of Sciences, 1992, pp. 1827-1831, vol. 89.
Gonzalgo et al., “Identification and Characterization of Differentially Methylated Regions of Genomic DNA by Methylation-sensitive Arbitrary Primed PCR,” Cancer Research, 1997, pp. 594-599, vol. 57.
Gonzalgo et al., “Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE),” Nucleic Acids Research, 1997, pp. 2529-2531, vol. 25.
Graff et al., “Mapping Patterns of CpG Island Methylation in Normal and Neoplastic Cells Implicates Both Upstream and Downstream Regions inde NovoMethylation,” Journal of Biological Chemistry, 1997, pp. 22322-22329, vol. 272.
Heller et al., “Discovery and analysis of inflammatory disease-related genes using cDNA microarrays,” The Proceedings of the National Academy of Sciences, 1997, pp. 2150-2155, vol. 94.
Herman et al., “Methylation-specific PCR: A Novel PCR Assay for Methylation Status of CpG Islands,” The Proceedings of the National Academy of Sciences, 1996, pp. 9821-9826, vol. 93.
Holliday et al., “Evidence for gene silencing by endogenous DNA methylation,” The Proceedings of the National Academy of Sciences, 1998, pp. 8727-8732, vol. 95.
Huang et al., “Identification of DNA Methylation Markers for Human Breast Carcinomas Using the Methylation-sensitive Restriction Fingerprinting Technique,” Cancer Research, 1997, pp. 1030-1034, vol. 57.
Huang et al., “Methylation Profiling of CpG Islands in Human Breast Cancer Cells,” Human Molecular Genetics, 1999, pp. 459-470, vol. 8.
Jones, “DNA Methylation Errors and Cancer,” Cancer Research. 1996, pp. 2463-2467, vol. 56.
Kawai et al., “Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method,” Nucleic Acids Research, 1993, pp. 5604-5608, vol. 21.
Kononen et al., “Tissue microa

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

High-throughput methods for detecting DNA methylation does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with High-throughput methods for detecting DNA methylation, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and High-throughput methods for detecting DNA methylation will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-4169979

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.