Personalized Oncogenomics: Clinical Experience with Malignant Peritoneal Mesothelioma Using Whole Genome Sequencing
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{"title"=>"Personalized oncogenomics: Clinical experience with malignant peritoneal mesothelioma using whole genome sequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Brandon S.", "last_name"=>"Sheffield", "scopus_author_id"=>"55096571400"}, {"first_name"=>"Anna V.", "last_name"=>"Tinker", "scopus_author_id"=>"7005427030"}, {"first_name"=>"Yaoqing", "last_name"=>"Shen", "scopus_author_id"=>"56015655700"}, {"first_name"=>"Harry", "last_name"=>"Hwang", "scopus_author_id"=>"36901597300"}, {"first_name"=>"Hector H.", "last_name"=>"Li-Chang", "scopus_author_id"=>"36545220100"}, {"first_name"=>"Erin", "last_name"=>"Pleasance", "scopus_author_id"=>"7801404201"}, {"first_name"=>"Carolyn", "last_name"=>"Ch'ng", "scopus_author_id"=>"55624460300"}, {"first_name"=>"Amy", "last_name"=>"Lum", "scopus_author_id"=>"56189521400"}, {"first_name"=>"Julie", "last_name"=>"Lorette", "scopus_author_id"=>"53984625300"}, {"first_name"=>"Yarrow J.", "last_name"=>"McConnell", "scopus_author_id"=>"25635890600"}, {"first_name"=>"Sophie", "last_name"=>"Sun", "scopus_author_id"=>"55650922600"}, {"first_name"=>"Steven J.M.", "last_name"=>"Jones", "scopus_author_id"=>"55732380600"}, {"first_name"=>"Allen M.", "last_name"=>"Gown", "scopus_author_id"=>"35425365400"}, {"first_name"=>"David G.", "last_name"=>"Huntsman", "scopus_author_id"=>"7003437964"}, {"first_name"=>"David F.", "last_name"=>"Schaeffer", "scopus_author_id"=>"56533353400"}, {"first_name"=>"Andrew", "last_name"=>"Churg", "scopus_author_id"=>"7102088472"}, {"first_name"=>"Stephen", "last_name"=>"Yip", "scopus_author_id"=>"7102134322"}, {"first_name"=>"Janessa", "last_name"=>"Laskin", "scopus_author_id"=>"7102409848"}, {"first_name"=>"Marco A.", "last_name"=>"Marra", "scopus_author_id"=>"55553154800"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84925833824", "sgr"=>"84925833824", "pui"=>"603282152", "isbn"=>"1932-6203", "pmid"=>"25798586", "doi"=>"10.1371/journal.pone.0119689"}, "id"=>"97c65a48-ff7c-36f2-b23d-23e91c718fd0", "abstract"=>"Peritoneal mesothelioma is a rare and sometimes lethal malignancy that presents a clinical challenge for both diagnosis and management. Recent studies have led to a better understanding of the molecular biology of peritoneal mesothelioma. Translation of the emerging data into better treatments and outcome is needed. From two patients with peritoneal mesothelioma, we derived whole genome sequences, RNA expression profiles, and targeted deep sequencing data. Molecular data were made available for translation into a clinical treatment plan. Treatment responses and outcomes were later examined in the context of molecular findings. Molecular studies presented here provide the first reported whole genome sequences of peritoneal mesothelioma. Mutations in known mesothelioma-related genes NF2, CDKN2A, LATS2, amongst others, were identified. Activation of MET-related signaling pathways was demonstrated in both cases. A hypermutated phenotype was observed in one case (434 vs. 18 single nucleotide variants) and was associated with a favourable outcome despite sarcomatoid histology and multifocal disease. This study represents the first report of whole genome analyses of peritoneal mesothelioma, a key step in the understanding and treatment of this disease.", "link"=>"http://www.mendeley.com/research/personalized-oncogenomics-clinical-experience-malignant-peritoneal-mesothelioma-using-whole-genome-s-5", "reader_count"=>24, "reader_count_by_academic_status"=>{"Librarian"=>1, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Other"=>4, "Student > Master"=>4, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Librarian"=>1, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Other"=>4, "Student > Master"=>4, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>12, "Medicine and Dentistry"=>5, "Arts and Humanities"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United Kingdom"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1981733"], "description"=>"<p>Circos Plots for patients 1 (A) and 2 (B). Copy number gains shown in red, copy number losses shown in green (height of bars is proportional to the number of copies gained or lost). Purple lines indicate interchromosomal translocations. Orange lines indicate intrachromosomal translocation.</p>", "links"=>[], "tags"=>["CDKN", "Whole Genome Sequencing Peritoneal mesothelioma", "molecular", "data", "nf", "understanding", "genome sequences", "translation", "Malignant Peritoneal Mesothelioma", "lats", "2a", "RNA expression profiles", "outcome"], "article_id"=>1350416, "categories"=>["Biological Sciences"], "users"=>["Brandon S. Sheffield", "Anna V. Tinker", "Yaoqing Shen", "Harry Hwang", "Hector H. Li-Chang", "Erin Pleasance", "Carolyn Ch’ng", "Amy Lum", "Julie Lorette", "Yarrow J. McConnell", "Sophie Sun", "Steven J. M. Jones", "Allen M. Gown", "David G. Huntsman", "David F. Schaeffer", "Andrew Churg", "Stephen Yip", "Janessa Laskin", "Marco A. Marra"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0119689.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Patient_1_and_2_large_scale_genomic_alterations_/1350416", "title"=>"Patient 1 and 2 large-scale genomic alterations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 04:21:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1981727"], "description"=>"<p>(A)Axial CT scan showing peritoneal-based pelvic mass. (B) Abdominal fluid aspiration biopsy showing papillary mesothelial proliferation (H&E stain on cell block preparation, 40X magnification). (C) Omental disease sampled at cytoreductive surgery showing malignant mesothelial cells forming gland-like structures, papillae, with spindle cell formation and sarcomatoid features. No treatment effect is appreciable (H&E 40X).</p>", "links"=>[], "tags"=>["CDKN", "Whole Genome Sequencing Peritoneal mesothelioma", "molecular", "data", "nf", "understanding", "genome sequences", "translation", "Malignant Peritoneal Mesothelioma", "lats", "2a", "RNA expression profiles", "outcome"], "article_id"=>1350411, "categories"=>["Biological Sciences"], "users"=>["Brandon S. Sheffield", "Anna V. Tinker", "Yaoqing Shen", "Harry Hwang", "Hector H. Li-Chang", "Erin Pleasance", "Carolyn Ch’ng", "Amy Lum", "Julie Lorette", "Yarrow J. McConnell", "Sophie Sun", "Steven J. M. Jones", "Allen M. Gown", "David G. Huntsman", "David F. Schaeffer", "Andrew Churg", "Stephen Yip", "Janessa Laskin", "Marco A. Marra"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0119689.g001", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Patient_1_pertinent_radiology_and_pathology_/1350411", "title"=>"Patient 1 pertinent radiology and pathology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 04:21:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1981742", "https://ndownloader.figshare.com/files/1981743", "https://ndownloader.figshare.com/files/1981744", "https://ndownloader.figshare.com/files/1981745", "https://ndownloader.figshare.com/files/1981746"], "description"=>"<div><p>Peritoneal mesothelioma is a rare and sometimes lethal malignancy that presents a clinical challenge for both diagnosis and management. Recent studies have led to a better understanding of the molecular biology of peritoneal mesothelioma. Translation of the emerging data into better treatments and outcome is needed. From two patients with peritoneal mesothelioma, we derived whole genome sequences, RNA expression profiles, and targeted deep sequencing data. Molecular data were made available for translation into a clinical treatment plan. Treatment responses and outcomes were later examined in the context of molecular findings. Molecular studies presented here provide the first reported whole genome sequences of peritoneal mesothelioma. Mutations in known mesothelioma-related genes <i>NF2</i>, <i>CDKN2A</i>, <i>LATS2</i>, amongst others, were identified. Activation of <i>MET</i>-related signaling pathways was demonstrated in both cases. A hypermutated phenotype was observed in one case (434 vs. 18 single nucleotide variants) and was associated with a favourable outcome despite sarcomatoid histology and multifocal disease. This study represents the first report of whole genome analyses of peritoneal mesothelioma, a key step in the understanding and treatment of this disease.</p></div>", "links"=>[], "tags"=>["CDKN", "Whole Genome Sequencing Peritoneal mesothelioma", "molecular", "data", "nf", "understanding", "genome sequences", "translation", "Malignant Peritoneal Mesothelioma", "lats", "2a", "RNA expression profiles", "outcome"], "article_id"=>1350425, "categories"=>["Biological Sciences"], "users"=>["Brandon S. Sheffield", "Anna V. Tinker", "Yaoqing Shen", "Harry Hwang", "Hector H. Li-Chang", "Erin Pleasance", "Carolyn Ch’ng", "Amy Lum", "Julie Lorette", "Yarrow J. McConnell", "Sophie Sun", "Steven J. M. Jones", "Allen M. Gown", "David G. Huntsman", "David F. Schaeffer", "Andrew Churg", "Stephen Yip", "Janessa Laskin", "Marco A. Marra"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0119689.s001", "https://dx.doi.org/10.1371/journal.pone.0119689.s002", "https://dx.doi.org/10.1371/journal.pone.0119689.s003", "https://dx.doi.org/10.1371/journal.pone.0119689.s004", "https://dx.doi.org/10.1371/journal.pone.0119689.s005"], "stats"=>{"downloads"=>12, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Personalized_Oncogenomics_Clinical_Experience_with_Malignant_Peritoneal_Mesothelioma_Using_Whole_Genome_Sequencing_/1350425", "title"=>"Personalized Oncogenomics: Clinical Experience with Malignant Peritoneal Mesothelioma Using Whole Genome Sequencing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-03-23 04:21:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1981735"], "description"=>"<p><i>NF2</i> loss-of-function mutations were common to both patients, as well as mutations in <i>CNTNAP3B</i> (shown in bold). For a complete list of SNVs see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119689#pone.0119689.s003\" target=\"_blank\">S1 File</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119689#pone.0119689.s004\" target=\"_blank\">S2 File</a>.</p><p>Select SNVs from patients 1 and 2.</p>", "links"=>[], "tags"=>["CDKN", "Whole Genome Sequencing Peritoneal mesothelioma", "molecular", "data", "nf", "understanding", "genome sequences", "translation", "Malignant Peritoneal Mesothelioma", "lats", "2a", "RNA expression profiles", "outcome"], "article_id"=>1350418, "categories"=>["Biological Sciences"], "users"=>["Brandon S. Sheffield", "Anna V. Tinker", "Yaoqing Shen", "Harry Hwang", "Hector H. Li-Chang", "Erin Pleasance", "Carolyn Ch’ng", "Amy Lum", "Julie Lorette", "Yarrow J. McConnell", "Sophie Sun", "Steven J. M. Jones", "Allen M. Gown", "David G. Huntsman", "David F. Schaeffer", "Andrew Churg", "Stephen Yip", "Janessa Laskin", "Marco A. Marra"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0119689.t001", "stats"=>{"downloads"=>18, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Select_SNVs_from_patients_1_and_2_/1350418", "title"=>"Select SNVs from patients 1 and 2.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-23 04:21:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1981732"], "description"=>"<p>(A)Vaginal mass biopsy showing malignant mesothelial cells with sarcomatoid features (H&E 20X). (B) CT/PET scan showing uptake in vaginal mass. (C) CT/PET showing additional uptake in the cecum. (D) Surgical specimen from the cecum showing epithelioid mesothelial proliferation with heavy lymphoplasmacytic infiltrate (H&E 20X). (E) Post-treatment CT/PET showing resolution of the vaginal mass (as compared to B). (F) Post-treatment CT/PET showing persistence of the cecal mass (compared with C). Imaging of associated inguinal lymphadenopathy not shown.</p>", "links"=>[], "tags"=>["CDKN", "Whole Genome Sequencing Peritoneal mesothelioma", "molecular", "data", "nf", "understanding", "genome sequences", "translation", "Malignant Peritoneal Mesothelioma", "lats", "2a", "RNA expression profiles", "outcome"], "article_id"=>1350415, "categories"=>["Biological Sciences"], "users"=>["Brandon S. Sheffield", "Anna V. Tinker", "Yaoqing Shen", "Harry Hwang", "Hector H. Li-Chang", "Erin Pleasance", "Carolyn Ch’ng", "Amy Lum", "Julie Lorette", "Yarrow J. McConnell", "Sophie Sun", "Steven J. M. Jones", "Allen M. Gown", "David G. Huntsman", "David F. Schaeffer", "Andrew Churg", "Stephen Yip", "Janessa Laskin", "Marco A. Marra"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0119689.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Patient_2_pertinent_radiology_and_pathology_/1350415", "title"=>"Patient 2 pertinent radiology and pathology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 04:21:44"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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