Update news for v4.14 (#1080)

oncokb · Feb 8, 2024 · 060b95e · 060b95e
1 parent f67a10d
commit 060b95e
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Showing 10 changed files with 239 additions and 7 deletions.
diff --git a/...__baseline_snapshots__/Precision Oncology Therapies Page without Login-snap.png b/...__baseline_snapshots__/Precision Oncology Therapies Page without Login-snap.png
diff --git a/src/main/webapp/app/config/constants.tsx b/src/main/webapp/app/config/constants.tsx
@@ -793,6 +793,7 @@ export type DataRelease = {
 };
 
 export const DATA_RELEASES: DataRelease[] = [
+  { date: '02082024', version: 'v4.14' },
   { date: '12212023', version: 'v4.13' },
   { date: '12062023', version: 'v4.12' },
   { date: '11132023', version: 'v4.11' },

diff --git a/src/main/webapp/app/pages/newsPage/ChangedAnnotatonListItem.tsx b/src/main/webapp/app/pages/newsPage/ChangedAnnotatonListItem.tsx
@@ -5,6 +5,7 @@ import {
   CHANGED_ANNOTATION_ADDITIONAL_DRUG_DIFF_LEVEL_COLUMNS,
   GENE,
   MUTATION,
+  CHANGED_ANNOTATION_DRUG_REMOVAL_COLUMNS,
 } from 'app/pages/newsPage/NewsPageContent';
 import { SimpleTable, SimpleTableRow } from 'app/components/SimpleTable';
 import { Row } from 'react-bootstrap';
@@ -24,6 +25,7 @@ export enum AnnotationColumnHeaderType {
   DRUG,
   ADDITIONAL_SAME_LEVEL_DRUG,
   ADDITIONAL_DIFF_LEVEL_DRUG,
+  DRUG_REMOVAL,
 }
 
 export const ChangedAnnotationListItem = (props: {
@@ -55,6 +57,12 @@ export const ChangedAnnotationListItem = (props: {
       useOneLineRowClass = false;
       defaultTitle = 'Changed Annotation';
       break;
+    case AnnotationColumnHeaderType.DRUG_REMOVAL:
+      annotationColumnHeader = CHANGED_ANNOTATION_DRUG_REMOVAL_COLUMNS;
+      useOneLineRowClass = false;
+      defaultTitle =
+        'Updated therapeutic implications - Removal of therapie(s) and changed tumor type-specific level of evidence for an alteration(s)';
+      break;
     case AnnotationColumnHeaderType.LEVEL:
     default:
       annotationColumnHeader = CHANGED_ANNOTATION_LEVEL_COLUMNS;

diff --git a/src/main/webapp/app/pages/newsPage/NewsPage.tsx b/src/main/webapp/app/pages/newsPage/NewsPage.tsx
@@ -91,6 +91,7 @@ export default class NewsPage extends React.Component<{
             <CitationText />
           </div>
           <div className="mt-2">
+            <NewsList date={'02082024'} />
             <NewsList date={'01172024'} />
             <NewsList date={'12212023'} />
             <NewsList date={'12062023'} />

diff --git a/src/main/webapp/app/pages/newsPage/NewsPageContent.tsx b/src/main/webapp/app/pages/newsPage/NewsPageContent.tsx
@@ -79,6 +79,7 @@ export const CURRENT_LEVEL_OF_EVIDENCE = 'Current Level of Evidence';
 export const PREVIOUS_LEVEL_OF_EVIDENCE = 'Previous Level of Evidence';
 export const DRUGS_ADDED_TO_ONCOKB = `Drug(s) added to ${ONCOKB_TM}`;
 export const DRUGS_CURRENTLY_IN_ONCOKB = `Drug(s) currently in ${ONCOKB_TM}`;
+export const DRUGS_REMOVED_FROM_ONCOKB = `Drug(s) removed from ${ONCOKB_TM}`;
 export const PREVIOUS_BIOMARKER_ASSOCIATION = 'Previous Biomarker Association';
 export const CURRENT_BIOMARKER_ASSOCIATION = 'Current Biomarker Association';
 
@@ -144,6 +145,17 @@ export const CHANGED_ANNOTATION_ADDITIONAL_DRUG_DIFF_LEVEL_COLUMNS = [
   { name: EVIDENCE },
 ];
 
+export const CHANGED_ANNOTATION_DRUG_REMOVAL_COLUMNS = [
+  { name: GENE },
+  { name: MUTATION },
+  { name: CANCER_TYPE },
+  { name: PREVIOUS_LEVEL },
+  { name: CURRENT_LEVEL_OF_EVIDENCE },
+  { name: DRUGS_CURRENTLY_IN_ONCOKB },
+  { name: DRUGS_REMOVED_FROM_ONCOKB },
+  { name: EVIDENCE },
+];
+
 export const CDX_COLUMNS = [
   { name: LEVEL },
   { name: GENE },
@@ -200,6 +212,215 @@ const EVIDENCE_COLUMN_SEPARATOR = '; ';
 // https://stackoverflow.com/questions/41947168/is-it-possible-to-use-keyof-operator-on-literals-instead-of-interfaces
 
 export const NEWS_BY_DATE: { [date: string]: NewsData } = {
+  '02082024': {
+    news: [
+      <span>
+        Updated therapeutic implications - Demotion of tumor type-specific level
+        of evidence for an alteration(s)
+        <Row className={'overflow-auto'}>
+          <table className="table">
+            <thead>
+              <tr>
+                <th>{GENE}</th>
+                <th>{MUTATION}</th>
+                <th>{CANCER_TYPE}</th>
+                <th>{DRUGS}</th>
+                <th>{PREVIOUS_LEVEL}</th>
+                <th>{CURRENT_LEVEL}</th>
+                <th>{REASON}</th>
+              </tr>
+            </thead>
+            <tbody>
+              <tr>
+                <td>
+                  <GenePageLink hugoSymbol="FGFR3" />
+                </td>
+                <td>
+                  <span>
+                    Fusions (excluding FGFR3-TACC3 Fusion and FGFR3-BAIAP2L1
+                    Fusion which remain Level 1)
+                  </span>
+                </td>
+                <td>Bladder Cancer</td>
+                <td>Erdafitinib</td>
+                <td>1</td>
+                <td>2</td>
+                <td>
+                  <WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
+                    <Linkout link="https://www.accessdata.fda.gov/drugsatfda_docs/label/2020/212018s001lbl.pdf">
+                      Adherence to FDA-drug label and CDx for Erdafitinib
+                    </Linkout>
+                    <span>
+                      Inclusion in NCCN Bladder Cancer Guidelines V3.2023
+                    </span>
+                    <PMIDLink pmids="37870920" />
+                  </WithSeparator>
+                </td>
+              </tr>
+            </tbody>
+          </table>
+        </Row>
+      </span>,
+      <span>
+        Updated therapeutic implications - Promotion of tumor type-specific
+        level of evidence for an alteration(s)
+        <Row className={'overflow-auto'}>
+          <table className="table">
+            <thead>
+              <tr>
+                <th>{GENE}</th>
+                <th>{MUTATION}</th>
+                <th>{CANCER_TYPE}</th>
+                <th>{DRUGS}</th>
+                <th>{PREVIOUS_LEVEL}</th>
+                <th>{CURRENT_LEVEL}</th>
+                <th>{REASON}</th>
+              </tr>
+            </thead>
+            <tbody>
+              <tr>
+                <td>
+                  <GenePageLink hugoSymbol="FGFR3" />
+                </td>
+                <td>
+                  <span>
+                    <WithSeparator separator={', '}>
+                      {['S371C', 'G380R', 'K650'].map(alt => (
+                        <AlterationPageLink
+                          hugoSymbol="FGFR3"
+                          alteration={alt}
+                        />
+                      ))}
+                    </WithSeparator>
+                  </span>
+                </td>
+                <td rowSpan={2}>Bladder Cancer</td>
+                <td rowSpan={2}>Erdafitinib</td>
+                <td>3A</td>
+                <td>2</td>
+                <td rowSpan={2}>
+                  {' '}
+                  <WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
+                    <Linkout link="https://www.accessdata.fda.gov/drugsatfda_docs/label/2020/212018s001lbl.pdf">
+                      Adherence to FDA-drug label and CDx for Erdafitinib
+                    </Linkout>
+                    <span>
+                      Inclusion in NCCN Bladder Cancer Guidelines V3.2023
+                    </span>
+                    <PMIDLink pmids="37870920" />
+                  </WithSeparator>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <GenePageLink hugoSymbol="FGFR3" />
+                </td>
+                <td>
+                  <span>
+                    Oncogenic Mutations (excluding G370C, R248C, S249C, Y373C
+                    which remain Level 1)
+                  </span>
+                </td>
+                <td>4</td>
+                <td>2</td>
+              </tr>
+              <tr>
+                <td>
+                  <GenePageLink hugoSymbol="MDM2" />
+                </td>
+                <td>
+                  <span>
+                    <AlterationPageLink
+                      hugoSymbol="MDM2"
+                      alteration="Amplification"
+                    />
+                  </span>
+                </td>
+                <td>
+                  Dedifferentiated Liposarcoma, Well-Differentiated Liposarcoma
+                </td>
+                <td>
+                  <div>
+                    <div style={{ fontStyle: 'italic' }}>
+                      {DRUGS_CURRENTLY_IN_ONCOKB}:
+                    </div>
+                    <div>Milademetan (Level 4)</div>
+                    <br></br>
+                    <div style={{ fontStyle: 'italic' }}>
+                      {DRUGS_ADDED_TO_ONCOKB}:
+                    </div>
+                    <div>Brigimadlin (Level 3A)</div>
+                  </div>
+                </td>
+                <td>4</td>
+                <td>3A</td>
+                <td>
+                  <PMIDLink pmids="37269344" />
+                </td>
+              </tr>
+            </tbody>
+          </table>
+        </Row>
+      </span>,
+    ],
+    changedAnnotations: [
+      {
+        columnHeaderType: AnnotationColumnHeaderType.DRUG_REMOVAL,
+        content: [
+          [
+            'FGFR2',
+            'Fusions',
+            'Bladder Cancer',
+            'Level 1',
+            'No Level',
+            <div>
+              <div>Erdafitinib (Level 1)</div>
+              <div>AZD4547 (Level 4)</div>
+            </div>,
+            'Erdafitinib, AZD4547',
+            <WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
+              <Linkout link="https://www.accessdata.fda.gov/drugsatfda_docs/label/2020/212018s001lbl.pdf">
+                Amendment to the FDA-drug label for Erdafitinib
+              </Linkout>
+              <span>
+                4/25 (16%) response rate for FGFR2/3 fusion+ bladder cancer, 0/6
+                (0%) response for FGFR2 fusion+ bladder cancer
+              </span>
+              <PMIDLink pmids="31340094" />
+            </WithSeparator>,
+          ],
+        ],
+      },
+    ],
+    updatedImplicationTitle:
+      'Updated therapeutic implications - New alteration(s) with a tumor type-specific level of evidence',
+    updatedImplication: [
+      [
+        '3A',
+        'MDM2',
+        'Amplification',
+        'Intimal Sarcoma',
+        'Milademetan',
+        <PMIDLink pmids={'37369013'} />,
+      ],
+    ],
+    newlyAddedGenes: [
+      'ANKRD26',
+      'ARHGAP26',
+      'ATIC',
+      'CD70',
+      'ERCC1',
+      'FGF1',
+      'FGF2',
+      'FGF5',
+      'HFE',
+      'HOXA11',
+      'MN1',
+      'PML',
+      'SRP72',
+      'TNFRSF17',
+    ],
+  },
   '01172024': {
     priorityNews: [
       <span>

diff --git a/src/main/webapp/app/pages/oncologyTherapiesPage/oncologyTherapiesPage.tsx b/src/main/webapp/app/pages/oncologyTherapiesPage/oncologyTherapiesPage.tsx
@@ -474,14 +474,15 @@ const OncologyTherapiesPage: React.FunctionComponent<{}> = props => {
                 'https://www.fda.gov/drugs/resources-information-approved-drugs/oncology-cancer-hematologic-malignancies-approval-notifications'
               }
             >
-              Content current as of 12/15/2023
+              Content current as of 1/19/2024
             </Linkout>
           </div>
           <div>
             The following US Food and Drug Administration (FDA)-approved
-            oncology drugs are categorized by drug class and mechanism of
-            action. Each drug is further classified as to whether it qualifies
-            as a targeted therapy or precision oncology therapy based on{' '}
+            oncology drugs post June 1998 are categorized by drug class and
+            mechanism of action. Each drug is further classified as to whether
+            it qualifies as a targeted therapy or precision oncology therapy
+            based on{' '}
             <Linkout link="https://aacrjournals.org/cancerdiscovery/article/doi/10.1158/2159-8290.CD-23-0467/729589/Quantifying-the-Expanding-Landscape-of-Clinical">
               Suehnholz et al., Cancer Discovery 2023
             </Linkout>{' '}

diff --git a/src/main/webapp/content/files/oncologyTherapies/fda_approved_oncology_therapies.json b/src/main/webapp/content/files/oncologyTherapies/fda_approved_oncology_therapies.json
@@ -1462,7 +1462,7 @@
   {
     "year": "2019",
     "tx": "Erdafitinib",
-    "biomarker": "FGFR2 Fusions, FGFR3 Fusions, S249C, R248C, G370C, Y373C",
+    "biomarker": "FGFR3-TACC3 Fusion, FGFR3-BAIAP2L1 Fusion, FGFR3 S249C, R248C, G370C, Y373C",
     "agentClass": "Small molecule kinase inhibitor",
     "drugTarget": "Multi-targeted kinase inhibitor (targets include FGFR1/2/3/4 among others)",
     "targetedTx": "Y",

diff --git a/src/main/webapp/content/files/oncologyTherapies/fda_approved_oncology_therapies.xlsx b/src/main/webapp/content/files/oncologyTherapies/fda_approved_oncology_therapies.xlsx
diff --git a/src/main/webapp/content/images/oncokb_summary.png b/src/main/webapp/content/images/oncokb_summary.png
diff --git a/src/main/webapp/index.html b/src/main/webapp/index.html
@@ -15,15 +15,15 @@
     <meta name="twitter:site" content="@oncokb">
     <meta name="twitter:title" content="OncoKB™ - MSK's Precision Oncology Knowledge Base">
     <meta name="twitter:description" content="OncoKB™ is a precision oncology knowledge base developed at Memorial Sloan Kettering Cancer Center that contains biological and clinical information about genomic alterations in cancer.">
-    <meta name="twitter:image" content="https://www.oncokb.org/content/images/oncokb_summary.png?20231221">
+    <meta name="twitter:image" content="https://www.oncokb.org/content/images/oncokb_summary.png?20240208">
     <meta name="twitter:url" content="https://www.oncokb.org/">
 
     <meta property="og:site_name" content="OncoKB™">
     <meta property="og:type" content="website">
     <meta property="og:url" content="https://www.oncokb.org/">
     <meta property="og:title" content="OncoKB™ - MSK's Precision Oncology Knowledge Base">
     <meta property="og:description" content="OncoKB™ is a precision oncology knowledge base developed at Memorial Sloan Kettering Cancer Center that contains biological and clinical information about genomic alterations in cancer.">
-    <meta property="og:image" content="https://www.oncokb.org/content/images/oncokb_summary.png?20231221">
+    <meta property="og:image" content="https://www.oncokb.org/content/images/oncokb_summary.png?20240208">
 
     <link rel="mask-icon" href="content/images/favicon/safari-pinned-tab.svg" color="#0968c3">
     <!-- Preload the customized fonts, so the html knows how to pain the page  -->