Codon-level co-occurrences of germline variants and somatic mutations in cancer are rare but often lead to incorrect variant annotation and underestimated impact prediction
Publication Date
March 28, 2017
Authors
Amanda Koire, Young Won Kim, Jarey Wang, Panagiotis Katsonis, et al
Volume
12
Issue
3
Pages
e0174766
DOI
https://dx.plos.org/10.1371/journal.pone.0174766
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0174766
Scopus
85016242610
Mendeley
http://www.mendeley.com/research/codonlevel-cooccurrences-germline-variants-somatic-mutations-cancer-rare-often-lead-incorrect-varian
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Mendeley | Further Information

{"title"=>"Codon-level co-occurrences of germline variants and somatic mutations in cancer are rare but often lead to incorrect variant annotation and underestimated impact prediction", "type"=>"journal", "authors"=>[{"first_name"=>"Amanda", "last_name"=>"Koire", "scopus_author_id"=>"42461625300"}, {"first_name"=>"Young Won", "last_name"=>"Kim", "scopus_author_id"=>"57193745072"}, {"first_name"=>"Jarey", "last_name"=>"Wang", "scopus_author_id"=>"57193746932"}, {"first_name"=>"Panagiotis", "last_name"=>"Katsonis", "scopus_author_id"=>"14029906400"}, {"first_name"=>"Haijing", "last_name"=>"Jin", "scopus_author_id"=>"57193719136"}, {"first_name"=>"Olivier", "last_name"=>"Lichtarge", "scopus_author_id"=>"7003903180"}], "year"=>2017, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"85016242610", "doi"=>"10.1371/journal.pone.0174766", "isbn"=>"1111111111", "pmid"=>"28350864", "issn"=>"19326203", "scopus"=>"2-s2.0-85016242610", "pui"=>"615010216"}, "id"=>"56667d43-a35b-3370-9ff3-77755b1cc0e6", "abstract"=>"Cancer cells explore a broad mutational landscape, bringing the possibility that tumor-specific somatic mutations could fall in the same codons as germline SNVs and leverage their presence to produce substitutions with a larger impact on protein function. While multiple, temporally consecutive mutations to the same codon have in the past been detected in the germline, this phenomenon has not yet been explored in the context of germline-somatic variant co-occurrences during cancer development. We examined germline context at somatic mutation sites for 1395 patients across four cancer cohorts (breast, skin, colon, and head and neck) and found 392 codon-level co-occurrences between germline and somatic variants, including over a dozen in well-known cancer genes. We found that for the majority of these co-occurrence events, traditional somatic calling led to an inaccurate representation of the protein site and a significantly lower predicted impact on protein fitness. We conclude that these events often lead to imprecise annotation of somatic variants but do not appear to be a frequent source of driver events during cancer development.", "link"=>"http://www.mendeley.com/research/codonlevel-cooccurrences-germline-variants-somatic-mutations-cancer-rare-often-lead-incorrect-varian", "reader_count"=>8, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Master"=>1, "Other"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Master"=>1, "Other"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>2, "Medicine and Dentistry"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Mathematics"=>{"Mathematics"=>1}}, "group_count"=>0}

Scopus | Further Information

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