Data processing: structural design – modeling – simulation – and em – Modeling by mathematical expression
Reexamination Certificate
2008-01-29
2008-01-29
Clow, Lori A. (Department: 1631)
Data processing: structural design, modeling, simulation, and em
Modeling by mathematical expression
C703S011000, C702S020000
Reexamination Certificate
active
09968627
ABSTRACT:
Methods and apparatus for classifying or predicting the classes for samples based on gene expression are described. Also described are methods and apparatus for ascertaining or discovering new, previously unknown classes based on gene expression. Methods, computer systems and apparatus for classifying or predicting whether a sample is treatment sensitive (e.g., chemosensitive) or treatment resistant (e.g., chemoresistant) are also provided. Classification occurs based on analysis of gene expression data from samples that have been subjected to one or more compounds.
REFERENCES:
patent: 5040133 (1991-08-01), Feintuch et al.
patent: 5179643 (1993-01-01), Homma et al.
patent: 5438629 (1995-08-01), Moed et al.
patent: 5631734 (1997-05-01), Stern et al.
patent: 5734796 (1998-03-01), Pao
patent: 5770722 (1998-06-01), Lockhart et al.
patent: 5819245 (1998-10-01), Peterson et al.
patent: 5832182 (1998-11-01), Zhang et al.
patent: 5871697 (1999-02-01), Rothberg et al.
patent: 5925525 (1999-07-01), Fodor et al.
patent: 6295514 (2001-09-01), Agrafiotis et al.
Shi et al. (Molecular Pharmacology (1998) vol. 53, pp. 241-251).
Borrow, Julian, et al., “The t(7;11) (p15;p15) translocation in acute myeloid leukaemia fuses the genes for nucleoporin NUP98 and class I homeoprotein HOXA9,”Nature Genetics, 12(2): 159-167 (1996).
Buccheri, Valeria, et al., “mb-1: A New Marker for B-Lineage Lymphoblastic Leukemia,”Blood, 82(3): 853-857 (1993).
Chu, S., et al., “The Transcriptional Program of Sporulation in Budding Yeast,”Science, 282: 699-705 (1998).
Cole, Kristina A., et al., “The genetics of cancer—a 3D model,”Nature Genetics, 21: 38-41 (1999).
Eisen, Michael, B., et al., “Cluster analysis and display of genome-wide expression patterns,”Proc. Natl. Acad. Sci., 95: 14863-14868 (1998).
Ermolaeva, Olga, et al., “Data management and analysis for gene expression arrays,”Nature Genetics, 20: 19-23 (1998).
Huang, Shang-Yi, et al., “Clinical, haematological and molecular studies in patients with chromosome translocation t(7;11): a study of four chinese patients in Taiwan,”British Journal of Haematology, 96: 682-687 (1997).
Iyer, Vishwanath R., et al., “The Transcriptional Program in the Response of Human Fibroblasts to Serum,”Science, 283: 83-87 (1999).
Khan, Javed, et al., “Expression profiling in cancer cDNA microarrays,”Electrophoresis, 20: 223-229 (1999).
Khan, Javed, et al., “Gene Expression Profiling of Alveolar Rhabdomyosarcoma with cDNA Microarrays,”Cancer Research, 58: 5009-5013 (1998).
Kononen, Juha, et al., “Tissue microarrays for high-throughput molecular profiling of tumor specimens,”Nature Medicine, 4: 844-847 (1998).
Kroon, Evert, et al., “Hoxa9 transforms primary bone marrow cells through specific collaboration with Meisla but not Pbx1b,”The EMBO Journal, 17(13): 3714-3725 (1998).
Lander, Eric S., “The New Genomics: Global Views of Biology,”Science, 274: 536-539 (1996).
Nakamura, Takuro, et al., “Fusion of the nucleoporin gene NUP98 to HoXA9 by the chromosome translocation t(7;11) (p15;p15) in human myeloid leukaemia”Nature Genetics, 12: 154-158 (1996).
Spellman, Paul T., et al., “Comprehensive Indentification of Cell Cycle-regulated Genes of the YeastSaccharomyces cerevisiaeby Microarray HybridizationD,”Molecular Biology of the Cell, 9(12): 3273-3297 (1998).
Tamayo, Pablo, et al., “Interpreting patterns of gene expression with self-organizing maps: Methods and appliation to hematopoietic differentiation,”Proc. Natl. Acad. Sci., 96: 2907-2912 (1999).
Tavazoie, Saeed, et al., “Systematic determination of genetic network architecture,”Nature Genetics, 22: 281-285 (1999).
Törönen, Petri, et al., “Analysis of gene expression data using self-organizing maps,”FEBS Letters, 451: 142-146 (1999).
Watson, Andrew, et al., “Technology for microarray analysis of gene expression,”Biotechnology, 9: 609-614 (1998).
Yang, George P., et al., “Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes,”Nucleic Acids Research, 27(6): 1517-1523 (1999).
“Affymetrix Launches New Genome Scanning Genechip® Expression Products,” [online], Sep. 1998 [retrieved on Oct. 14, 1998]. Retrieved from the Internet:<URL:http://www.affymetrix.com/press/pr980918.html>.
Stipp, D., “Gene Chip Breakthrough,” [online], Mar. 1997 [retrieved Oct. 15, 1998]. Retrieved from the Internet: <URL:http://www.pathfinder.com/@@NJC11CgcA1QLIOjS3/fortune/1997/970331/bio.html>.
Zheng, P. et al., “Proto-oncogene PML controls genes devoted to MHC class I antigen presentation,”Nature, 396: 373-376 (Nov. 26, 1998).
Lockhart, D.J. et al., “Expression monitoring by hybridization to high-density oligonucleotide arrays,”Nature Biotechnology, 14: 1675-1680 (Dec. 1996).
DeRisi, J.L., et al., “Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale,”Science, 278: 680-686 (Oct. 1997).
Lashkari, D.A., et al., “Yeast microarrays for genome wide parallel genetic and gene expression analysis,”Proc. Natl. Acad. Sci. USA, 94: 13057-13062 (Nov. 1997).
Miyata, Y., et al., “Phosphorylation of the immunosuppressant FK506-binding protein FKBP52 by casein kinase II: Regulation of HSP90-binding activity of FKBP52,”Proc. Natl. Acad. Sci. USA, 94: 14500-14505 (Dec. 1997).
Kok, K., et al., “A gene in the chromosomal region 3p21 with greatly reduced expression in lung cancer is similar to the gene for ubiquitin-activating enzyme,”Proc. Natl. Acad. Sci. USA, 6071-6075 (Jul. 1993).
Wodicka, L., et al., “Genome-wide expression monitoring inSaccoarmyces cerevisiae,” Nature Biotechnology, 15: 1359-1367 (Dec. 1997).
Jin, Y., et al., “Molecular cloning of a 25-kDa high affinity rapamycin binding protein, FKBP25,”J. Bio. Chem., 267(16): 10942-10945 (1992).
Pennisi, E., “DNA Chips Give New View of Classic Test,”Science, 283: 17-18 (Jan. 1999).
Jobson, J.D., “Cluster Analysis” in Applied Multivariate Data Analysis, vol. II: Categorical and Multivariate Methods, (NY:Springer-Verlag) pp. 518-568 (1992).
Gordon, A.D., “Introduction” and “Measuring dissimilarity.” InClassification, (Chapman and Hall) pp. 1-53 (1981).
Kohonen, T., “Self-Organizing Maps,” 2nd Edition, T.S. Huang et al., eds. (NY: Springer-Verlag, 1997).
Loos, H.S. and B. Fritzke, DemoGNG (Version 1.5), [online] [Retrieved Jan. 29, 1999]. Retrieved from the Internet: <URL: http://www.neuroinformatik.ruhr-uni-bochum.de/ini/VDM/research/gns/DemoGNG/GNG.html>.
Kaski, S., et al., “Bibliography of Self-Organizing Map (SOM) Papers: 1981-1997,” [online] Sep. 1998 [retrieved on Mar. 5, 1999]. Retrieved from the Internet: <URL: http://www.icsi.berkeley.edu/˜jagota/NCS/VOL1/P4—html/ vol1—4.html>.
Cho, R., et al., “A genome-wide transcriptional analysis of the mitotic cell cycle,”Molecular Cell, 2: 65-73 (Jul. 1998).
de Thé, H., et al., “The PML-RAR Fusion mRNA Generated by the t(15;17) Translocation in Acute Promyelocytic Leukemia Encodes a Functionally Altered RAR,”Cell, 66: 675-684 (Aug. 1991).
Hartigan, J., “Clustering” inClustering Algorithms, (NY:J. Wiley, 1975) pp. 1-27, 155-176.
Bamdad, C., “Surface Plasmon Resonance for Measurements of Biological Interest” inCurrent Protocols in Molecular Biology, (John Wiley & Sons, Inc.) pp. 20.4.1-20.4.12 (1997).
Eisen, M.B., et al., “Cluster analysis and display of genome-wide expression patterns,”Proc. Natl. Acad. Sci. USA, 95: 14863-14868 (Dec. 1998).
Jain, A.K. and R.C. Dubes, “Algorithms for Clustering Data,” (Prentice-Hall), pp. 1-27, 118-142, 262-274 (198
Coller Hilary A.
Golub Todd R.
Lander Eric S.
Mesirov Jill P.
Slonim Donna K.
Clow Lori A.
Dana-Farber Cancer Institute Inc.
Ropes & Gray LLP
Whitehead Institute for Biomedical Research
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