Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2010-08-18
2011-11-22
Clow, Lori A (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S013000, C702S015000, C703S002000, C703S011000
Reexamination Certificate
active
08065092
ABSTRACT:
A method of diagnosing, predicting, or prognosticating about a disease that includes obtaining experimental data, wherein the experimental data is high dimensional data, filtering the data, reducing the dimensionality of the data through use of one or more methods, training a supervised pattern recognition method, ranking individual data points from the data, wherein the ranking is dependent on the outcome of the supervised pattern recognition method, choosing multiple data points from the data, wherein the choice is based on the relative ranking of the individual data points, and using the multiple data points to determine if an unknown set of experimental data indicates a diseased condition, a predilection for a diseased condition, or a prognosis about a diseased condition.
REFERENCES:
patent: 6794137 (2004-09-01), Blumenberg
patent: 7062384 (2006-06-01), Rocke et al.
patent: 7229774 (2007-06-01), Chinnaiyan et al.
patent: 7341552 (2008-03-01), Zhang et al.
patent: 7370021 (2008-05-01), Reeve et al.
patent: 7384736 (2008-06-01), Hakonarson
patent: 7402388 (2008-07-01), Gillis et al.
patent: 7402399 (2008-07-01), Mukherjeei et al.
patent: 7774143 (2010-08-01), Khan et al.
patent: 7783431 (2010-08-01), Khan et al.
patent: 2003/0207278 (2003-11-01), Khan et al.
patent: 2004/0009154 (2004-01-01), Khan et al.
patent: 2008/0181896 (2008-07-01), Khan et al.
Agilent Technology Webpage, dated Aug. 16, 2007.
Ancoca et al., “On the statistical assessment of classifiers using DNA microarray data”,BMC Bioinformatics, 7:387 (2006).
Blast Alignment between GenBank Accession No. NM—000612 and SEQ ID No. 72, dated Aug. 16, 2007.
Chen et al., “Diagnosis of the Small Round Blue Cell Tumors Using Multiplex Polymerase Chain Reaction”,Journal of Molecular Diagnostics, 9(1):80-88 (2007).
Cover page of Nature Medicine, vol. 7, No. 6, Jun. 2001.
ECgene Summary for CCND1 available via URL: <genome.ewha.ac.kr/cgi-bin/ECquery.cgi?organism=human&query=CCND1>, printed May 29, 2008.
ECgene Summary for IGF2 available via URL: <genome.ewha.ac.kr/cgi-bin/ECquery.cgi?organism=human&query=IGF2>, printed May 29, 2008.
Furey et al.,Bioinformatics, 16(10):906-914 (2000).
GenBank Accession No. N54901, dated Jan. 28, 1997.
GenBank Accession No. NM—000612, dated Oct. 31, 2000.
GenBank Sequence Revision History page printed Aug. 15, 2007.
GeneCard Database Record IGF2 printed Aug. 15, 2007.
GeneCard for IGF2 via URL: <genecards.org/cgi-bin/carddisp.pl?gene=IGF2&snp=93#snp>, printed May 29, 2008.
GeneCard for CCND1 available via URL: <genecards.org/cgi-bin/carddisp.pl?gene=Ccnd1&snp=97#snp>, printed May 29, 2008.
Golub et al., “Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring”, Science, 286:531-537 (1999).
Gruvberger et al., “Estrogen Receptor Status in Breast Cancer is Associated with Remarkably Distinct Gene Expression Patterns”, Cancer Research, 61:5979-5984 (2001).
Herrero et al.,Bioinformatics, 17(2):126-136 (2001).
Image Consortium Record printed Aug. 15, 2007.
Image Id. No. record printed Sep. 21, 2006.
Kim et al., “ECgene: genome annotation for alternative splicing”,Nucleic Acids Research, 33:D75-D79 (2005).
Khan et al., “Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks”, Nature Medicine, 7(6):673-679 (2001).
Kwon et al., “DNA Microarray Data Analysis for Cancer Classification Based on Stepwise Discriminant Analysis and Bayesian Decision Theory”, Genome Informatics, 12:252-254 (2001).
Li et al., Human Pathology, 2008, 39:1792-1801.
Mateos et al., “Supervised Neural Networks for Clustering Conditions in DNA Array Data after Reducing Noise by Clustering Gene Expression Profiles”,Microarray data analysis II, Kluwer Academic Publ., pp. 91-103 (2002).
Muller et al.,IEEE Transactions on Neural Networks, 12(2):181-201 (2001).
NHGRI Protocol, http://www.nhgri.hih.gov/DIR/LGG/SK/HTML/protocol.html, 27 pages (Apr. 25, 2002).
Peterson et al., “JETNET 3.0—A versatile artificial neural network package”, Computer Physics Communications, 81:185-220 (1994).
Raychaudhuri et al., Pacific Symposium on Biocomputing (2000) pp. 455-466.
Raychaudhuri et al.,Trends in Biotechnology, 19(5):189-193 (2001).
Sequence Alignment printed Sep. 11, 2006.
Sperduti et al., “Supervised Neural Networks for the Classification of Structures”, IEEE Transaction on Neural Networks, 8(3):714-735 (1997).
Tips for cDNA sequences printed Sep. 21, 2006.
Tusher et al., “Significance analysis of microarrays applied to the ionizing radiation response”, PNAS, 98(9):5116-5121 (2001).
U.S. Appl. No. 10/133,937 Office Action dated Jan. 22, 2009.
U.S. Appl. No. 10/159,563 Office Action dated Feb. 12, 2009.
U.S. Appl. No. 10/159,653 Form PTO-892 from Office Action dated Jun. 10, 2008, should be U.S. Appl. No. 10/159,563.
Van Gelder et al., “Amplified RNA synthesized from limited quantities of heterogeneous cDNA”, Proc. Natl. Acad. Sci. USA, 87(5):1663-1667 (1990).
Wang et al., Human Genetics, 2006, 120:297-300.
Khan Javed
Meltzer Paul
Peterson Carsten
Ringner Markus
Clow Lori A
Merchant & Gould P.C.
The United States of America as represented by the Department of
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