title: Predicting the recurrence of noncoding regulatory mutations in cancer.
abstract: BACKGROUND
  One of the greatest challenges in cancer genomics is to distinguish driver mutations from passenger mutations. Whereas recurrence is a hallmark of driver mutations, it is difficult to observe recurring noncoding mutations owing to a limited amount of whole-genome sequenced samples. Hence, it is required to develop a method to predict potentially recurrent mutations.
  
  
  RESULTS
  In this work, we developed a random forest classifier that predicts regulatory mutations that may recur based on the features of the mutations repeatedly appearing in a given cohort. With breast cancer as a model, we profiled 35 quantitative features describing genetic and epigenetic signals at the mutation site, transcription factors whose binding motif was disrupted by the mutation, and genes targeted by long-range chromatin interactions. A true set of mutations for machine learning was generated by interrogating publicly available pan-cancer genomes based on our statistical model of mutation recurrence. The performance of our random forest classifier was evaluated by cross validations. The variable importance of each feature in the classification of mutations was investigated. Our statistical recurrence model for the random forest classifier showed an area under the curve (AUC) of ~0.78 in predicting recurrent mutations. Chromatin accessibility at the mutation sites, the distance from the mutations to known cancer risk loci, and the role of the target genes in the regulatory or protein interaction network were among the most important variables.
  
  
  CONCLUSIONS
  Our methods enable to characterize recurrent regulatory mutations using a limited number of whole-genome samples, and based on the characterization, to predict potential driver mutations whose recurrence is not found in the given samples but likely to be observed with additional samples.
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
authors.forename: Woojin
authors.initials: W
authors.lastname: Yang
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
authors.forename: Hyoeun
authors.initials: H
authors.lastname: Bang
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
authors.forename: Kiwon
authors.initials: K
authors.lastname: Jang
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
authors.forename: Min Kyung
authors.initials: MK
authors.lastname: Sung
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea. jungkyoon@kaist.ac.kr.
authors.forename: Jung Kyoon
authors.initials: JK
authors.lastname: Choi
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D002843:Chromatin / Q000235:genetics; D005260:Female; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D015233:Models, Statistical; D009154:Mutation; D014157:Transcription Factors / Q000235:genetics
chemical_list: D002843:Chromatin; D014157:Transcription Factors