Title:
SYSTEMS AND METHODS FOR ANALYZING GENE EXPRESSION DATA FOR CLINICAL DIAGNOSTICS
Document Type and Number:
WIPO Patent Application WO2005084171
Kind Code:
A3
Abstract:
Methods, computer program products and computer systems for constructing a classifier for classifying a specimen into a class are provided. The classifiers are models. Each model includes a plurality of tests. Each test specifies a mathematical relationship (e.g., a ratio) between the characteristics of specific cellular constituents. Each test is polled using characteristic values of these specified cellular constituents from the biological specimen to be classified. In some embodiments, each test has a positive threshold and a negative threshold. When the value of the test exceeds the positive threshold, the test polls positive. When the value of the test is below the negative threshold, the test polls negative. When the value of the test is between the negative threshold and the positive threshold, the test polls indeterminate. The value of each test is combined to provide a composite score. In some embodiments, positive composite score indicate that the specimen belongs in the class associated with the model.
Inventors:
ANDERSON GLENDA G (US)
MORALEDA JORGE (US)
MORALEDA JORGE (US)
Application Number:
PCT/US2004/032007
Publication Date:
September 14, 2006
Filing Date:
September 29, 2004
Export Citation:
Assignee:
PATHWORK INFORMATICS INC (US)
ANDERSON GLENDA G (US)
MORALEDA JORGE (US)
ANDERSON GLENDA G (US)
MORALEDA JORGE (US)
International Classes:
G01N33/48; G16B40/20; C12Q1/68; G06F19/00; G16B20/40; G16B25/10; G16B25/30; G16B40/10
Other References:
VAN 'T VEER L.J. ET AL.: "Gene Expression Profiling Predicts Clinical Outcome of Breast Cancer", NATURE, vol. 415, 2002, pages 530 - 536, XP002297133
TAMAYO P. ET AL.: "Interpreting Patterns of Gene Expression with Self-organizing Maps: Methods and Application to Hematopoietic Differentiation", PROC. NATL. ACAD. SCI. USA, vol. 96, 1999, pages 2907 - 2912, XP002980673
SU A.I. ET AL.: "Molecular Classification of Human Carcinomas by Use of Gene Expression Signatures", CANCER RESEARCH, vol. 61, 2001, pages 7388 - 7393, XP002242441
RICHER J.K. ET AL.: "Differential Gene Regulation by the Two Progesterone Receptor Isoforms in Human Breast Cancer Cells", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 277, 2002, pages 5209 - 5218, XP003000394
RAMASWAMY S. ET AL.: "DNA Microarrays in Clinical Oncology", JOURNAL OF CLINICAL ONCOLOGY, vol. 20, 2002, pages 1932 - 1941, XP003000395
GOLUB T.R. ET AL.: "Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring", SCIENCE, vol. 286, 1999, pages 531 - 537, XP002207658
CLAVERIE J.-M.: "Computational Methods for the Identification of Differential and Coordinated Gene Expression", HUMAN MOLECULAR GENETICS, vol. 8, 1999, pages 1821 - 1832, XP002202819
BEN-DOR A.: "Tissue Classification with Gene Expression Profiles", JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 7, 2000, pages 559 - 583, XP009047442
TAMAYO P. ET AL.: "Interpreting Patterns of Gene Expression with Self-organizing Maps: Methods and Application to Hematopoietic Differentiation", PROC. NATL. ACAD. SCI. USA, vol. 96, 1999, pages 2907 - 2912, XP002980673
SU A.I. ET AL.: "Molecular Classification of Human Carcinomas by Use of Gene Expression Signatures", CANCER RESEARCH, vol. 61, 2001, pages 7388 - 7393, XP002242441
RICHER J.K. ET AL.: "Differential Gene Regulation by the Two Progesterone Receptor Isoforms in Human Breast Cancer Cells", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 277, 2002, pages 5209 - 5218, XP003000394
RAMASWAMY S. ET AL.: "DNA Microarrays in Clinical Oncology", JOURNAL OF CLINICAL ONCOLOGY, vol. 20, 2002, pages 1932 - 1941, XP003000395
GOLUB T.R. ET AL.: "Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring", SCIENCE, vol. 286, 1999, pages 531 - 537, XP002207658
CLAVERIE J.-M.: "Computational Methods for the Identification of Differential and Coordinated Gene Expression", HUMAN MOLECULAR GENETICS, vol. 8, 1999, pages 1821 - 1832, XP002202819
BEN-DOR A.: "Tissue Classification with Gene Expression Profiles", JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 7, 2000, pages 559 - 583, XP009047442
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