Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2005-07-08
2010-02-16
Kapushoc, Stephen (Department: 1634)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091200, C536S024330
Reexamination Certificate
active
07662561
ABSTRACT:
Methods for identifying expression of markers indicative of the presence of esophageal, a squamous cell cancer, a squamous cell cancer of the head and neck, colon cancer and melanoma are provided. Also provided are articles of manufacture useful in such methods and compositions containing primers and probes useful in such methods.
REFERENCES:
patent: 5314809 (1994-05-01), Erlich et al.
patent: 5814491 (1998-09-01), Vijg et al.
patent: 5837442 (1998-11-01), Tsang
patent: 5843761 (1998-12-01), Barnett et al.
patent: 5854033 (1998-12-01), Lizardi
patent: 5882856 (1999-03-01), Shuber
patent: 5958349 (1999-09-01), Petersen et al.
patent: 6040138 (2000-03-01), Lockhart et al.
patent: 6057105 (2000-05-01), Hoon et al.
patent: 6183960 (2001-02-01), Lizardi
patent: 6210884 (2001-04-01), Lizardi
patent: 6245517 (2001-06-01), Chen et al.
patent: 6251601 (2001-06-01), Bao et al.
patent: 6261776 (2001-07-01), Pirrung et al.
patent: 6306643 (2001-10-01), Gentalen et al.
patent: 6309823 (2001-10-01), Cronin et al.
patent: 6344329 (2002-02-01), Lizardi
patent: 6346413 (2002-02-01), Fodor et al.
patent: 6374684 (2002-04-01), Dority et al.
patent: 6403037 (2002-06-01), Chang et al.
patent: 6406844 (2002-06-01), Pirrung et al.
patent: 6416952 (2002-07-01), Pirrung et al.
patent: 6431476 (2002-08-01), Taylor et al.
patent: 6440725 (2002-08-01), Pourahmadi et al.
patent: 7101663 (2006-09-01), Godfrey et al.
patent: 2001/0051344 (2001-12-01), Shalon et al.
patent: 2006/0068418 (2006-03-01), Godfrey et al.
patent: 1050587 (2000-11-01), None
patent: WO 95/11687 (1995-05-01), None
patent: WO 98/08970 (1998-03-01), None
patent: WO 99/13104 (1999-03-01), None
patent: WO 00/44774 (2000-08-01), None
patent: WO 00/72970 (2000-12-01), None
patent: WO 00/73412 (2000-12-01), None
patent: WO 00/73413 (2000-12-01), None
patent: WO 01/01129 (2001-01-01), None
patent: WO 01/45845 (2001-06-01), None
patent: WO 01/57253 (2001-08-01), None
patent: WO 01/84463 (2001-11-01), None
patent: WO 02/18902 (2002-03-01), None
patent: WO 02/052030 (2002-07-01), None
patent: WO 02/070751 (2002-09-01), None
patent: WO 03/055973 (2003-07-01), None
patent: WO 03/072253 (2003-09-01), None
patent: WO 03/077055 (2003-09-01), None
patent: WO 2004/048931 (2004-06-01), None
Enard W et al. ‘Intra- and interspecific variation in primate gene expression patterns.’ Science. Apr. 12, 2002;296(5566):340-3.
Thisted RA (1998) ‘What is a P-value?’ available online at www.stat.uchicago.edu/˜thisted, pp. 1-6.
Juppner H ‘Functional properties of the PTH/PTHrP receptor.’ Bone. Aug.1995; 17(2 Suppl):39S-42S.
Cheung VG et al ‘Natural variation in human gene expression assessed in lymphoblastoid cells.’ Nat Genet. Mar. 2003;33(3):422-5.
HuGeneFL Array from www.affymetrix.com, p. 1.
Details for HUGENEFL:M93036—AT, from www.affymetrix.com, pp. 1-5.
Details for HUGENEFL:M76482—AT, from www.affymetrix.com, pp. 1-3.
de Vos S et al ‘Gene expression profile of serial samples of transformed B-cell lymphomas.’ Lab Invest. Feb. 2003;83(2):271-85.
ABI Prism 7700 Sequence Detection System User Bulletin #5, “Multiplex PCR with TaqMan VIC Probes,” Applied Biosystems (1998/2001).
Baner, Johan et al. “Signal amplification of padlock probes by rolling circle replication,” Nucleic Acids Research (1998), vol. 26, No. 22, pp. 5073-5078.
Bercovich, Dani et al. “Quantitative Ratio of Primer Pairs and Annealing Temperature Affecting PCR Products in Duplex Amplification,” BioTechniques (Oct. 1999), vol. 27, pp. 762-770.
Braun, D. et al. “Exponential DNA Repliction by Laminar Convection,” Physical Review Letters, 91:158103.
Brink, A. A. T. P. et al. “Nucleic Acid Sequence-Based Amplification, a New Method for Analysis of Spliced and Unspliced [EBV] . . . ” Journal of Clinical Microbiology (Nov. 1998), pp. 3164-3169.
Canter, David et al., “On-Chip Amplification of Genomic DNA with Short Tandem Repeat and Single Nucleotide Polymorphism Analysis,” Nangoen, Inc., San Diego, CA.
Christian, Allen T. et al. “Detection of DNA point mutations and mRNA expression levels by rolling circle amplification in individual cells,” PNAS (Dec. 2001), vol. 98, No. 25, pp. 14238-14243.
DeBaar, Michel P. et al. “Single Rapid Real-Time Monitored Isothermal RNA Amplification Assay for Quantification of [HIV] Type 1 . . . ” Journal of Clinical Microbiology (Apr. 2001), pp. 1378-1384.
DeBarr, M.P. et al. “One-Tube Real-Time Isothermal Amplification Assay To Identify and Distinguish [HIV] Type 1 Subtypes . . . ”Journal of Clinical Microbiology (May 2001), pp. 1895-1902.
Demidov, Vadim V., “Rolling-circle ampliction in DNA diagnostics: the power of simplicity,” Future Drugs Ltd., Expert Rev. Mol. Diagn. (Nov. 2002) 2 (6):542-548.
Dessau, R. B. et al. “Coronaviruses in spinal fluid of patients with acute monosymptomatic optic neuritis,” Acta Neurol Scand (1999), vol. 100, pp. 88-91.
Efron, B. and Tibshirani, R.J. An Introduction to the Bootstrap. Boca Raton: Chapman and Hall, 1993: 247-252.
Godfrey, T.E. et al. “Prognostic Value of Quantitative Reverse Transcription-Polymerase Chain Reaction . . . ” Clinical Cancer Research (Dec. 2001), vol. 7, pp. 4041-4048.
Greijer, Astrid E. et al. “Multiplex real-time NASBA for monitoring expression dynamics of human cytomegalovirus encoded IE1 and pp67 RNA,” Journal of Clinical Virology (2002) vol. 24, pp. 57-66.
Harris, Eva et al. “Typing of Dengue Viruses in Clinical Specimens and Mosquitoes by Single-Tube Multiplex Reverse Transcriptase PCR,” Journal of Clinical Microbiology (Sep. 1998), pp. 2634-2639.
Hoshikawa, Yasushi, et al. “Hypoxia induces different genes in the lungs of rates compared with mice,” Phyisical Genomics (Dec. 3, 2002). vol. 10, p. 1152.
Krishnan, Madhavi, et al. “PCR in Rayleigh-Benard Convection Cell,” Science (Oct. 2002), vol. 298, p. 793.
Leone, G. et al. “Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection . . . ” Nucleic Acids Research (1998), vol. 26, No. 9, pp. 2150-2155.
Little, Michael C. et al. “Molecular Diagnostics and Genetics,” Clinical Chemistry (1999) vol. 45, No. 6, pp. 777-784.
Lockley, Andrew K. et al. “Colormetric detection of immobilized PCR products generated on a solid support,” Nucleic Acids Research, (1997), vol. 25, No. 6, pp. 1313-1314.
Luketich, James D., et al. “Detection of Micrometastases in Histologically Negative Lymph Nodes in Esophageal Cancer,” Ann Thorac Surg (1998); vol. 66, pp. 1715-1718.
Mitas M et al. “Quantitative real-time RT-PCR detection of breast cancer micrometastasis using a multigene marker panel.” Int J Cancer 2001; 93(2):162-171.
Miyake, Y.. et al. “Quantification of Micrometastases in Lymph Nodes of Colorectal Cancer Using Real-Time Fluorescence Polymerase Chain Reaction,” Int. J. Oncol (Feb. 2000), vol. 16, No. 2, pp. 289-293.
Mondesire, Roy R. et al. “Solid-phase nucleic acid extraction, amplification, and detection,” IVD Technology Magazine (May 2000).
Morrison TB et al. “Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification,” Biotechniques, (Jun. 1998); vol. 24, No. 6, pp. 954-962.
Nagaraju, J. et al. “FISSR-PCR: a simple and sensitive assay for highthroughput genotyping and genetic mapping,” Molecular and Cellular Proves (2002) vol. 16, pp. 67-72.
Nallur, Girish et al. “Signal amplification by rolling circle amplification on DNA microarrays,” Nucleic Acids Research, (2001) vol. 29, No. 23 e118.
Nilsson, M. et al. “Making Ends Meet in Genetic Analysis Using Padlock Probes,” Human Mutation (2002) 19:410-415.
Oehlenschlager, Frank et al.“Detection of HIV-1 RNA by nucleic acid sequence-based amplification combined with fluorescence corr
Godfrey Tony E.
Gooding William E.
Hughes Steven J.
Raja Siva
Xi Liqiang
Hirshman Jesse A.
Hirshman Law, LLC
Kapushoc Stephen
University of Pittsburgh-Of the commonwealth System of Higher Ed
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