SEMINAR 2008

Jan 18 (Fri) 2008, 11AM- BS 303

Microarray-Based Method for the Diagnosis of Cancers of Unknown Primary: Hello Computer! Goodbye Microscope?

Dr. Torik Ayoubi, Head Transcriptomics Unit, Genome Center Maastricht Assistant Professor, Division of Genetics & Cell Biology Maastricht University, The Netherlands

Abstract:

Cancer of Unknown Primary site (CUP) is one of the 10 most frequent cancer diagnoses worldwide, and constitutes 3–4% of all human malignancies. Patients with CUP present themselves at the clinic with metastatic disease for which the primary tumor site remains unknown even after extensive attempts to determine the site of tumor origin. Effective treatment of cancer, however, fundamentally depends on the primary anatomical site of the tumor and, therefore, determination of cancer subtype is important for optimal cancer management and therapy. Current diagnostic standards rely largely on morphological and immunocytochemical analysis.

With the completion of the human genome project, molecular pathology has dramatically increased its arsenal of novel molecular markers that can be used to determine the phenotype of human tumors. Gene expression profiling using high-density microarray technology is an extremely powerful tool enabling the comprehensive analysis of every transcript expressed in a cell or tumor simultaneously. It is, therefore, very useful for the identification of expression patterns characteristic for a particular tissue or physiological condition.

We have developed a multi-class tumor classifier using publicly available Affymetrix 133 Plus 2.0 microarray data of primary and metastatic tumors. After sequential rounds of training and validation involving multiple independent data sets and over a thousand primary and metastatic tumors the classifier achieved a robust accuracy higher than 80%. The tumors types that are recognized include: lung (squamous, adenoma or endocrine), breast (estrogen receptor positive /negative or ERBB2 receptor positive / negative), ovary, endometrium, cervix, prostate, liver, pancreas, colon/rectum, stomach, kidney, bladder, adrenal, sarcoma, (GIST, leiomyoma, liposarcoma), skin (melanoma, squamous), lymphoma (B cell, T cell), and Central Nervous System tumors. We are still in the process to increase the capability of the classifier to recognize additional tumor subtypes.

Contact for more details: rnarayan@fau.edu, URL: http://www.science.fau.edu/fbrcf/