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Merge pull request #241 from zhx828/hotfix
Update the news
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‎app/index.html

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<a href="#/terms" class="">Usage Terms</a>
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<a href="mailto:[email protected]" target="_top">Contact us</a>
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<a href="https://twitter.com/OncoKB" target="_blank">Twitter</a>
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<a href="#/dataAccess">API</a>
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<a href="api/v1/swagger-ui.html">API</a>
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</div>
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<p style="margin-top: -30px"><a href="#/news" class="">Last update: {{data.lastUpdate}}</a></p>
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</div>
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</a>
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</div>
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<div class="col-md-4 col-lg-4 col-sm-12 col-xs-12 mskcc">
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<span>© 2018 Memorial Sloan Kettering Cancer Center</span>
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<span>© 2019 Memorial Sloan Kettering Cancer Center</span>
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</div>
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</div>
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</div>

‎app/scripts/app.js

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@@ -145,8 +145,8 @@ angular.module('oncokbStaticApp').run(
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}, {content: '3855 Variants'}, {content: '60 Tumor Types'}]
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};
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$rootScope.data = {
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lastUpdate: 'December 14, 2018',
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version: '1.18',
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lastUpdate: 'January 24, 2019',
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version: '1.19',
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levelColors: {
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'1': '#33A02C',
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'2A': '#1F78B4',
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},
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citationURL: 'When using OncoKB, please cite: ' +
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'<a href="http://ascopubs.org/doi/full/10.1200/PO.17.00011" ' +
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'target="_blank">Chakravarty et al., JCO PO 2017</a>'
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'target="_blank">Chakravarty et al., JCO PO 2017</a>.'
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};
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api.getNumbers('main')

‎app/scripts/controllers/news.js

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'KDM6A - Oncogenic Mutations - Bladder Cancer - EZH2 inhibitors (<b>new association</b>)',
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]
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},
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'01242019': {
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'Level 1': [
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'November 2, 2018: <a target="_blank" ' +
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'href="https://www.fda.gov/Drugs/InformationOnDrugs/ApprovedDrugs/ucm625027.htm">' +
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'the FDA approved lorlatinib</a> for patients with anaplastic lymphoma kinase (ALK)-positive metastatic non-small cell lung cancer (NSCLC) whose disease has progressed on crizotinib and at least one other ALK inhibitor or whose disease has progressed on alectinib or ceritinib for metastatic disease.'
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]
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},
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};
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$scope.data.newlyAddedLevelFour = [
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{
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'10012018': ['HIST1H1E','SETD6','SETD5','SETD7','SETDB2','SETDB1','SETD4','SETD3','SETD1B','U2AF2','TET3','NFE2','IRF8','IRF1','IKZF3','JARID2','NCSTN','HIST1H2BO','HIST1H2AC','HIST1H2BG','HIST1H2BJ','HIST1H2BK','HIST1H2BC','HIST1H2AG','HIST1H2AL','HIST1H2AM','TYK2'],
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'10262018': ['NT5C2','P2RY8','PCBP1','PDS5B','PTPN1','PTPN2 ','STAG1','TRAF3','TRAF5'],
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'12142018': ['KSR2','LCK','LTB','MGAM','MOB3B','MPEG1','NCOR2','PIGA','PLCG1','POT1','ROBO1','RUNX1T1','SAMHD1','SETD1A','SGK1','SMC1A','SMC3','SMG1','SP140','STAT6','TBL1XR1','UBR5','VAV1','VAV2','XBP1'],
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'01242019': ['ECT2L','RELN','TAL1','MLLT10','TLX3','TLX1','TRA','TRB','TRD','TRG','EPOR','ABL2','MECOM','DEK','RBM15','BCL9'],
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};
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});

‎app/styles/_team.scss

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.item-1 {
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padding-left: 15px;
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}
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h5 {
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margin-top: 30px;
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}
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.row {
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margin-bottom: 0;
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}
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@media (min-width: $range-min-lg-width) {
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.col-lg-3.item-1 {
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width: 22%;

‎app/views/cancerGenes.html

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</div>
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<div class="row" style="margin-bottom: 0;">
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<div class="col-lg-12">
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<div style="margin-bottom: 10px">1019 genes, last update 12/14/2018</div>
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<div style="margin-bottom: 10px">1019 genes, last update 1/24/2019</div>
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<div>The following genes are considered to be cancer genes by OncoKB, based on their inclusion in
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various different sequencing panels, the Sanger Cancer Gene Census, or
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<a href="http://science.sciencemag.org/content/339/6127/1546.full">

‎app/views/dataaccess.html

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<div class="container">
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<div class="data-access">
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<div class="header">
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<h5>By using OncoKB data, you are agreeing to the OncoKB <a href="#/terms"><u>usage
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terms</u></a>.</h5>
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<h3 class="title">Annotating Your Files</h3>
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<div>You can annotate your data files (mutations, copy number alterations, fusions, and clinical data) with
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<a href="https://github.com/oncokb/oncokb-annotator" target="_blank">OncoKB Annotator</a>.
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</div>
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<h3 class="title">Data Download</h3>
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<div>OncoKB annotations are fully available for download. Please review the <a href="#/terms"><u>usage
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terms</u></a> before downloading. Previous versions are available <a
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href="https://github.com/oncokb/oncokb-public/tree/master/data" target="_blank">here</a>.
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</div>
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<div ng-bind-html="data.citationURL" style="margin-bottom: 10px"></div>
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<div class="top-download">
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<a class="btn btn-sm download waves-effect waves-light"
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ng-href="{{apiLink}}utils/allCuratedGenes.txt"
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download><i
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class="fa fa-cloud-download"></i> All Curated Genes</a>
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<a class="btn btn-sm download waves-effect waves-light"
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ng-href="{{apiLink}}utils/allAnnotatedVariants.txt"
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download><i
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class="fa fa-cloud-download"></i> All Alterations</a>
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class="fa fa-cloud-download"></i> All Curated Alterations</a>
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<a class="btn btn-sm download waves-effect waves-light"
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ng-href="{{apiLink}}utils/allActionableVariants.txt"
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download><i
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class="fa fa-cloud-download"></i> Actionable Alterations</a>
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<a class="btn btn-sm download waves-effect waves-light"
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ng-href="{{apiLink}}utils/allCuratedGenes.txt"
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download><i
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class="fa fa-cloud-download"></i> All Curated Genes</a>
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</div>
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<h3 class="title">Annotating Your Files</h3>
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<div>You can annotate your data files (mutations, copy number alterations, fusions, and clinical data) with
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<a href="https://github.com/oncokb/oncokb-annotator" target="_blank">OncoKB Annotator</a>.
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</div>
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<h3 class="title">Data API</h3>
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</div>
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<div class="swagger" swagger-ui url="swaggerUrl" api-explorer="true"></div>
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</div>
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</div>

‎app/views/news.html

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</p>
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<p ng-bind-html="data.citationURL"></p>
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</div>
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<h3>January 24, 2019</h3>
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<div>
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<ul>
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<li>Updated Actionable Genes
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<div class="row">
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<table class="table">
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<thead>
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<th class="col-lg-1 col-sm-2 col-xs-3">Level</th>
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<th class="col-lg-11 col-sm-10 col-xs-9">Update</th>
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</thead>
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<tbody>
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<tr ng-repeat="(key, value) in data.updatedActionableGenes['01242019']">
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<td>{{key}}</td>
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<td>
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<ul>
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<li ng-repeat="item in value"><span ng-bind-html="item"></span></li>
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</ul>
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</td>
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</tr>
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</tbody>
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</table>
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</div>
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</li>
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<li>Addition of {{data.newlyAddedGenes['01242019'].length}} new heme-associated genes:
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<div class="newly-added-genes">
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<span class="gene" ng-repeat="hugo in data.newlyAddedGenes['01242019']"><a
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href="#/gene/{{hugo}}">{{hugo}}</a></span>
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</div>
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</li>
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</ul>
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</div>
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<h3>December 14, 2018</h3>
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<div>

‎app/views/team.html

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<h2>OncoKB Team</h2>
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<p>
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OncoKB is developed and maintained by the Knowledge Systems group in the <a
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href="https://www.mskcc.org/research-areas/programs-centers/molecular-oncology">Marie Josée
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and Henry R. Kravis Center for Molecular Oncology</a> at Memorial Sloan Kettering Cancer Center.</p>
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href="https://www.mskcc.org/research-areas/programs-centers/molecular-oncology">Marie Josée
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and Henry R. Kravis Center for Molecular Oncology</a> at Memorial Sloan Kettering Cancer Center. Disclosure
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of conflicts of interest of all OncoKB contributors is available <a
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href="https://docs.google.com/spreadsheets/d/1FaOIvQmLXA7Z9rM_WkgP9QPbfkDHoTLKEUGlr0G2UT0/edit?usp=sharing"
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target="_blank">here.</a></p>
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</div>
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</div>
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<div class="row">
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<li>Paul Sabbatini, MD</li>
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<li>Nikolaus Schultz, PhD</li>
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</ul>
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<h5>Core Curators</h5>
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<ul>
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<li>Kinisha Gala, PhD</li>
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<li>Hannah Johnsen</li>
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<li>Phillip Jonsson, PhD</li>
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<li>Lindsay M. LaFave, PhD</li>
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<li>David Knorr, MD, PhD</li>
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<li>Linde Miles</li>
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</ul>
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<h5>Past Contributors</h5>
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<ul>
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<li>Tara Soumerai, MD</li>
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<li>Aphrothiti Hanrahan, PhD</li>
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<li>Anton Henssen, MD</li>
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<li>Tripti Shrestha Bhattarai, PhD</li>
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<li>Fiona Brown, PhD</li>
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<li>Iñigo Landa-Lopez, PhD</li>
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<li>Neel Shah, PhD</li>
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<li>Eneda Toska, PhD</li>
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<li>Jiaojiao Wang, MSc</li>
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</ul>
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</div>
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<div class="col-lg-4 col-md-4 col-sm-6 item-2">
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<h5>Clinical Genomics Annotation Committee</h5>
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<ul>
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<li>Margaret Callahan, MD, PhD</li>
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<li>Sarat Chandarlapaty, MD, PhD</li>
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<li>Ping Chi, MD, PhD</li>
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<li>Daniel Danila, MD</li>
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<li>Mrinal Gounder, MD</li>
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<li>James Harding, MD</li>
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<li>Matthew Hellman, MD</li>
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<li>Alan Ho, MD, PhD</li>
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<li>Gopa Iyer, MD</li>
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<li>Yelena Janjigian, MD</li>
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<li>Thomas Kaley, MD</li>
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<li>Vicky Makker, MD</li>
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<li>Paul Paik, MD</li>
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<li>Michael Postow, MD</li>
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<li>Dana Rathkopf, MD</li>
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<li>Alexander Shoushtari, MD</li>
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<li>Neerav Shukla, MD</li>
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<li>Tiffany Traina, MD</li>
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<li>Martin Voss, MD</li>
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<li>Rona Yaeger, MD</li>
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<li>Carol Aghajanian, MD</li>
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<li>Maria Arcila, MD</li>
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<li>Michael Berger, PhD</li>
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<li>Margaret Callahan, MD, PhD</li>
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<li>Timothy A. Chan, MD, PhD</li>
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<li>Sarat Chandarlapaty, MD, PhD</li>
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<li>Ping Chi, MD, PhD</li>
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<li>Daniel Danila, MD</li>
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<li>Lisa DeAngelis, MD</li>
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<li>Luis Alberto Diaz, Jr., MD</li>
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<li>Ahmet Dogan, MD, PhD</li>
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<li>Alexander Drilon, MD</li>
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<li>James A. Fagin, MD</li>
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<li>Mrinal M. Gounder, MD</li>
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<li>James J. Harding, MD</li>
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<li>Matthew D. Hellmann, MD</li>
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<li>Alan L. Ho, MD, PhD</li>
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<li>David Hyman, MD</li>
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<li>Gopa Iyer, MD</li>
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<li>Edgar A. Jaimes, MD</li>
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<li>Yelena Y. Janjigian, MD</li>
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<li>Philip Kantoff, MD</li>
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<li>David S. Klimstra, MD</li>
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<li>Andrew Kung, MD, PhD</li>
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</ul>
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</div>
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<div class="col-lg-4 col-md-4 col-sm-6 item-3">
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<h5>Core Curators</h5>
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<ul>
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<li>Kinisha Gala, PhD</li>
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<li>Hannah Johnsen</li>
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<li>Phillip Jonsson, PhD</li>
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<li>Lindsay Saunders, PhD</li>
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</ul>
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</div>
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<div class="col-lg-4 col-md-4 col-sm-6 item-4">
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<h5>Alumni</h5>
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<div class="col-lg-4 col-md-4 col-sm-6 item-2">
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<h5>Clinical Genomics Annotation Committee (continued)</h5>
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<ul>
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<li>Douglas Levine, MD, FACOG, FACS</li>
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<li>Alexandra Charen-Snyder, MD</li>
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<li>Maeve Lowery, MD</li>
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<li>Tara Soumerai, MD</li>
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<li>Aphrothiti Hanrahan, PhD</li>
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<li>Anton Henssen, MD</li>
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<li>Shrujal Baxi, MD, MPH</li>
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<li>Tripti Shrestha Bhattarai, PhD</li>
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<li>Fiona Brown, PhD</li>
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<li>Iñigo Landa-Lopez, PhD</li>
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<li>Neel Shah</li>
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<li>Eneda Toska, PhD</li>
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<li>Jiaojiao Wang, MSc</li>
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<li>Antonio Omuro, MD</li>
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<li>Marc Ladanyi, MD</li>
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<li>C. Ola Landgren, MD, PhD</li>
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<li>Ingo K. Mellinghoff, MD</li>
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<li>Kenneth Offit, MD</li>
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<li>Paul K. Paik, MD</li>
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<li>David G. Pfister, MD</li>
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<li>Dana E. Rathkopf, MD</li>
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<li>Gregory J. Riely, MD, PhD</li>
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<li>Mark E. Robson, MD</li>
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<li>Neal Rosen, MD, PhD</li>
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<li>Leonard Saltz, MD</li>
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<li>Maurizio Scaltriti, PhD</li>
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<li>Howard I. Scher, MD</li>
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<li>Sohrab Shah, PhD</li>
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<li>Alexander N. Shoushtari, MD</li>
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<li>Neerav N. Shukla, MD</li>
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<li>Martin S. Tallman, MD</li>
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<li>William D. Tap, MD</li>
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<li>Barry S. Taylor, PhD</li>
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<li>Tiffany A. Traina, MD</li>
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<li>Martin H. Voss, MD</li>
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<li>Jedd D. Wolchok, MD, PhD</li>
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<li>Rona D. Yaeger, MD</li>
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<li>Anas Younes, MD</li>
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</ul>
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</div>
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</div>

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