{"id":"AIBD-0808","title":"FDA found that the Pathwork Tissue of Origin Test, built with machine learning, agreed with the known diagnosis for most of 545 tumor specimens","summary":"In FDA's review of the Pathwork Tissue of Origin Test, results agreed with the available diagnosis for 86.3% of metastatic and 92.0% of primary tumor specimens among 545.","date_observed":"2008-07-30","date_basis":"source publication","date_precision":"day","benefit_status":"intended","source_collection":null,"source_entry":null,"account":"Pathwork Diagnostics developed the Tissue of Origin Test, which compares the RNA expression of a fresh-frozen tumor with a database of 15 tumor types. Its 1550 marker probesets were selected with machine learning, and its model was built on 2039 specimens split into training and test sets. Four processing laboratories ran the test on poorly differentiated, undifferentiated and metastatic tumor specimens. Of 659 specimens processed, 545 met the labeling limits and quality checks. FDA reviewers report that results agreed with the available diagnosis for 86.3% of metastatic and 92.0% of primary specimens. A similarity score of 30 or more marked the right tissue 92.9% of the time. FDA cleared the test on 30 July 2008. Tumors from tissues outside the panel often scored as a panel tissue, including 48 of 49 endometrial cancers. The test is not intended for tumors that current practice cannot diagnose.","category":"aggregate result","unexpected":false,"purpose":"Pathwork Diagnostics built the Tissue of Origin Test to measure how closely a tumor's RNA expression pattern resembles each of 15 common tumor types, for use with other diagnostic tests.","system":"Pathwork Tissue of Origin Test","model_version":null,"developer":"Pathwork Diagnostics, Inc.","deployer":"Pathwork Diagnostics (clinical validation at four processing laboratories)","location":null,"domain":"Healthcare","segment":null,"benefit_type":"Improved Task Accuracy","work_activities":["4.A.1.b.1"],"taxonomy_note":null,"registry_ids":{},"ratings":[{"group":"organizational","depth":null,"reason":"The study measured agreement with available diagnoses on processed specimens, and no change in diagnosis or treatment is reported."}],"ai_role":{"status":"unassessed","statement":"The study compared the test's results with the available diagnosis for each specimen. It did not compare diagnosis with and without the test."},"evidence":[{"kind":"regulatory document","citation":"U.S. Food and Drug Administration, Center for Devices and Radiological Health. 510(k) substantial equivalence determination decision summary for the Pathwork Tissue of Origin Test (K080896). Cleared 2008-07-30.","title":"510(k) Substantial Equivalence Determination Decision Summary, K080896: Pathwork Diagnostics Tissue of Origin Test","url":"https://www.accessdata.fda.gov/cdrh_docs/reviews/K080896.pdf","date":"2008-07-30","written_by":"independent","quote":"Based on the n = 545 results, the probability that a true positive tissue call was obtained when a Similarity Score of ≥ 30 was reported was 92.9%, 95% CI [90.3, 95.0], and the probability that a true negative tissue call was obtained when a Similarity Score of ≤ 5 was reported was 99.7%, 95% CI [99.6, 99.8]."}],"replication":{"produced_by":["RNA from fresh-frozen tumor tissue was hybridized to the Pathchip microarray and scanned.","Laboratories processed specimens as the Pathwork Specimen Processing Guide sets out."],"must_hold":["The tumor can be diagnosed according to current clinical and pathological practice.","A qualified clinician reads the result in the context of the patient's clinical history and other tests."],"echoes":[]},"paired_incident":null,"headline":"*Pathwork Tissue of Origin Test* matched the known origin of most tumors","metric":"86.3% of metastatic and 92.0% of primary tumor specimens","comparator":{"against":"The available diagnosis for each specimen","before":"Available diagnosis (reference)","after":"Agreement for 86.3% of metastatic and 92.0% of primary tumor specimens","basis":"measured","quote":"To assess the accuracy of the results reported by each laboratory, the Physician Guided Conclusions were compared to available diagnosis established for each specimen. Each laboratory was expected to achieve the overall acceptance criteria of at least 80% agreement with the available diagnosis, with no more than 10% non- agreement. As can be seen in the table below, all four laboratories achieved the criteria, with Site 2 as the poorest performer with 87.8% agreement. No laboratory reported more than 5% non-agreement. Table 3 Physician Guided Conclusion (PGC) agreement with available diagnosis Stratification # Specimens % Agreement % Non- % Indeterminate agreement Site 1 48 93.8% (45/48) 2.1% (1/48) 4.2% (2/48) Site 2 49 87.8% (43/49) 4.2% (2/49) 8.2% (4/49) Site 3 48 91.7% (44/48) 2.1% (1/48) 6.3% (3/48) Site 4 47 91.5% (43/47) <0.1% (0/47) 8.55 (4/47) Overall 192 91.2% (175/192) 2.1% (4/192) 6.9% (13/192) b. Linearity/assay reportable range: Linearity is not applicable for this range of assay. c. Traceability, Stability, Expected values (controls, calibrators, or methods): Quality Control Specimen Processing Controls: The following quality control checks are required during specimen processing to assure reliable results: 1) Amount of total RNA extracted from tissue specimens: minimum of 1.0 μg. 6 2) Amount of fragmented, labeled cRNA used for hybridization to Pathchip microarrays: 10 μg. To ensure that a sufficient quantity of high quality labeled cRNA is obtained for hybridization to Pathchip microarrays, it is recommended that: 1) All procedures in the Pathwork Specimen Processing Guide are followed efficiently to reduce RNase degradation. 2) No more than 60 minutes between excision and freezing of the biopsy specimen. 3) A minimum of 100 mg tissue be used as starting material for extraction of total RNA. 4) Biopsy specimen should contain at least 60% tumor and no more than 20% necrosis 5) Absorbance measurements of total RNA give an A260/A280 ratio of at least 1.7. 6) Amount of labeled cRNA used for fragmentation: minimum of 15 μg. Endogenous Pathchip Controls: In addition to these external controls, the Pathwork Tissue of Origin test utilizes endogenous mRNA markers that are found in human tissue specimens and are captured on the Pathchip microarray to perform a series of data verifications that detect laboratory processing anomalies found to unfavorably influence the accuracy of the Pathwork Tissue of Origin test. These data verifications include the detection of regional discontinuities and low overall signal. When a submitted file fails one or more of the data verifications, the system software will return a Tissue of Origin Test Report flagged as follows: \"The gene expression data file submitted failed data verification. This can be caused by a poor quality specimen or an error in laboratory processing. Specifics shown in CAUTION below.” Device stability: The shelf life of Pathchip is one year from the date of manufacture when stored at 2º C to 8ºC. d. Detection limit: Dilution study _ Labeled cRNA: Dilution study was performed to demonstrate that the Tissue of Origin test is robust against reasonable variations in the amount of labeled cRNA used in hybridization. The study used 15 different frozen human tissue (FHT) specimens, three (3) each from breast, colorectal, lung, lymphoma and pancreas tissues of origin. RNA was extracted and processed to the point of labeled cRNA. For each specimen, Pathchip arrays were hybridized with each of the five dilutions (20, 15, 10, 7.5 and 5 μg) of labeled cRNA. Subsequent processing of all 15 specimens x 5 dilutions (= 75 arrays) were performed per the recommended protocol. Four samples from one specimen were excluded because of low data verification values. The data was analyzed using linear regression and correlation analysis to assess equivalence. Based on the data, the Tissue of Origin Test User Guide specifies 10 ± 2 μg cRNA. e. Analytical specificity: Several potential interfering substances in tumor biopsy were evaluated for potential adverse effects. Adipose Tissue: To examine whether the adipose tissue in breast tumors is a 7 potential interferrent and produce adverse effects in the Tissue of Origin test, Physician Guided Conclusion (PGC) from 69 breast-related specimens included in the clinical validation were compared to its available clinical diagnosis. Available clinical diagnosis from Breast-related specimens were in 94.2% agreement with PGC, compared to all specimens which had 87.8% agreement. RNases: To examine whether RNases in pancreas tumors produce adverse effects in Tissue of Origin test, the results from FHT biopsy specimens were stratified to evaluate pancreatic tumors for RNases interference. The clinical validation included 25 pancreas-related specimens. Available clinical diagnoses from pancreas-related specimens were in 72% agreement with PGC, compared to all specimens which had 87.8% agreement. Since there is a lower performance than for all the other specimens, this is cited under Limitations in the user guide. Fibrous material: To examine whether fibrous material in skin-related specimens, produce adverse effects in the Tissue of Origin Test, the results from FHT biopsy specimens used in the clinical validation were stratified to evaluate the effect from melanomas and skin-related biopsies. The clinical validation included 27 skin-related specimens. Available clinical diagnoses from skin-related specimens were in 81.5% agreement with PGC, compared to all specimens which had 87.8% agreement. Tissue of Origin Test does not demonstrate apparent adverse effects with this interfering substance. Necrotic tissue: To examine whether necrotic tissue produce adverse effects in use of the Tissue of Origin Test, the results from the FHT biopsy specimens used in the clinical validation study were stratified by percent necrosis. Based on the % agreement, a cut-off of 20% necrosis or less is recommended as a quality control measure for biopsy specimen inclusion criteria for this test. f. Assay cut-off: Guide to Report Interpretation: The Similarity Score (SS) is a measure of the similarity of the RNA expression pattern of the specimen to the RNA expression pattern of the indicated tissue. Similarity Scores range from 0 (very low similarity) to 100 (very high similarity) and sum to 100 across all 15 tissues on the panel. SS ≥ 30: A single SS greater than or equal to 30 indicates the likely tissue of origin. If two or three SS’s are greater than or equal to 30, then one of those results indicates the likely tissue of origin. 5 < SS < 30: If every SS is between 5 and 30, then the test result is indeterminate and no tissue of origin is indicated. SS ≤ 5: An SS less than or equal to 5 rules out that tissue type as the likely tissue of origin. 2. Comparison studies: a. Method comparison with available diagnosis: The clinical validation involved a total of four different processing sites. The study included 25 to 69 samples per tissue on the panel, with an average of 36 specimens 8 per tissue. The specimens included poorly differentiated, undifferentiated and metastatic tumor specimens. Of the total 659 tumor specimens processed in this study, 545 specimens met the labeling limitations for tumor grade and available diagnosis and passed the data verification quality tests. To assess the accuracy of the results reported by each laboratory, the Physician Guided Conclusions were compared to available diagnosis established for each specimen. Based","url":"https://www.accessdata.fda.gov/cdrh_docs/reviews/K080896.pdf"},"later":null,"value":null,"developer_country":"United States","deployer_country":"United States","unrated_because":"The test was run on processed specimens and guided no care, so no realized outcome is reported for any group.","brief_notes":null,"brief":null,"revisions":[{"date":"2026-10-31","change":"Added the record from the finding of the U.S. Food and Drug Administration.","source":"https://www.accessdata.fda.gov/cdrh_docs/reviews/K080896.pdf","editor":"AIBD"}],"confidence":"found","shade":"high","claim_status":"Found by a regulator","claim_basis":"Sources: one independent regulatory document. 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