Abstract
Abstract Somatic copy number variations (CNVs) are frequently observed in cancer, likely a result high genomic and structural instability characteristic of cancer. CNVs have been shown to be important drivers for many oncogenic pathways and are associated with drug sensitivity and resistance. Therefore, these genetic alterations are valuable candidate biomarkers for patient stratification and predictors for therapeutic responses to targeted therapies. A fundamental challenge for copy number determination in tumor FFPE DNA is that the material is often degraded and modified by fixation, processing and storage. Here we present a PCR-based copy number assay utilizing target specific pre-amplification and a microfluidics detection system. 45 genes were selected based on literature and their potential relevance to therapeutic targets. This high-throughput platform showed excellent specificity and dynamic range from 1 to 100ng input genomic DNA. A panel of matched frozen and FFPE DNAs from cell lines were used for cross -validation with copy number identified by array CGH. A medium-center method is employed to calculate copy number and assess the extent of degradation in sample DNAs. To evaluate clinical utility of the technology, copy number alteration from a collection of matched primary and metastatic breast tumors as well as correlation between copy number changes and gene expression will be reported. We will also report results from a survey of other tumor types, including gastric cancer, mesothelioma, and HER2+ breast cancer. Citation Format: Ling-Yuh Huw, Rajesh Patel, Carol O'Brien, Ling Fu, Rajiv Raja, Lukas Amler, Garret Hampton, Mark Lackner. Development of robust copy number assays for tumor FFPE tissues. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3505. doi:10.1158/1538-7445.AM2013-3505
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