Abstract 1148: Development and validation of a second generation microRNA-based assay for diagnosing tumor tissue origin

Background: Cancer of unknown primary (CUP) constitutes 3%-5% of all newly diagnosed cancer cases. It presents a major diagnostic challenge due to the therapeutic implications of the tissue origin of the cancer. MicroRNAs are a family of non-coding, regulatory RNA genes that are involved in development, differentiation and cell cycle and were shown to be involved in oncogenesis. MicroRNAs are highly tissue-specific and therefore ideal candidates for CUP diagnosis. We have previously presented a biologically-motivated classification assay to identify the tissue of origin using a set of 48 microRNAs measured on a qRT-PCR platform. This assay can differentiate 25 different tumor types from 17 origins. We present here the development and validation of a second generation assay that can identify 42 different tumor types using a custom array platform. Methods: Over 1200 primary and metastatic tumor FFPE samples were used for the training and development of the assay. High-quality RNA, including the well-preserved microRNA fraction, was extracted from the FFPE blocks using proprietary protocols. Expression levels of all known and additional Rosetta's proprietary microRNAs were profiled using a custom array platform. A combination of a decision tree classifier with a KNN classifier was developed to identify the tissue of origin based on the microRNA expression patterns. A validation set of more than 500 independent FFPE samples of primary tumors and metastases was analyzed blindly and classified using the developed assay. Results: The assay is able to identify 42 tumor types based on the expression of only several dozens microRNAs with very high accuracy. Based on the validation set, the sensitivity (positive agreement) for identifying the tumor origin is 85%. In more than 80% of the cases, a single answer was reported, and for these cases, the sensitivity is 90%. Conclusions: Previous studies have highlighted the tissue-specificity of microRNA expression, and have demonstrated their potential use for classification of human malignancies. An assay utilizing microRNA expression in paraffin-embedded tissue for identification of the tissue of origin was previously developed. Here we present the development and the performance of a second generation assay, designed to identify 42 tumor types. This assay will provide an important new tool for diagnosing tumor tissue origin. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1148. doi:10.1158/1538-7445.AM2011-1148