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Merge pull request #215 from zhx828/rc
Release 1.16
2 parents f1277cb + 1ec48b5 commit 67d6c53

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lines changed

‎app/scripts/app.js

+2-2
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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: 'August 20, 2018',
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version: '1.15',
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lastUpdate: 'October 1, 2018',
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version: '1.16',
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levelColors: {
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'1': '#33A02C',
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'2A': '#1F78B4',

‎app/scripts/controllers/about.js

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* Controller of the oncokbStaticApp
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*/
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angular.module('oncokbStaticApp')
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.controller('AboutCtrl', function() {
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.controller('AboutCtrl', function($scope, $rootScope) {
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$scope.numOfGenes = $rootScope.meta.numbers.main.gene;
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});

‎app/scripts/controllers/cancerGenes.js

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@@ -11,7 +11,7 @@
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* Controller of the oncokbStaticApp
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*/
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angular.module('oncokbStaticApp')
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.controller('CancerGenesCtrl', function($scope, _, api, $q) {
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.controller('CancerGenesCtrl', function($scope, _, api, $q, apiLink) {
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// DataTable initialization & options
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$scope.dt = {};
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$scope.dt.dtOptions = {
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};
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function displayConvert(obj, keys) {
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if (obj.oncokbAnnotated === true) {
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obj.occurrenceCount += 1;
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}
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_.each(keys, function(key) {
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obj[key] = obj[key] === true ? 'Yes' : 'No';
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});
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$scope.cancerGeneList = [];
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$scope.doneLoading = true;
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});
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$scope.download = function() {
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var tempArr = ['Hugo Symbol', '# of occurence within resources', 'OncoKB Annotated', 'OncoKB Oncogene', 'OncoKB TSG', 'MSK-IMPACT', 'MSK-HEME', 'Foundation One', 'Foundation One Heme', 'Vogelstein', 'Sanger CGC'];
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var content = [tempArr.join('\t')];
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_.each($scope.cancerGeneList, function(item) {
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tempArr = [item.hugoSymbol, item.occurrenceCount, item.oncokbAnnotated, item.oncogene, item.tsg, item.mSKImpact, item.mSKHeme, item.foundation,
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item.foundationHeme, item.vogelstein, item.sangerCGC];
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content.push(tempArr.join('\t'));
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});
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var blob = new Blob([content.join('\n')], {
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type: 'text/plain;charset=utf-8;',
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});
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saveAs(blob, 'CancerGenesList.txt');
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};
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$scope.apiLink = apiLink;
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});

‎app/scripts/controllers/news.js

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@@ -90,12 +90,12 @@ angular.module('oncokbStaticApp')
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],
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'Level 3': [
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'EGFR - Exon 20 insertions - Non-small cell lung cancer - Poziotinib (<b>added as new association</b>)',
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'EGFR - Exon 20 insertions - Non-small cell lung cancer - Poziotinib (<b>added as new association</b>)',
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'ALK - G1202R - Non-small cell lung cancer - Lorlatinib (<b>added as new association</b>)',
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'KIT - D816 mutations - Mastocytosis - Avapritinib (<b>added as new association</b>)',
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'MTOR - E2014K, E2419K - Bladder cancer - Everolimus (<b>updated association</b>)',
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'MTOR - E2014K, E2419K - Bladder cancer - Everolimus (<b>updated association</b>)',
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'MTOR - L1460P, L2209V, L2427Q - Renal cell carcinoma - Temsirolimus (<b>updated association</b>)',
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'MTOR - Q2223K -Renal cell carcinoma - Everolimus (<b>updated association</b>)'
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'MTOR - Q2223K - Renal cell carcinoma - Everolimus (<b>updated association</b>)'
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]
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},
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'08172018': {
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'href="https://www.fda.gov/Drugs/InformationOnDrugs/ApprovedDrugs/ucm614128.htm">' +
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'the FDA approved ivosidenib</a> for adult patients with relapsed or refractory acute myeloid leukemia (AML) with a susceptible IDH1 mutation as detected by an FDA-approved test.',
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]
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},
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'10012018': {
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'Level 3': [
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'RET - Oncogenic Mutations - Medullary Thyroid Cancer - LOXO-292 (<b>added as new association</b>)',
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]
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}
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};
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$scope.data.newlyAddedLevelFour = [
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}
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];
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$scope.data.newlyAddedGenes = {
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'08172018': ['ACTG1', 'ARHGEF28', 'ARID3A', 'ARID3B', 'ARID3C', 'ARID4A', 'ARID4B', 'ARID5A', 'ATP6AP1', 'ATP6V1B2', 'ATXN2', 'BACH2', 'BCL11B', 'BCORL1', 'BCR', 'BTG1', 'CD28', 'CD58', 'CIITA', 'CRBN', 'CUX1', 'DDX3X', 'DTX1', 'DUSP22', 'EGR1', 'EP400', 'ESCO2', 'ETNK1', 'FANCD2', 'FAS', 'FBXO11', 'FURIN', 'GNA12', 'GNA13', 'GNB1', 'GTF2I', 'HDAC1', 'HDAC4', 'HDAC7', 'HIF1A', 'HIST1H1B', 'HIST1H1D']
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'08172018': ['ACTG1', 'ARHGEF28', 'ARID3A', 'ARID3B', 'ARID3C', 'ARID4A', 'ARID4B', 'ARID5A', 'ATP6AP1', 'ATP6V1B2', 'ATXN2', 'BACH2', 'BCL11B', 'BCORL1', 'BCR', 'BTG1', 'CD28', 'CD58', 'CIITA', 'CRBN', 'CUX1', 'DDX3X', 'DTX1', 'DUSP22', 'EGR1', 'EP400', 'ESCO2', 'ETNK1', 'FANCD2', 'FAS', 'FBXO11', 'FURIN', 'GNA12', 'GNA13', 'GNB1', 'GTF2I', 'HDAC1', 'HDAC4', 'HDAC7', 'HIF1A', 'HIST1H1B', 'HIST1H1D'],
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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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};
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});

‎app/styles/_cancerGenes.scss

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float: left;
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line-height: 50px;
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}
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button {
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a {
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height: 30px;
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margin: 10px;
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float: right;

‎app/views/about.html

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2020
and Henry R. Kravis Center for Molecular Oncology</a> at Memorial Sloan Kettering Cancer
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Center (MSK), in partnership with Quest Diagnostics.</p>
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<p>Curated by a network of clinical fellows, research fellows, and faculty members at MSK, OncoKB contains
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detailed information about specific alterations in 477 cancer genes. The information is curated from various
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detailed information about specific alterations in {{numOfGenes}} cancer genes. The information is curated from various
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sources, such as guidelines from the FDA, NCCN, or ASCO, <a href="https://clinicaltrials.gov/">ClinicalTrials.gov</a>
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and the scientific literature.</p>
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<p>For each alteration, we have curated the biological effect, prevalence and prognostic information, as well as

‎app/views/cancerGenes.html

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<div class="row" style="margin-bottom: 0;">
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<div class="col-lg-12 title">
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<span>OncoKB Cancer Gene List</span>
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<button class="btn btn-sm download waves-effect waves-light"
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ng-click="download()"><i class="fa fa-cloud-download"></i> Cancer Gene List
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</button>
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<a class="btn btn-sm download waves-effect waves-light"
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ng-href="{{apiLink}}utils/cancerGeneList.txt"
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download> <i class="fa fa-cloud-download"></i> Cancer Gene List</a>
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</div>
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</div>
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<div class="row" style="margin-bottom: 0;">

‎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>October 1, 2018</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['10012018']">
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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 27 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['10012018']"><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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<li>OncoKB is monitoring the following drugs that were granted <a target="_blank"
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href="https://www.fda.gov/forpatients/approvals/fast/ucm405397.htm">Breakthrough
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Therapy</a> designation by the
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FDA:
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<ul class="bullet" style="margin-top: 10px">
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<li>Sept 5, 2018: <a target="_blank"
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href="https://www.onclive.com/web-exclusives/fda-grants-loxo292-breakthrough-designation-for-nsclc-mtc">
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LOXO-292 for RET fusion–positive non–small cell lung cancer (NSCLC) or RET-mutant medullary
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thyroid cancer (MTC)</a></li>
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</ul>
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</li>
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</ul>
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</div>
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<h3>August 20, 2018</h3>
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<div>
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<ul>

‎data/v1.16/README.md

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# v1.16
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## Related releases
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[OncoKB Public Website, October 1, 2018 Updates](https://github.com/oncokb/oncokb-public/releases/tag/0.10)
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[OncoKB Core/Curate v0.3.3 Release](https://github.com/oncokb/oncokb/releases/tag/v0.3.3)
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‎data/v1.16/allActionableVariants.json

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