title: Chromatin structure-based prediction of recurrent noncoding mutations in cancer.
abstract: Recurrence is a hallmark of cancer-driving mutations. Recurrent mutations can arise at the same site or affect the same gene at different sites. Here we identified a set of mutations arising in individual samples and altering different cis-regulatory elements that converge on a common gene via chromatin interactions. The mutations and genes identified in this fashion showed strong relevance to cancer, in contrast to noncoding mutations with site-specific recurrence only. We developed a prediction method that identifies potentially recurrent mutations on the basis of the features shared by mutations whose recurrence is observed in a given cohort. Our method was capable of accurately predicting recurrent mutations at the level of target genes but not mutations recurring at the same site. We experimentally validated predicted mutations in distal regulatory regions of the TERT gene. In conclusion, we propose a novel approach to discovering potential cancer-driving mutations in noncoding regions.
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
authors.forename: Kwoneel
authors.initials: K
authors.lastname: Kim
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: Woojin
authors.initials: W
authors.lastname: Yang
authors.affiliation: Specific Organs Cancer Branch, Research Institute, National Cancer Center, Gyeonggi, Republic of Korea.
authors.forename: Eun-Young
authors.initials: EY
authors.lastname: Choi
authors.affiliation: Specific Organs Cancer Branch, Research Institute, National Cancer Center, Gyeonggi, Republic of Korea.
authors.forename: Seong-Min
authors.initials: SM
authors.lastname: Park
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.|Specific Organs Cancer Branch, Research Institute, National Cancer Center, Gyeonggi, Republic of Korea.
authors.forename: Mingyun
authors.initials: M
authors.lastname: Bae
authors.affiliation: Specific Organs Cancer Branch, Research Institute, National Cancer Center, Gyeonggi, Republic of Korea.
authors.forename: Youn-Jae
authors.initials: YJ
authors.lastname: Kim
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
authors.forename: Jung Kyoon
authors.initials: JK
authors.lastname: Choi
mesh_terms: D002843:Chromatin / Q000737:chemistry; D015331:Cohort Studies; D004252:DNA Mutational Analysis / Q000379:methods*; D004273:DNA, Neoplasm; D004742:Enhancer Elements, Genetic; D005820:Genetic Testing / Q000379:methods; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid
chemical_list: D002843:Chromatin; D004273:DNA, Neoplasm