Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2008-01-29
2008-01-29
Shibuya, Mark L. (Department: 1639)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
Reexamination Certificate
active
07323306
ABSTRACT:
Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.
REFERENCES:
patent: 5508169 (1996-04-01), Deugau et al.
patent: 5858656 (1999-01-01), Deugau et al.
patent: 6261782 (2001-07-01), Lizardi et al.
patent: 6498013 (2002-12-01), Velculescu et al.
patent: 6613520 (2003-09-01), Ashby
patent: 6677121 (2004-01-01), Lizardi et al.
patent: 2003/0165923 (2003-09-01), Li et al.
patent: 2003/0186251 (2003-10-01), Dunn et al.
patent: 2005/0059022 (2005-03-01), Ruan et al.
patent: 2005/0255501 (2005-11-01), Ng et al.
patent: 2006/0084083 (2006-04-01), Ruan et al.
patent: 2006/0084111 (2006-04-01), Ruan et al.
Zhou et al., Journal of Applied Microbiology, 2001, vol. 90, pp. 96-105.
Dunn, et al., “Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA”, Genome Research, 12: 1756-1765, (Nov. 2002).
Wang, et al., “Digital karyotyping”, PNAS, Dec. 10, 2002, vol. 99, No. 25, pp. 16156-16161.
Takai, et al., “Comprehensive Analysis of CpG Islands in Human Chromosomes 21 and 22”, PNAS, Mar. 19, 2002, vol. 99, No. 6, pp. 3740-3745.
Prashar, et al., “Analysis of differential gene expression by display of 3′ end restrictions fragments of cDNAs”, Proc. Natl. Acad. Sci. USA, Jan. 1996, vol. 93, pp. 659-663.
White, et al., “Genome Sequence of the Radioresistant BacteriumDeinococcus radioduransR1”, Science., Nov. 1999, vol. 286, pp. 1571-1577.
Masny, et al., “Fingerprinting of Bacterial Genomes by Amplification of DNA Fragments Surrounding Rare Restriction Sites”, BioTechniques, vol. 31, No. 4, 2001, pp. 930-936.
Ronaghi, et al., “A Sequencing Method Based on Real-Time Pyrophosphate”, Science, vol. 281, Jul. 17, 1998, pp. 363-365.
Ren, et al., “Genome-Wide Location and Function of DNA Binding Proteins”, Science, vol. 290, Dec. 22, 2000, pp. 2306-2309.
Spinella, et al., “Tandem arrayed ligation of expressed sequence tags (TALEST): a new method for generating global gene expression profiles”, Nucleic Acids Research, 1999, vol. 27, No. 18, pp. i-viii.
Rouillard, et al., “Virtual Genome Scan: A Tool for Restriction Landmark-Based Scanning of the Human Genome”, Genome Research, 2001, pp. 1453-1459.
Wimmer, et al., “Combined Restriction Landmark Genomic Scanning and Virtual Genome Scans Identify a Novel Human Homeobox Gene, ALX3, That is Hypermethylated in Neuroblastoma”, Genes, Chromosomes & Cancer, 33, 2002, pp. 285-294.
Tucholski, et al., “MmeI, a class-IIS restriction endonuclease: purification and characterization”, Gene, 157, 1995, pp. 87-92.
Parkhill, et al., “Genome Sequence ofYersinia pestis, the causative agent of plague”, Nature, vol. 413, Oct. 4, 2001, pp. 523-527.
Wang, et al., “A strategy for genome-wide gene analysis: Integrated procedure for gene identification”, Proc. Natl. Sci. USA, vol. 95, Sep. 1998, pp. 11909-11914.
Shiraishi, et al., “Isolation of DNA fragments associated with methylated CpG islands in human adenocarcinomas of the lung using a methylated DNA binding column and denaturing gradient gel electrophoresis”, Proc. Natl. Acad. Sci. USA, vol. 96, Mar. 1999, pp. 2913-2918.
Vos, et al., “AFLP: a new technique for DNA fingerprinting”, Nucleic Acids Ressarch, 1995, vol. 23, No. 21, pp. 4407-4414.
Asakawa, et al., “Genetic variation detected by quantitative analysis of end-labeled genomic DNA fragments”, Proc. Natl. Acad. Sci. USA, vol. 91, Sep. 1994, pp. 9052-9056.
Hatada, et al., “A genomic scanning method for higher organisms using restriction sites as landmarks”, Proc. Natl. Acad. Sci. USA, vol. 88, Nov. 1991, pp. 9523-9527.
Yakimov, et al., “Upstream-independent ribosomal RNA amplification analysis (URA): a new approach to characterizing the diversity of natural microbial communities”, Environmental Microbiology, 3(10), 2001, pp. 662-666.
Van der Lelie, et al., “Use of Single-Point Genome Signature Tags as a Universal Tagging Method for Microbial Genome Surveys”, Applied and Environmental Microbiology, Mar. 2006, pp. 2092-2101.
Impey, et al., “Defining the CREB Regulon: A Genome-Wide Analysis of Transcription Factor Regulatory Regions”, Cell, vol. 119, Dec. 29, 2004, pp. 1041-1054.
Dunn John J
Krause Maureen K.
McCorkle Sean R.
van der Lelie Daniel
Brookhaven Science Associates LLC
Neiger Lori-Anne
Shibuya Mark L.
LandOfFree
Genome signature tags does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Genome signature tags, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Genome signature tags will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2768621