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The Pathwork® Tissue of Origin Test is an in vitro diagnostic intended to measure the degree of similarity between the RNA expression patterns in a patient's formalin-fixed, paraffin-embedded (FFPE) tumor and the RNA expression patterns in a database of fifteen tumor types (poorly differentiated, undifferentiated and metastatic cases) that were diagnosed according to then current clinical and pathological practice. This test should be evaluated by a qualified physician in the context of the patient's clinical history and other diagnostic test results. Limitations: The Pathwork Tissue of Origin Test is not intended to establish the origin of tumors (e.g. cancer of unknown primary) that cannot be diagnosed according to current clinical and pathological practice. It is not intended to subclassify or modify the classification of tumors that can be diagnosed by current clinical and pathological practice, nor to predict disease course or survival or treatment efficacy, nor to distinguish primary from metastatic tumor. Tumor types not in the Pathwork Tissue of Origin Test database may have RNA expression patterns that are similar to patterns in the database; therefore, results cannot be used to distinguish tumor types in the database from tumor types not in the database.

The Pathwork® Tissue of Origin Test Kit-FFPE is a test kit consisting of the Pathchip microarray, reagents, software, and labeling. The Pathchip is a custom-designed microarray manufactured by Affymetrix, Inc. (Santa Clara, CA) per Pathwork design requirements and functions in a manner similar to GeneChip HG-U133A. The Pathchip has over 500,000 unique oligonucleotide features (18-micron in size), covering over 18,400 transcript variants (across 22.300 probesets) which in turn represent 14,500 of the best characterized human genes. Each transcript is represented by a probeset, comprised of 11-16 pairs of oligonucleotide probes. The probesets are spatially distributed over the arrav and are used to measure the level of transcription of each sequence represented on the array. For each array, there are 2000 probesets representing 2000 human genes which are used by the Tissue of Origin Test Kit - FFPE algorithm as markers to identify the tissue of origin of the specimen being tested. These probesets were selected using machine learning methods and each set has between 11 and 16 probe pairs of 25 bases whose sequences are matched to mRNA species that are found in human tissue. In addition, the array has 29 probesets that are used for normalization and data verification. The algorithm of the Pathwork® Tissue of Origin Test was developed using a database of 2196 specimens, divided into independent training and test datasets. The test development used a machine learning approach based on marker selection to build a predictive model. The model consists of a list of markers, a set of reference (support) samples and a set of coefficients. These components are combined to produce 15 Similarity Scores, one for each of the possible tissues on the test panel. Each similarity score ranges from 0 to 100, with a higher score being associated with a higher likelihood that the input specimen has a molecular signature of the corresponding tissue of origin. The 15 similarity scores are scaled to sum up to 100. Each is based on the microarray standardized expression (SE) values of selected biomarkers. The process consists of the following steps: - Read SE values for the biomarkers used in the Tissue of Origin Test from 1. the input file. - Compute a decision function ("score") for each of 105 possible pairings of 2. the 15 tissues on the test panel with respect to the sample described by the input SE values. - Convert the 105 pairwise scores into pairwise probabilities. 3. - Reduce the 105 pairwise probabilities to 15 Similarity Scores, one for each 4. Tissue of Origin. These are the final 15 Similarity Scores presented in the Tissue of Origin Test Report.

The Pathwork® Tissue of Origin Test is an in vitro diagnostic intended to measure the degree of similarity between the RNA expression patterns in a patient's formalin-fixed, paraffin-embedded (FFPE) tumor and the RNA expression patterns in a database of fifteen tumor types (poorly differentiated, undifferentiated and metastatic cases) that were diagnosed according to then current clinical and pathological practice. This test should be evaluated by a qualified physician in the context of the patient's clinical history and other diagnostic test results. Limitations: The Pathwork Tissue of Origin Test is not intended to establish the origin of tumors (e.g. cancer of unknown primary) that cannot be diagnosed according to current clinical and pathological practice. It is not intended to subclassify or modify the classification of tumors that can be diagnosed by current clinical and pathological practice, nor to predict disease course or survival or treatment efficacy, nor to distinguish primary from metastatic tumor. Tumor types not in the Pathwork Tissue of Origin Test database may have RNA expression patterns that are similar to patterns in the database; therefore, results cannot be used to distinguish tumor types in the database from tumor types not in the database.

The Pathwork® Tissue of Origin Test Kit-FFPE (Origin Test Kit-FFPE) is a test kit consisting of the Pathchip microarray, reagents, software, Pathwork Specimen Processing Guide and Guide to Report Interpretation (GRI). The Pathchip is a custom-designed microarray that functions in a manner similar to GeneChip HG-U133A. The Pathchip has over 500,000 unique oligonucleotide features covering over 18,400 transcript variants (across 22,300 probesets) which in turn represent 14,500 of the best characterized human genes. For each array, there are 2000 probesets representing 2000 human genes which are used by the Origin Test Kit-FFPE algorithm as markers to identify the tissue of origin of the specimen being tested. These probesets were selected using machine learning methods. The algorithm of the Origin Test Kit-FFPE was developed using a database of 2196 specimens, divided into independent training and test datasets. The test development used a machine learning approach based on marker selection to build a predictive model consists of a list of markers, a set of reference (support) samples and a set of coefficients. These components are combined to produce 15 Similarity Scores, one for each of the possible tissues on the test panel. Each Similarity Score ranges from 0 to 100, with a higher score being associated with a higher likelihood that the input specimen has a molecular signature of the corresponding tissue of origin. The 15 Similarity Scores are scaled to sum up to 100. Each is based on the microarray standardized expression (SE) values of selected biomarkers. The process consists of reading SE values, computing a decision function for pairwise tissue pairings, converting pairwise scores to probabilities, and reducing pairwise probabilities to 15 Similarity Scores. The Pathwork Specimen Processing Guide (SPG) contains instructions for processing tissue specimens. The specimen used is a formalin-fixed, paraffin-embedded (FFPE) specimen containing at least 60% viable tumor. Total RNA is isolated and processed through a two-cycle RNA amplification, hybridization to the Pathchip microarray, washing and scanning, data acquisition, data verification, standardization of signal intensities, determination of similarity to 15 tissues of origin, and generation of a Report. The CEL file from each laboratory is transported to Pathwork Diagnostics for analysis using the Pathwork System Software (PSS). The PSS converts the CEL file to gene expression measurements, performs data verification, normalizes the data, performs statistical tests, and produces a report summarizing the 15 Similarity Scores. The report quantifies the similarity of the RNA expression pattern in a tumor specimen to expression patterns found in tumor specimens from 15 known tissues of origin and is provided back to the laboratory over a secure internet connection in pdf format. Clinical laboratory customers use the report for incorporation into the surgical pathology report delivered to the requesting physician. The report presents the 15 computed Similarity Scores in a graphical format. The ordering physician interprets the report using the Guide to Report Interpretation (GRI).

The Pathwork® Tissue of Origin Test is intended to measure the degree of similarity between the RNA expression pattern in a patient's fresh-frozen tumor and the RNA expression patterns in a database of tumor samples (poorly differentiated, undifferentiated and metastatic cases) that were diagnosed according to then current clinical and pathological practice. The database contains examples of RNA expression patterns for fifteen common malignant tumor types: bladder, breast, colorectal, gastric, hepatocellular, kidney, non-small cell lung, ovarian, pancreatic, prostate, and thyroid carcinomas, melanoma, testicular germ cell tumor, non-Hodgkins lymphoma (not otherwise specified), and soft tissue sarcoma (not otherwise specified). The Pathwork® Tissue of Origin Test result is intended for use in the context of the patient's clinical history and other diagnostic tests evaluated by a qualified clinician. Limitations: The Pathwork Tissue of Origin Test is not intended to establish the origin of tumors that cannot be diagnosed according to current clinical and pathological practice. (e.g. carcinoma of unknown primary). It is not intended to subclassify or modify the classification of tumors that can be diagnosed by current clinical and pathological practice, nor to predict disease course or survival or treatment efficacy, nor to distinguish primary from metastatic tumor. Tumor types not in the Pathwork Tissue of Origin Test database may have RNA expression patterns that are similar to RNA expression patterns in tumor types in the database, leading to indeterminate results or misclassifications,

The Pathwork® Tissue of Origin Test is a microarray and analytics "kit" that quantifies the similarity of tumor specimens to 15 cancer types representing 60 morphologies. Frozen biopsy specimens are processed by the clinical laboratory as described in the User Guide. In brief, mRNA is extracted, amplified, labeled and hybridized to the Pathchip® microarray, which is then scanned using one of the instrument systems validated for use with this test. The resulting data file is transmitted via secure internet transfer protocol to the Pathwork® System Software for data quality control and analysis. Test results are available for clinical interpretation via a secure password protected website. Components included in the kit: Microarray: Pathchip microarrays, packaged in boxes of 5 or 10. Tissue of Origin Test Report produced by the Pathwork System Software (by licensed agreement): The Pathwork® System Software receives data from the scanned Pathchip™ microarray and performs data quality control and analysis. The System Software then generates a Pathwork® Tissue of Origin Test Report which provides a Similarity Score for each of the 15 tissues on the test panel. The test report is accessible for clinical interpretation via a secure password protected website. Tissue of Origin Test Reagents: Reagents for specimen processing and RNA extraction.