title: Rank-based miRNA signatures for early cancer detection.
abstract: We describe a new signature definition and analysis method to be used as biomarker for early cancer detection. Our new approach is based on the construction of a reference map of transcriptional signatures of both healthy and cancer affected individuals using circulating miRNA from a large number of subjects. Once such a map is available, the diagnosis for a new patient can be performed by observing the relative position on the map of his/her transcriptional signature. To demonstrate its efficacy for this specific application we report the results of the application of our method to published datasets of circulating miRNA, and we quantify its performance compared to current state-of-the-art methods. A number of additional features make this method an ideal candidate for large-scale use, for example, as a mass screening tool for early cancer detection or for at-home diagnostics. Specifically, our method is minimally invasive (because it works well with circulating miRNA), it is robust with respect to lab-to-lab protocol variability and batch effects (it requires that only the relative ranking of expression value of miRNA in a profile be accurate not their absolute values), and it is scalable to a large number of subjects. Finally we discuss the need for HPC capability in a widespread application of our or similar methods.
authors: The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068 Rovereto, Italy.
authors: Mario
authors: 0000-0001-5983-7292
authors: M
authors: Lauria
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics; D003955:Diagnostic Tests, Routine; D055088:Early Detection of Cancer / Q000379:methods*; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D012984:Software; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs