Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer
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Mendeley | Further Information

{"title"=>"Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer", "type"=>"journal", "authors"=>[{"first_name"=>"Rebecca F.", "last_name"=>"Lowdon", "scopus_author_id"=>"37031488600"}, {"first_name"=>"Ting", "last_name"=>"Wang", "scopus_author_id"=>"7405563383"}], "year"=>2017, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"85016145714", "doi"=>"10.1371/journal.pone.0174032", "pui"=>"614970132", "pmid"=>"28333948", "scopus"=>"2-s2.0-85016145714", "issn"=>"19326203", "isbn"=>"1111111111"}, "id"=>"18c496d9-5976-36a7-9a0d-458b7352167a", "abstract"=>"Evidence that noncoding mutation can result in cancer driver events is mounting. However, it is more difficult to assign molecular biological consequences to noncoding mutations than to coding mutations, and a typical cancer genome contains many more noncoding mutations than protein-coding mutations. Accordingly, parsing functional noncoding mutation signal from noise remains an important challenge. Here we use an empirical approach to identify putatively functional noncoding somatic single nucleotide variants (SNVs) from liver cancer genomes. Annotation of candidate variants by publicly available epigenome datasets finds that 40.5% of SNVs fall in regulatory elements. When assigned to specific regulatory ele-ments, we find that the distribution of regulatory element mutation mirrors that of nonsynon-ymous coding mutation, where few regulatory elements are recurrently mutated in a patient population but many are singly mutated. We find potential gain-of-binding site events among candidate SNVs, suggesting a mechanism of action for these variants. When aggre-gating noncoding somatic mutation in promoters, we find that genes in the ERBB signaling and MAPK signaling pathways are significantly enriched for promoter mutations. Altogether, our results suggest that functional somatic SNVs in cancer are sporadic, but occasionally occur in regulatory elements and may affect phenotype by creating binding sites for tran-scriptional regulators. Accordingly, we propose that noncoding mutation should be formally accounted for when determining gene-and pathway-mutation burden in cancer.", "link"=>"http://www.mendeley.com/research/epigenomic-annotation-noncoding-mutations-identifies-mutated-pathways-primary-liver-cancer", "reader_count"=>20, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>8, "Mathematics"=>1, "Agricultural and Biological Sciences"=>7, "Medicine and Dentistry"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Mathematics"=>{"Mathematics"=>1}}, "group_count"=>2}

Scopus | Further Information

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