Diagnostic and Prognostic Tests

a prognostic test and diagnostic technology, applied in the field of diagnostic and prognostic tests, can solve problems such as patient death, and achieve the effects of simple, powerful, and easy adaptation to clinical settings

Inactive Publication Date: 2009-04-23
THE BRIGHAM & WOMEN S HOSPITAL INC +1
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  • Abstract
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Benefits of technology

[0009]The diagnostic and prognostic methods that were developed utilize gene expression data from as few as two genes through the use of expression level ratios and rationally chosen thresholds. The effectiveness of unit-less ratios in diagnosing cancer types was demonstrated and confirmed using real time quantitative reverse-transcriptase polymerase chain reaction (RT-PCR). This is a simple, but powerful, use of microarray data that can be easily adapted to a clinical setting to diagnose cancer (and non-cancer tissue or diseases) and predict patient outcome without complex computer software or hardware. Accordingly, diagnostic assays for classification of tumors, prediction of tumor outcome, selecting and monitoring treatment regimens, and monitoring tumor progression / regression can now be based on the ratios of expression of a small number of genes.

Problems solved by technology

MPM is a mesodermally derived, neoplastic disease that arises in the pleura and relentlessly grows into adjacent structures until it ultimately results in the death of the patient.

Method used

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Examples

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example 1

REFERENCES FOR EXAMPLE 1

[0147]1. Aisner, J. Diagnosis, staging, and natural history of pleural mesothelioma. In: J. Aisner, R. Arriagada, M. R. Green, N. Martini, and M. C. Perry (eds.), Comprehensive Textbook of Thoracic Oncology, pp. 799-785. Baltimore: Williams and Wilkins, 1996.[0148]2. Pass, H. Malignant pleural mesothelioma: Surgical roles and novel therapies, Clin Lung Cancer. 3: 102-117, 2001.[0149]3. Ordonez, N. G. The immunohistochemical diagnosis of epithelial mesothelioma, Hum Pathol. 30: 313-323, 1999.[0150]4. Nguyen, G.-K., Akin, M.-R. M., Villanueva, R. R., and Slatnik, J. Cytopathology of malignant mesothelioma of the pleura in fine-needle aspiration biopsy, Diagn Cytopathol. 21: 253-259, 1999.[0151]5. Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., Bloomfield, C. D., and Landers, E. S. Molecular classification of cancer: class discovery and class prediction by gene expressi...

example 2

REFERENCES FOR EXAMPLE 2

[0195]1. Golub, T. R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531-537 (1999).[0196]2. Perou, C. M. et al. Molecular portraits of human breast tumours. Nature 406, 747-752 (2000).[0197]3. Hedenfalk, I. et al. Gene expression profiles in hereditary breast cancer. N Engl J Med 344, 539-548 (2001).[0198]4. Khan, J. et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 7, 673-679 (2001).[0199]5. Quackenbush, J. Computational analysis of microarray data. Nat Rev Genet. 2, 418-427 (2001).[0200]6. Corson, J. M. & Renshaw, A. A. Pathology of mesothelioma in Comprehensive Textbook of Thoracic Oncology (eds Aisner, J., Arriagada, R. Green, M. R., Martini, N. & Perry, M. C.) 757-758 (Williams and Wilkins, Baltimore, Md., 1996).[0201]7. Virtaneva, K. et al. Expression profiling reveals fundamental biological diffe...

example 3

REFERENCES FOR EXAMPLE 3

[0236]1. Pass H. Malignant pleural mesothelioma: Surgical roles and novel therapies. Clin Lung Cancer 2001; 3:102-117.[0237]2. Aisner J. Diagnosis, staging, and natural history of pleural mesothelioma. In: Aisner J, Arriagada R, Green M R, et al, Aisner J, Arriagada R, Green M R, et als. Comprehensive Textbook of Thoracic Oncology. Baltimore (Md.): Williams and Wilkins; 1996.799-785.[0238]3. Ong S-T, Vogelsang N J. Current therapeutic approaches to unresectable (primary and recurrent) disease. In: Aisner J, Arriagada R, Green M R, et al, Aisner J, Arriagada R, Green M R, et als. Comprehensive Textbook of Thoracic Oncology, Baltimore (Md.): Williams and Wilkins; 1996.799-814.[0239]4. Peto J, Hodgson J T, Matthews F E, Jones J R. Continuing increase in mesothelioma mortality in Britain. Lancet 1995; 345:535-539.[0240]5. Sugarbaker D J, Flores R M, Jaklitsch M T, Richards W G, Strauss G M, Corson J M, et al. Resection margins, extrapleural nodal status, and cell...

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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.

Description

RELATED APPLICATIONS[0001]This application claims the benefit under 35 U.S.C. § 119(e) of U.S. provisional application 60 / 317,389, filed Sep. 5, 2001, and U.S. provisional application 60 / ______, filed Aug. 30, 2002, the entire disclosures of which are incorporated herein by reference.GOVERNMENT SUPPORT[0002]This invention was made in part with government support under grant number DK58849 from the National Institutes of Health. The United States government may have certain rights in this invention.FIELD OF THE INVENTION[0003]The invention relates to methods for diagnosing conditions, predicting prognoses and optimizing treatment strategies using ratios of gene expression data. The invention also relates to nucleic acid markers for cancer, particularly for distinguishing malignant pleural mesothelioma from other lung cancers or from normal lung tissue, and for distinguishing between subclasses of malignant pleural mesothelioma.BACKGROUND OF THE INVENTION[0004]Although much progress h...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68G01N33/574
CPCC12Q1/6837G01N33/574C12Q2600/158C12Q1/6886
Inventor GORDON, GAVIN J.JENSEN, RODERICK V.GULLANS, STEVEN R.HSIAO, LI-LIBUENO, RAPHAEL
Owner THE BRIGHAM & WOMEN S HOSPITAL INC
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