Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2005-02-18
2011-10-25
Babic, Christopher M. (Department: 1637)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
Reexamination Certificate
active
08043808
ABSTRACT:
The invention can be summarized as follows. There is provided a method for amplifying hypomethylated genomic nucleotide sequences and/or hypermethylated genomic nucleotide sequences and comparing the methylation state between different samples, for example control and test samples. Also disclosed is a microarray based method for analyzing hypo and/or hypermethylated genomic nucleotide sequence. Further, kits comprising reagents for practicing the method are provided.
REFERENCES:
patent: 5874215 (1999-02-01), Kuiper et al.
patent: 6110680 (2000-08-01), Sutcliffe et al.
patent: 6605432 (2003-08-01), Huang
patent: 6617137 (2003-09-01), Dean et al.
patent: 2003/0099997 (2003-05-01), Bestor
patent: 97/45560 (1997-12-01), None
patent: WO 00/26401 (2000-05-01), None
patent: WO 03/027259 (2003-04-01), None
patent: WO 03/064701 (2003-08-01), None
Yan et al. (J Nutr. Aug. 2002;132(8 Suppl):2430S-2434S).
Chotai et al. (J Med Genet. Jun. 1998;35(6):472-5).
Yan et al. (2002) “Applications of CpG Island Microarrays for High-Throughput Analysis of DNA Methylation” J. Nutrition 132(8) Suppl.:2430S-2434S.
Chotai & Payne (1998) “A rapid, PCR based test for differential molecular diagnosis of Prader-Willi and Angelman syndromes” J. Med. Genet. 35(6):472-475.
International Search Report and Written Opinion for PCT/CA2005/000211.
Adorj an, P., et al., Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res, 2002. 30(5): p. e21.
Balog, R.P., et al., Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays. Anal Biochem, 2002. 309(2): p. 301-10.
Bird, A.P., CpG-rich islands and the function of DNA methylation. Nature, 1986. 321(6067): p. 209-13.
Chen C. et al. Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes. Am J Pathol. Jul. 2003. vol. 163, No. 1, pp. 37-45.
Frommer, M., et al., A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. PNAS USA, 1992. 89(5): p. 1827-31.
Gitan, R.S., et al., Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res, 2002. 12(1): p. 158-64.
Hatada, I., et al., A microarray-based method for detecting methylated loci. J Hum Genet, 2002.47(8): p. 448-51.
Hou, P., et al., A microarray to analyze methylation patterns of p16(Ink4a) gene 5′-CpG islands. Clin Biochem , 2003 . 36(3): p. 197-202.
Kruger et al. McrB: a prokaryotic protein specifically recognizing DNA containing modified cytosine residues. EMBO J, 1995. 14(11): p. 2661-9.
Shi, H., et al., Triple analysis of the cancer epigenome: an integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation. Cancer Res, 2003. 63(9): p. 2164-71.
Stewart & Raleigh, Dependence of McrBC cleavage on distance between recognition elements . Biol Chem, 1998. 379(4-5): p. 611-6.
Sutherland et al., McrBC: a multisubunit GTP-dependent restriction endonuclease. J Mol Biol , 1992. 225(2): p. 327-48.
Tompa, R., et al ., Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr Biol, 2002. 12(I): p. 65-8.
Toyota, M., et al ., Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res, 1999. 59(10): p. 2307-12.
Van Steensel et al., Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet, 2001. 27(3): p. 304-8.
Van Steensel & Henikoff, Epigenomic profiling using microarrays. Biotechniques , 2003. 35(2): p. 346-50, 352-4, 356-7.
Yamada, Y. et al. A comprehensive analysis of allelic Methylation status of CpG islands on human chromosome 21q. Genome Res. Feb. 2004, vol. 14, No. 2, pp. 247-266.
Yan, P.S., et al., Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res, 2001. 61(23): p. 8375-80.
Yan, P.S., et al., Use of CpG island microarrays to identify colorectal tumors with a high degree of concurrent methylation. Methods, 2002. 27(2): p. 162-9.
Frigola, Jordi et al., Methylome Profiling of Cancer Cells by Amplification of Inter-Methylated Sites (AIMS), Oxford University Press, Nucleic Acids Research, 2002, vol. 30, No. 7 e28, 2002, pp. 1-7.
Supplemental European Search Report for EP 05 70 6493 dated Dec. 3, 2007.
Petronis Arturas
Schumacher Axel
Babic Christopher M.
Centre for Addiction and Mental Health
Smith , Gambrell & Russell, LLP
Sundby Suzannah K.
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