Prospective study of a 10-gene molecular assay to predict tissue of origin in patients with carcinoma of unknown primary (CUP)

21096 Background: Carcinoma of unknown primary (CUP) where metastatic disease presents without an identifiable primary represents ∼ 3–5% of all cancers. Identifying the origin of the primary tumor in CUP pts can facilitate rational choice of therapeutic regimens. Veridex developed an optimized set of 10 gene markers for a quantitative reverse transcriptase polymerase chain reaction (qRTPCR) assay, and demonstrated high accuracy in predicting the tissue of origin with formalin-fixed, paraffin-embedded (FFPE) metastatic carcinoma samples (J Mol Diagn 2006, 8: 320–9). In this study, the 10-gene assay was prospectively evaluated in CUP pts. Methods: We collected FFPE biopsy tissue specimens from consenting CUP pts at MD Anderson. Eligibile pts met our definition for CUP with adenocarcinoma or poorly differentiated carcinoma. Samples were obtained prior to treatment. 51 pts have been enrolled so far and 11 were ineligible [insufficient samples].Of the 40 pts, qRTPCR assay has been performed on 33 pts. Data on 27/33 is available. A statistical model was used to determine the probability that the metastatic carcinoma tissue assayed originated from 1 of the following 7 categories: lung, pancreas, colon, breast, prostate, ovarian, and other. Subsequently, prediction of the primary by qRTPCR was independently compared with metastatic pattern spread, tumor pathological features, and results of clinical and pathology diagnostic workups. Results: Assay results on 27 prospectively collected CUP patient biopsy specimens are available. In total, CUP tissue of origin prediction by the assay correlated with clinical and pathological assessment in 21 out of 27 evaluated pts (78 %). The most common cancer type predicted by the assay was colon cancer, which correlated with predominantly intra-abdominal metastatic spread in this pt cohort. Conclusions: This prospective study demonstrated the feasibility of conducting gene analysis to predict metastatic carcinoma tissue of origin in FFPE tissue specimens derived from CUP patients. Overall distribution of various primary cancer types as predicted by the assay was consistent with the historical distribution reported for CUP. Assay prediction was concordant with clinical and pathological assessment in 78 % CUP pts. No significant financial relationships to disclose.

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A quantitative reverse transcriptase polymerase chain reaction assay to identify metastatic carcinoma tissue of origin

Journal of Clinical Oncology ◽

10.1200/jco.2006.24.18_suppl.20024 ◽

2006 ◽

Vol 24 (18_suppl) ◽

pp. 20024-20024

Author(s):

D. Talantov ◽

J. Baden ◽

T. Jatkoe ◽

J. Yu ◽

D. Atkins ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Reverse Transcriptase ◽

Primary Tumor ◽

Metastatic Carcinoma ◽

Unknown Primary ◽

Chain Reaction ◽

Gene Markers ◽

Carcinoma Of Unknown Primary ◽

Polymerase Chain ◽

Tissue Of Origin

20024 Background: Carcinoma of unknown primary (CUP) wherein metastatic disease presents without an identifiable primary tumor site represents approximately 3–5% of all cancers. Identifying the origin of the primary tumor in patients with CUP can enable rational choice of therapeutic regimens. We developed an optimized set of ten gene markers for a quantitative reverse transcriptase polymerase chain reaction (qRTPCR) assay, and demonstrated high accuracy in predicting the tissue of origin when used on with formalin-fixed, paraffin-embedded (FFPE) metastatic carcinoma samples. Methods: Twenty-three putative tissue-specific markers for lung, colon, pancreas, breast, prostate and ovarian carcinomas were nominated by querying a gene expression profile database and by performing a literature search. Ten of these marker candidates were then selected based on validation by qRTPCR on 205 FFPE metastatic carcinomas of known tissue origin. Next, we optimized the RNA isolation and qRTPCR methods for these ten markers, and tested the qRTPCR assay on two sets of FFPE metastatic tumors. Results: We applied the 10-gene qRTPCR assay to a set of 260 metastatic tumors of known origin, generating an overall accuracy of 78%. Furthermore we tested an independent set of 48 metastatic samples, including thirty-seven samples where either the tissue of origin was known or which initially presented as CUP but were subsequently resolved. In these 48 samples, our assay demonstrated an accuracy of 76%. Conclusions: Our results suggested that optimized ten-gene markers qRTPCR assay reliably predicts tissue of origin of metastatic carcinomas in FFPE tissues. Such assay can significantly improve the rate of tissue of origin identification for carcinoma of unknown primary. [Table: see text]

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Estimation of expected survival time using gene expression profiling for tumor site origin.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.10584 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. 10584-10584

Author(s):

William David Henner ◽

J. Scott Nystrom ◽

John D. Hainsworth ◽

Gauri R. Varadhachary ◽

Frank A. Greco ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Patient Survival ◽

Unknown Primary ◽

Cancer Type ◽

Carcinoma Of Unknown Primary ◽

Tissue Of Origin ◽

The Relationship ◽

Similarity Scores

10584 Background: Expected survival is an important factor in treatment selection and patient decision making. Gene expression profiling for tissue of origin (GEP TOO) can be used to classify metastatic and poorly-differentiated tumors according to the most likely primary site for difficult-to-diagnose tumors. The Pathwork Tissue of Origin Test, (Redwood City, CA) generates Similarity Scores (SS), one for each of the 15 tissues on the Tissue of Origin Test Panel and sum to 100. The highest SS has been validated as the most likely tissue of origin in a large validation study (Pillai et al. 2010). This abstract reports the relationship between the highest SS for a sample and patient survival. Methods: Two cohorts were analyzed in IRB-approved studies. Cohort 1 consisted of 45 patients with carcinoma of unknown primary treated empirically with therapy for carcinoma of unknown primary with known outcome data including survival. Cohort 2 consisted of 107 patients receiving the TOO test in routine clinical practice and included in a decision impact registry study. The relationship between the highest SS generated by the TOO test was examined using parametric (Gamma) and non-parametric (Cox Proportional Hazards) regression models with covariates of age, gender and median survival of the cancer type indicated. Logrank tests were performed to compare survival in patients with SS above or below 50 in each cohort. Results: The highest SS generated by the TOO Test was strongly and positively correlated with patient survival in both Cohort 1 (p = 0.0093, Cox PH) and in Cohort 2 (p=0.0045, Gamma). In Cohort 1, survival for patients with a SS < 50 was 5.9 mos and for patients with a SS ≥ 50 was 9.7 mos (p=0.03, logrank). In Cohort 2, survival for patients with a SS < 50 was 10.6 mos and 22.6 mos for patients with a SS ≥ 50 (p=0.0073, logrank). Conclusions: The Similarity Scores generated by GEP TOO Test have been validated as an aid to diagnosis for difficult-to-diagnose malignancies. Two independent studies of this GEP TOO Test demonstrated a strong positive relationship between the highest SS and survival. This has the potential to expand the clinical utility of this test beyond diagnosis to include prognosis. Further studies to examine this question are underway.

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