Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving antigen-antibody binding – specific binding protein...
Reexamination Certificate
2002-09-05
2009-11-24
Aeder, Sean E (Department: 1642)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving antigen-antibody binding, specific binding protein...
C435S006120
Reexamination Certificate
active
07622260
ABSTRACT:
The invention provides methods for diagnosing biological states or conditions based on ratios of gene expression data from tissue samples, such as cancer tissue samples. The invention also provides sets of genes that are expressed differentially in malignant pleural mesothelioma. These sets of genes can be used to discriminate between normal and malignant tissues, and between classes of malignant tissues. Accordingly, diagnostic assays for classification of tumors, prediction of tumor outcome, selecting and monitoring treatment regimens and monitoring tumor progression/regression also are provided.
REFERENCES:
patent: 5770176 (1998-06-01), Nargessi
patent: 5840484 (1998-11-01), Seilhamer et al.
patent: 6040138 (2000-03-01), Lockhart et al.
patent: 2009/0104617 (2009-04-01), Gordon et al.
patent: WO 00/55633 (2000-09-01), None
patent: WO 03/021229 (2003-03-01), None
Reimer et al (Cancer Research, Feb. 15, 2000, 60:822-826).
Beer et al., Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med. Aug. 2002; 8(8):816-24.
Bhattacharjee et al., Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A. Nov. 20, 2001;98(24):13790-5.
Clark et al., Genomic analysis of metastasis reveal an essential role for RhoC. Nature. Aug. 3, 2000;406(6795):532-5.
Dhanasekaran et al., Delineation of prognostic biomarkers in prostate cancer. Nature. Aug. 23, 2001;412(6849):822-6.
Dudoit et al., Comparison of discrimination methods for the classification of tumors using gene expression data. J Am Stat Assoc. 2002; 97(457):77-87.
Fodor et al., Massively parallel genomics. Science. 1997; 277:393-5.
Golub et al., Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. Oct. 15, 1999;286(5439):531-7.
Gordon et al., Translation of microarray data into clinically relevant cancer diagnostic test using gene expression ratios in lung cancer and mesothelioma. Cancer Res. Sep. 1, 2002;62(17):4963-7.
Gordon et al., Validation of genomics-based prognostic tests in malignant pleural mesothelioma. Clin Cancer Res. Jun. 15, 2005;11(12):4406-14.
Gordon et al., Using gene expression ratios to predict outcome among patients with mesothelioma. J Natl Cancer Inst. Apr. 16, 2003;95(8):598-605.
Gullans et al., Of microarrays and meandering data points. Nat Genet. Sep. 2000;26(1):4-5.
Gwynne et al., Microarray Analysis: the next revolution in Molecular Biology. Science eMarketplace. Science. Aug. 6, 1999. (science.org/feature/e-market/benchtop/micro.shl).
Hedenfalk et al., Gene-expression profiles in hereditary breast cancer. N Engl J Med. Feb. 22, 2001;344(8):539-48.
Hough et al., Large-scale serial analysis of gene expression reveals genes differentially expressed in ovarian cancer. Cancer Res. Nov. 15, 2000;60(22):6281-7.
Hsiao et al., A compendium of gene expression in normal human tissues. Physiol Genomics. Dec. 21, 2001;7(2):97-104.
Khan et al., Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med. Jun. 2001;7(6):673-9.
O'Dell et al., Associations of IGF2 Apal RFLP and INS VNTR class I allele size with obesity. Eur J Hum Genet. Oct.-Nov. 1999;7(7):821-7.
Perou et al., Molecular portraits of human breast tumours. Nature. Aug. 17, 2000;406(6797):747-52.
Pomeroy et al., Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. Jan. 24, 2002;415(6870):436-42.
Quackenbush et al., Computational analysis of microarray data. Nat Rev Genet. Jun. 2001;2(6):418-27.
Rosenwald et al., The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med. Jun. 20, 2002;346(25):1937-47.
Shipp et al., Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med. Jan. 2002;8(1):68-74.
Sugarbaker et al., Extrapleural pneumonectomy in the multimodality therapy of malignant pleural mesothelioma. Results in 120 consecutive patients. Ann Surg. Sep. 1996;224(3):288-94; discussion 294-6.
Sugarbaker et al., Node status has prognostic significance in the multimodality therapy of diffuse, malignant mesothelioma. J Clin Oncol. Jun. 1993;11(6):1172-8.
Sugarbaker et al., Resection margins, extrapleural nodal status, and cell type determine postoperative long-term survival in trimodality therapy of malignant pleural mesothelioma: results in 183 patients. J Thorac Cardiovasc Surg. Jan. 1999;117(1):54-63; discussion 63-5.
Tusher et al., Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A. Apr. 24, 2001;98(9):5116-21.
Van 'T Veer et al., Gene expression profiling predicts clinical outcome of breast cancer. Nature. Jan. 31, 2002;415(6871):530-6.
Virtaneva et al., Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics. Proc Natl Acad Sci U S A. Jan. 30, 2001;98(3):1124-9.
Wang et al., Monitoring gene expression profile changes in ovarian carcinomas using cDNA microarray. Gene. Mar. 18, 1999;229(1-2):101-8.
Warrington et al., Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genomics. Apr. 27, 2000;2(3):143-7.
Welsh et al., Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci U S A. Jan. 30, 2001;98(3):1176-81.
Welsh et al., Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res. Aug. 15, 2001;61(16):5974-8.
Calvo, R. et al., Altered HOX and WNT7A expression in human lung cancer. Proc Natl Acad Sci U S A. Nov. 7, 2000;97(23):12776-81.
Frank, S. et al., Identification of a differential expression of two cDNAs between malignant mesothelioma and normal mesothelial cells using the RNA fingerprint method. Tumour Biol. 1998;19(3):153-9.
Frank, S. et al., Identification of genes involved in human mesothelial cancer progression using a modified differential display technique. Cancer Lett. Jan. 16, 1998;123(1):7-14.
Kettunen, E. et al., Gene expression profiling of malignant mesothelioma cell lines: cDNA array study. Int J Cancer. Feb. 15, 2001;91(4):492-6.
Liu, Z et al. Expression and activity of matrix metalloproteases in human malignant mesothelioma cell lines. Int J Cancer. Mar. 1, 2001;91(5):638-43.
Mohr, S et al. [Gene expression profiling in human mesothelioma cells using DNA microarray and high-density filter array technologies] Bull Cancer. Mar. 2001;88(3):305-13. French.
Rihn, BH et al. Differential gene expression in mesothelioma. FEBS Lett. Sep. 1, 2000;480(2-3):95-100.
Sandhu, H. et al., mRNA expression patterns in different stages of asbestos-induced carcinogenesis in rats. Carcinogenesis. May 2000;21(5):1023-9.
Sun, X. et al., Upregulation of 9 genes, including that for thioredoxin, during epithelial differentiation of mesothelioma cells. Differentiation. Dec. 2000;66(4-5):181-8.
Goetz, M.P. et al., A two-gene expression ratio of homeobox 13 and interleukin-17B receptor for prediction of recurrence and survival in women receiving adjuvant tamoxifen. Clin Cancer Res. Apr. 1, 2006;12(7 Pt. 1):2080-7.
Granville, C.A. and Dennis, P.A. An overview of lung cancer genomics and proteomics. Am J Respir Cell Mol Biol. Mar. 2005;32(3):169-76.
Groskopf, J. et al., APTIMA PCA3 molecular urine test: development of a method to aid in the diagnosis of prostate cancer. Clin Chem. Jun. 2006;52(6):1089-95. Epub Apr. 20, 2006.
Groskopf, J. et al., PCA3 Molecular Urine Assay: Characterization of a Method to Aid in the Diagnosis of Prostate Cancer, Poster 2006 European Association of Urology, Paris France.
Hofmann, H. S. et al., Discrimination of human lung neoplasm from normal lung by two target genes. Am J Respir Crit Care Med. Sep. 1, 2004;170(5):516-9.
Jansen, M.P. et al., Re: Limits of predictive models using microarr
Bueno Raphael
Gordon Gavin J.
Gullans Steven R.
Hsiao Li-Li
Jensen Roderick V.
Aeder Sean E
The Brigham and Women's Hospital, Inc.
Wesleyan University
Wolf Greenfield & Sacks P.C.
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