November 23, 2018 Journal article Open Access

Kuijjer, Marieke Lydia

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    "description": "<p>This dataset contains gene and pathway mutation scores for 5,805 primary tumors from 23 different cancer types from The Cancer Genome Atlas (TCGA).<br>\n<br>\nGene mutation scores of 2,219 cancer-associated genes were calculated by normalizing the number of non-silent mutations in a gene (obtained from .maf files from TCGA) by the gene&#39;s length. We used SAMBAR (Subtyping Agglomerated Mutations By Annotation Relations) to calculate pathway mutation scores. In short, SAMBAR takes the sum of mutation scores of all genes belonging to a biological pathway and then corrects these scores for the pathway&#39;s gene set size and the number of times a gene is represented in the complete set of pathways. Please see <a href=\"https://www.nature.com/articles/s41416-018-0109-7\">our publication</a> in the <em>British Journal of Cancer</em> for methodological details.</p>\n\n<p>In the RData file &quot;TCGA_SAMBAR.RData&quot;, we share the following objects:</p>\n\n<p>- <strong>gene_scores</strong>: a 2219 by 5805 numeric matrix including gene (rows) mutation scores for each sample (columns).</p>\n\n<p>- <strong>pathway_scores</strong>: a 1066 by 5805 numeric matrix including pathway (rows) mutation scores for each sample (columns).<br>\n<br>\nThe file &quot;sample_tumor_annotation.RData&quot; contains the object:<br>\n<br>\n- <strong>sample_annotation</strong>: a 5805 by 2 character matrix including sample names (first column) and the tumor type the sample belongs to (<a href=\"https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations\">TCGA Study Abbreviations</a>).</p>", 
    "contributors": [
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        "orcid": "0000-0001-8221-7139", 
        "affiliation": "Genentech Inc.", 
        "type": "Researcher", 
        "name": "Paulson, Joseph Nathaniel"
      }, 
      {
        "affiliation": "Bristol-Myers Squibb", 
        "type": "Researcher", 
        "name": "Salzman, Peter"
      }, 
      {
        "affiliation": "University of Massachusetts Boston", 
        "type": "Researcher", 
        "name": "Ding, Wei"
      }, 
      {
        "orcid": "0000-0002-2702-5879", 
        "affiliation": "Harvard TH Chan School of Public Health", 
        "type": "Researcher", 
        "name": "Quackenbush, John"
      }
    ], 
    "title": "Gene and pathway mutation scores for 5,805 primary tumors from TCGA", 
    "license": {
      "id": "CC-BY-3.0"
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    "journal": {
      "volume": "118", 
      "issue": "11", 
      "pages": "1492-1501", 
      "title": "British Journal of Cancer"
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    "references": [
      "Kuijjer, Marieke Lydia, et al. Br J Cancer. 2018 May;118(11):1492-1501"
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    "keywords": [
      "somatic mutations", 
      "mutations", 
      "SAMBAR", 
      "de-sparsification", 
      "cancer", 
      "TCGA", 
      "mutation data", 
      "mutation scores", 
      "pathway mutation scores", 
      "biological pathways", 
      "gene mutation scores", 
      "subtypes", 
      "cancer subtypes", 
      "pan-cancer"
    ], 
    "publication_date": "2018-11-23", 
    "creators": [
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        "orcid": "0000-0001-6280-3130", 
        "affiliation": "Centre for Molecular Medicine Norway, University of Oslo", 
        "name": "Kuijjer, Marieke Lydia"
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    "notes": "This work was funded through a grant from the NVIDIA foundation (grant no. 2014-133322 (3953)). This work was additionally supported by a Postdoctoral Fellowship Program from the Charles A. King Trust Fund, Sara Elizabeth O'Brien Trust, Bank of America, N.A., co-Trustees.", 
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