COPE is a framework of Context-Oriented Predictor for variant Effect. To the best of our knowledge, COPE is the first fully functional element-centric variant annotation tool that integrates the entire sequence context to evaluate the functional impact of multiple variants in a context-sensitive approach. Different from current variant-centric approach that assesses the functional consequence of each variant independently, COPE takes each functional element as the basic annotation unit and considers that multiple variants in the same functional element may interfere each other and have different effects in combination than individually (complementary rescue effect). Currently, COPE could be applied to both protein-coding gene and transcription factor binding site.
Cheng SJ, Shi FY, Liu H, Ding Y, Jiang S, Liang N, Gao G. Accurately annotate compound effects of genetic variants using a context-sensitive framework. Nucleic acids research 2017. Full Text
Cheng SJ, Jiang S, Shi FY, Ding Y, Gao G. Systematically identify and annotate multiple-variant compound effect at transcription factor binding sites in human genome. (Under Review)