CIRCULATING DNA AMPLIFICATION & COLON CA DETECTION

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DESCRIPTION (provided by applicant): This 2-year R21 project will demonstrate that newly developed genome amplification and analysis technologies lead to highly improved sensitivity in detecting circulating nucleic acids of tumor origin in the plasma of patients with cancer. In particular, we have developed a new technology, Restriction and Circularization-Aided Rolling Circle Amplification, RCA-RCA that allows comprehensive whole genome amplification from DNA that has undergone fragmentation (i.e. the method is tolerant to sample degradation). As such, it can amplify fragmented nucleic acids circulating in human plasma, including tumor-derived DNA that is used as a biomarker for early tumor detection and disease monitoring in cancer. In a modified protocol, RCA-RCA can also achieve whole methylome amplification, i.e., it preserves epigenetic changes so that methylation can be studied on a high throughput basis in the amplified material. We aim to demonstrate that whole genome/methylome amplification enables highly improved detection of tumor-derived genetic or epigenetic alterations in blood plasma by providing unlimited material for high- throughput molecular analysis and by allowing high sensitivity and identification of new biomarkers via microarray analysis of plasma-circulating DNA. The proposed study will focus on colon cancer. The premise of this proposal is that, in early colon cancer, tumor DNA is circulating in the plasma but often goes undetected due to limitations in the detection method(s) and the material available. By enabling 'target magnification' and application of high-throughput genome analysis we aim to achieve highly improved sensitivity and reliability in detecting circulating nucleic acids of tumor origin in plasma. Furthermore, the present whole genome amplification enables plasma-DNA archives to be established that enable future retrospective studies to be conducted on the same samples for evaluation of new biomarkers and sharing of material among investigators.