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4.23 (#1189)
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* 4.23

* Addressed PR Comments
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@jfkonecn
jfkonecn authored Nov 25, 2024
1 parent 05cfa25 commit 97bd3c1
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Showing 7 changed files with 171 additions and 23 deletions.
1 change: 1 addition & 0 deletions src/main/webapp/app/config/constants.tsx
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Expand Up @@ -864,6 +864,7 @@ export type DataRelease = {
};

export const DATA_RELEASES: DataRelease[] = [
{ date: '11262024', version: 'v4.23' },
{ date: '10242024', version: 'v4.22' },
{ date: '09252024', version: 'v4.21' },
{ date: '08152024', version: 'v4.20' },
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2 changes: 1 addition & 1 deletion src/main/webapp/app/pages/newsPage/Links.tsx
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Expand Up @@ -6,7 +6,7 @@ export const FdaApprovalLink: React.FunctionComponent<{
approval: string;
year?: string;
}> = props => {
let linkText = 'FDA-approval ';
let linkText = 'FDA approval ';
if (props.year) {
linkText += `(${props.year}) `;
}
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5 changes: 3 additions & 2 deletions src/main/webapp/app/pages/newsPage/NewsPage.tsx
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Expand Up @@ -3,7 +3,7 @@ import { CitationText } from 'app/components/CitationText';
import NewsList, { getNews, getNewsTitle } from 'app/pages/newsPage/NewsList';
import {
DRUGS_ADDED_TO_ONCOKB,
DRUGS_CURRENTLY_IN_ONCOKB,
DRUGS_REMAINING_IN_ONCOKB,
NEWS_BY_DATE,
} from 'app/pages/newsPage/NewsPageContent';
import {
Expand Down Expand Up @@ -87,6 +87,7 @@ export default class NewsPage extends React.Component<{
<CitationText />
</div>
<div className="mt-2">
<NewsList date={'11262024'} />
<NewsList date={'10242024'} />
<NewsList date={'09252024'} />
<NewsList date={'08152024'} />
Expand Down Expand Up @@ -187,7 +188,7 @@ export default class NewsPage extends React.Component<{
<th>Mutation</th>
<th>Cancer Type</th>
<th>Current Level of Evidence</th>
<th>{DRUGS_CURRENTLY_IN_ONCOKB}</th>
<th>{DRUGS_REMAINING_IN_ONCOKB}</th>
<th>{DRUGS_ADDED_TO_ONCOKB}</th>
<th>Evidence</th>
</tr>
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165 changes: 147 additions & 18 deletions src/main/webapp/app/pages/newsPage/NewsPageContent.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ import {
YearEndReviewPageLink,
getAlterationPageLink,
getAlternativeAllelesPageLinks,
getAlternativeGenePageLinks,
} from 'app/shared/utils/UrlUtils';
import { PMIDLink } from 'app/shared/links/PMIDLink';
import { Linkout } from 'app/shared/links/Linkout';
Expand Down Expand Up @@ -85,7 +86,7 @@ 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_UPDATE_IN_ONCOKB = `Drug(s) updated in ${ONCOKB_TM}`;
export const DRUGS_CURRENTLY_IN_ONCOKB = `Drug(s) currently in ${ONCOKB_TM}`;
export const DRUGS_REMAINING_IN_ONCOKB = `Drug(s) remaining in ${ONCOKB_TM}`;
export const DRUGS_REMOVED_FROM_ONCOKB = `Drug(s) removed from ${ONCOKB_TM}`;
export const DRUGS_DEMOTED_IN_ONCOKB = `Drug(s) demoted in ${ONCOKB_TM}`;
export const DRUGS_PROMOTED_IN_ONCOKB = `Drug(s) promoted in ${ONCOKB_TM}`;
Expand Down Expand Up @@ -156,7 +157,7 @@ export const CHANGED_ANNOTATION_DRUG_SAME_HIGHEST_LEVEL_COLUMNS = [
{ name: GENE },
{ name: MUTATION },
{ name: CANCER_TYPE },
{ name: DRUGS_CURRENTLY_IN_ONCOKB },
{ name: DRUGS_REMAINING_IN_ONCOKB },
{ name: DRUGS_CHANGED_IN_ONCOKB },
{ name: EVIDENCE },
];
Expand All @@ -166,7 +167,7 @@ export const CHANGED_ANNOTATION_ADDITIONAL_DRUG_SAME_LEVEL_COLUMNS = [
{ name: MUTATION },
{ name: CANCER_TYPE },
{ name: CURRENT_LEVEL_OF_EVIDENCE },
{ name: DRUGS_CURRENTLY_IN_ONCOKB },
{ name: DRUGS_REMAINING_IN_ONCOKB },
{ name: DRUGS_ADDED_TO_ONCOKB },
{ name: EVIDENCE },
];
Expand All @@ -177,7 +178,7 @@ export const CHANGED_ANNOTATION_ADDITIONAL_DRUG_DIFF_LEVEL_COLUMNS = [
{ name: CANCER_TYPE },
{ name: PREVIOUS_LEVEL_OF_EVIDENCE },
{ name: CURRENT_LEVEL_OF_EVIDENCE },
{ name: DRUGS_CURRENTLY_IN_ONCOKB },
{ name: DRUGS_REMAINING_IN_ONCOKB },
{ name: DRUGS_ADDED_TO_ONCOKB },
{ name: EVIDENCE },
];
Expand All @@ -188,7 +189,7 @@ export const CHANGED_ANNOTATION_DRUG_REMOVAL_COLUMNS = [
{ name: CANCER_TYPE },
{ name: PREVIOUS_LEVEL },
{ name: CURRENT_LEVEL_OF_EVIDENCE },
{ name: DRUGS_CURRENTLY_IN_ONCOKB },
{ name: DRUGS_REMAINING_IN_ONCOKB },
{ name: DRUGS_REMOVED_FROM_ONCOKB },
{ name: EVIDENCE },
];
Expand All @@ -198,16 +199,16 @@ export const CHANGED_ANNOTATION_DRUG_REMOVAL_SAME_HIGHEST_LEVEL_COLUMNS = [
{ name: MUTATION },
{ name: CANCER_TYPE },
{ name: CURRENT_LEVEL_OF_EVIDENCE },
{ name: DRUGS_CURRENTLY_IN_ONCOKB },
{ name: DRUGS_REMOVED_FROM_ONCOKB },
{ name: DRUGS_REMAINING_IN_ONCOKB },
{ name: EVIDENCE },
];

export const CHANGED_ANNOTATION_SENSITIVITY_LEVEL_COLUMNS = [
{ name: GENE },
{ name: MUTATION },
{ name: CANCER_TYPE },
{ name: DRUGS_CURRENTLY_IN_ONCOKB },
{ name: DRUGS_REMAINING_IN_ONCOKB },
{ name: DRUGS_ADDED_TO_ONCOKB },
{ name: UPDATED_SENSITIVITY_LEVEL },
{ name: UPDATED_RESISTANCE_LEVEL },
Expand Down Expand Up @@ -300,6 +301,134 @@ 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 } = {
'11262024': {
changedAnnotations: [
{
columnHeaderType: AnnotationColumnHeaderType.NEW_ALTERATION_WITH_LEVEL,
content: [
[
'1',
'KMT2A',
'Fusions',
'Mixed Phenotype Acute Leukemia',
'Revumenib',
[
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<FdaApprovalLink
approval="revumenib"
link="https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-revumenib-relapsed-or-refractory-acute-leukemia-kmt2a-translocation?"
/>
<PMIDLink pmids="39121437 " />
</WithSeparator>,
],
],
],
},
{
columnHeaderType:
AnnotationColumnHeaderType.ADDITIONAL_SENSITIVITY_LEVEL_DRUG,
content: [
[
'NTRK1',
'G595R',
'All Solid Tumors',
'Larotrectinib (Level R1), Entrectinib (Level R2)',
<div>
<div>Selitrectinib (Level 3A)</div>
<br />
<div>Zurletrectinib (Level 4)</div>
</div>,
'3A',
'R1',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<PMIDLink pmids="32133433, 33004339, 28578312, 38902532, 34625502" />
</WithSeparator>,
],
[
'NTRK3',
'G623R',
'All Solid Tumors',
'Larotrectinib (Level R1)',
<div>
<div>Selitrectinib (Level 3A)</div>
<br />
<div>Zurletrectinib (Level 4)</div>
</div>,
'3A',
'R1',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<PMIDLink pmids="28578312, 34030125, 37262390, 38902532, 34625502" />
</WithSeparator>,
],
],
},
{
useOneLineRowClass: false,
title:
'Updated therapeutic implications - Promotion of tumor type-specific level of evidence for an alteration(s)',
headers: CHANGED_ANNOTATION_LEVEL_WITH_EVIDENCE_COLUMNS,
content: [
[
'KMT2A',
'Fusions',
'Acute Myeloid Leukemia, B-cell Lymphoblastic Leukemia/Lymphoma',
'Revumenib (Level 3A)',
'3A',
'1',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<FdaApprovalLink
approval="revumenib"
link="https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-revumenib-relapsed-or-refractory-acute-leukemia-kmt2a-translocation?"
/>
<PMIDLink pmids="39121437" />
</WithSeparator>,
],
],
},
{
columnHeaderType: AnnotationColumnHeaderType.UPDATED_SAME_LEVEL_DRUG,
content: [
[
'1',
<WithSeparator separator={', '}>
{getAlternativeGenePageLinks('NTRK1/2/3')}
</WithSeparator>,
<WithSeparator separator={', '}>
<AlterationPageLink hugoSymbol="NTRK1" alteration="Fusions">
Fusions
</AlterationPageLink>
</WithSeparator>,
'All Solid Tumors',
'Entrectinib, Larotrectinib, Repotrectinib (Level 1)',
'Zurletrectinib (Level 4)',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<PMIDLink pmids="38902532" />
</WithSeparator>,
],
],
},
{
columnHeaderType:
AnnotationColumnHeaderType.DRUG_REMOVAL_SAME_HIGHEST_LEVEL,
content: [
[
'PIK3CA',
'H1047R',
'All Solid Tumors',
'4',
'LOXO-783, LOXO-783 + Aromatase Inhibition Therapy + Abemaciclib, LOXO-783 + Fulvestrant, LOXO-783 + Fulvestrant + Abemaciclib, LOXO-783 + LY3484356, LOXO-783 + LY3484356 + Abemaciclib, LOXO-783 + Paclitaxel (Level 4)',
'RLY-2608, RLY-2608 + Fulvestrant (Level 4)',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<Linkout link="https://www.oncologypipeline.com/apexonco/lilly-down-not-out-pi3k-alpha-inhibition">
Discontinuation of LOXO-783 development
</Linkout>
</WithSeparator>,
],
],
},
],
newlyAddedGenes: ['ADGRG4', 'AFDN', 'AGGF1', 'MAGI2', 'PRKCB', 'ZNF292'],
},
'10242024': {
priorityNews: [
<span>
Expand Down Expand Up @@ -398,7 +527,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
'Breast Cancer',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div>
Alpelisib + Fulvestrant, Capivasertib + Fulvestrant (Level 2)
Expand Down Expand Up @@ -743,7 +872,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
'Oligodendroglioma',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div>Ivosidenib (Level 2)</div>
<br></br>
Expand All @@ -770,7 +899,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
'Astrocytoma',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div>Vorasidenib (Level 3A), Ivosidenib (Level 3A)</div>
<br></br>
Expand Down Expand Up @@ -816,7 +945,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
'Endometrial Cancer, Ovarian Cancer',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div>Lunresertib (Level 4), BLU-222 (Level 4)</div>
<br></br>
Expand Down Expand Up @@ -1101,7 +1230,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
'Colorectal Cancer',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div style={{ textDecoration: 'underline' }}>Sensitivity</div>
<div>
Expand Down Expand Up @@ -1686,7 +1815,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
'Breast Cancer',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div>
Capivasertib + Fulvestrant (Level 1), Alpelisib + Fulvestrant
Expand Down Expand Up @@ -1758,7 +1887,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
'Non-Small Cell Lung Cancer',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div>Osimertinib (Level R2), Afatinib (Level 4)</div>
<br></br>
Expand Down Expand Up @@ -1932,7 +2061,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
<td>
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div>Milademetan (Level 4)</div>
<br></br>
Expand Down Expand Up @@ -2116,7 +2245,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
'Breast Cancer',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div>GSK2636771, AZD8186 (Currently Level 4)</div>
<br></br>
Expand Down Expand Up @@ -2257,7 +2386,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
<th>{MUTATION}</th>
<th>{CANCER_TYPE}</th>
<th>{CURRENT_LEVEL_OF_EVIDENCE}</th>
<th>{DRUGS_CURRENTLY_IN_ONCOKB}</th>
<th>{DRUGS_REMAINING_IN_ONCOKB}</th>
<th>{DRUGS_ADDED_TO_ONCOKB}</th>
<th>{EVIDENCE}</th>
</tr>
Expand Down Expand Up @@ -2345,7 +2474,7 @@ export const NEWS_BY_DATE: { [date: string]: NewsData } = {
'Colorectal Cancer',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
{DRUGS_REMAINING_IN_ONCOKB}:
</div>
<div>Adagrasib + Cetuximab (Level 3A)</div>
<br></br>
Expand Down
17 changes: 17 additions & 0 deletions src/main/webapp/app/shared/utils/UrlUtils.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -176,6 +176,23 @@ export const getAlternativeAllelesPageLinks = (
}
};

export const getAlternativeGenePageLinks = (genes: string) => {
const splits = genes.split('/');
const temp = splits[0];
const baseHugoSymbol = temp.substring(0, temp.length - 1);
const geneLinks = [temp[temp.length - 1], ...splits.slice(1)].map(
(ending, index) => {
const hugoSymbol = `${baseHugoSymbol}${ending}`;
return (
<GenePageLink hugoSymbol={hugoSymbol}>
{index === 0 ? hugoSymbol : ending}
</GenePageLink>
);
}
);
return <WithSeparator separator={'/'}>{geneLinks}</WithSeparator>;
};

export type GenePagePath = {
hugoSymbol?: string;
geneticType?: GENETIC_TYPE;
Expand Down
Binary file modified src/main/webapp/content/images/oncokb_summary.png
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4 changes: 2 additions & 2 deletions src/main/webapp/index.html
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Expand Up @@ -14,15 +14,15 @@
<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?20241024">
<meta name="twitter:image" content="https://www.oncokb.org/content/images/oncokb_summary.png?20241126">
<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?20241024">
<meta property="og:image" content="https://www.oncokb.org/content/images/oncokb_summary.png?20241124">

<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 -->
Expand Down

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