title: iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes.
abstract: Cancer results from the acquisition of somatic driver mutations. Several computational tools can predict driver genes from population-scale genomic data, but tools for analyzing personal cancer genomes are underdeveloped. Here we developed iCAGES, a novel statistical framework that infers driver variants by integrating contributions from coding, non-coding, and structural variants, identifies driver genes by combining genomic information and prior biological knowledge, then generates prioritized drug treatment. Analysis on The Cancer Genome Atlas (TCGA) data showed that iCAGES predicts whether patients respond to drug treatment (P = 0.006 by Fisher's exact test) and long-term survival (P = 0.003 from Cox regression). iCAGES is available at http://icages.wglab.org .
authors.affiliation: Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, 90089, USA.|Biostatistics Graduate Program, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
authors.forename: Chengliang
authors.initials: C
authors.lastname: Dong
authors.affiliation: Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, 90089, USA.|Biostatistics Graduate Program, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, 90089, USA.|Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, 90089, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Yang
authors.affiliation: Department of Computer Science, New York University, New York, NY, 10012, USA.
authors.forename: Zeyu
authors.initials: Z
authors.lastname: He
authors.affiliation: Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.|Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Liu
authors.affiliation: Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, 90089, USA. kw2701@cumc.columbia.edu.|Institute for Genomic Medicine, Columbia University, 630 W. 168th St, Room 11-451, New York, NY, 10032, USA. kw2701@cumc.columbia.edu.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
mesh_terms: D030541:Databases, Genetic; D052138:Genes, Neoplasm; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000628:therapy; D012984:Software
keywords: Cancer genomics; Machine learning; Precision medicine; Precision oncology; TCGA