Skip to content

Commit

Permalink
Update news for v4.15 (#1095)
Browse files Browse the repository at this point in the history
  • Loading branch information
@calvinlu3
calvinlu3 authored Mar 20, 2024
1 parent 064184d commit 68e1695
Show file tree
Hide file tree
Showing 7 changed files with 295 additions and 8 deletions.
1 change: 1 addition & 0 deletions src/main/webapp/app/config/constants.tsx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -793,6 +793,7 @@ export type DataRelease = {
};

export const DATA_RELEASES: DataRelease[] = [
{ date: '03212024', version: 'v4.15' },
{ date: '02082024', version: 'v4.14' },
{ date: '12212023', version: 'v4.13' },
{ date: '12062023', version: 'v4.12' },
Expand Down
23 changes: 23 additions & 0 deletions src/main/webapp/app/pages/newsPage/ChangedAnnotatonListItem.tsx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@ import {
GENE,
MUTATION,
CHANGED_ANNOTATION_DRUG_REMOVAL_COLUMNS,
CHANGED_ANNOTATION_LEVEL_WITH_EVIDENCE_COLUMNS,
CHANGED_ANNOTATION_SENSITIVITY_LEVEL_COLUMNS,
} from 'app/pages/newsPage/NewsPageContent';
import { SimpleTable, SimpleTableRow } from 'app/components/SimpleTable';
import { Row } from 'react-bootstrap';
Expand All @@ -25,7 +27,10 @@ export enum AnnotationColumnHeaderType {
DRUG,
ADDITIONAL_SAME_LEVEL_DRUG,
ADDITIONAL_DIFF_LEVEL_DRUG,
ADDITIONAL_SENSITIVITY_LEVEL_DRUG,
DRUG_REMOVAL,
DEMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE,
PROMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE,
}

export const ChangedAnnotationListItem = (props: {
Expand Down Expand Up @@ -57,12 +62,30 @@ export const ChangedAnnotationListItem = (props: {
useOneLineRowClass = false;
defaultTitle = 'Changed Annotation';
break;
case AnnotationColumnHeaderType.ADDITIONAL_SENSITIVITY_LEVEL_DRUG:
annotationColumnHeader = CHANGED_ANNOTATION_SENSITIVITY_LEVEL_COLUMNS;
useOneLineRowClass = false;
defaultTitle =
'Updated therapeutic implications - Addition of sensitivity-associated therapy(s) for an alteration(s) with a tumor type-specific resistance level of evidence';
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.PROMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE:
annotationColumnHeader = CHANGED_ANNOTATION_LEVEL_WITH_EVIDENCE_COLUMNS;
useOneLineRowClass = false;
defaultTitle =
'Updated therapeutic implications - Promotion of tumor type-specific level of evidence for an alteration(s)';
break;
case AnnotationColumnHeaderType.DEMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE:
annotationColumnHeader = CHANGED_ANNOTATION_LEVEL_WITH_EVIDENCE_COLUMNS;
useOneLineRowClass = false;
defaultTitle =
'Updated therapeutic implications - Demotion of tumor type-specific level of evidence for an alteration(s)';
break;
case AnnotationColumnHeaderType.LEVEL:
default:
annotationColumnHeader = CHANGED_ANNOTATION_LEVEL_COLUMNS;
Expand Down
1 change: 1 addition & 0 deletions src/main/webapp/app/pages/newsPage/NewsPage.tsx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,7 @@ export default class NewsPage extends React.Component<{
<CitationText />
</div>
<div className="mt-2">
<NewsList date={'03212024'} />
<NewsList date={'02082024'} />
<NewsList date={'01172024'} />
<NewsList date={'12212023'} />
Expand Down
262 changes: 262 additions & 0 deletions src/main/webapp/app/pages/newsPage/NewsPageContent.tsx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@ export const MUTATION = 'Mutation';
export const CANCER_TYPE = 'Cancer Type';
export const DRUG = 'Drug';
export const LEVEL = 'Level';
export const LEVELS = 'Level(s)';
export const DRUGS = 'Drug(s)';
export const EVIDENCE = 'Evidence';
export const PREVIOUS_LEVEL = 'Previous Level';
Expand All @@ -80,6 +81,10 @@ 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 DRUGS_DEMOTED_IN_ONCOKB = `Drug(s) demoted in ${ONCOKB_TM}`;
export const DRUGS_PROMOTED_IN_ONCOKB = `Drug(s) promoted in ${ONCOKB_TM}`;
export const CURRENT_SENSITIVITY_LEVEL = 'Current Sensitivity Level';
export const CURRENT_RESISTANCE_LEVEL = 'Current Resistance Level';
export const PREVIOUS_BIOMARKER_ASSOCIATION = 'Previous Biomarker Association';
export const CURRENT_BIOMARKER_ASSOCIATION = 'Current Biomarker Association';

Expand Down Expand Up @@ -114,6 +119,16 @@ export const CHANGED_ANNOTATION_LEVEL_COLUMNS = [
{ name: REASON },
];

export const CHANGED_ANNOTATION_LEVEL_WITH_EVIDENCE_COLUMNS = [
{ name: GENE },
{ name: MUTATION },
{ name: CANCER_TYPE },
{ name: DRUGS },
{ name: PREVIOUS_LEVEL },
{ name: CURRENT_LEVEL },
{ name: EVIDENCE },
];

export const CHANGED_ANNOTATION_DRUG_COLUMNS = [
{ name: LEVEL },
{ name: GENE },
Expand Down Expand Up @@ -156,6 +171,17 @@ export const CHANGED_ANNOTATION_DRUG_REMOVAL_COLUMNS = [
{ name: EVIDENCE },
];

export const CHANGED_ANNOTATION_SENSITIVITY_LEVEL_COLUMNS = [
{ name: GENE },
{ name: MUTATION },
{ name: CANCER_TYPE },
{ name: DRUGS_CURRENTLY_IN_ONCOKB },
{ name: DRUGS_ADDED_TO_ONCOKB },
{ name: CURRENT_SENSITIVITY_LEVEL },
{ name: CURRENT_RESISTANCE_LEVEL },
{ name: EVIDENCE },
];

export const CDX_COLUMNS = [
{ name: LEVEL },
{ name: GENE },
Expand Down Expand Up @@ -212,6 +238,242 @@ 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 } = {
'03212024': {
priorityNews: [
<span>
Updated therapeutic implications - New alteration(s) with a tumor
type-specific level of evidence
<Row className={'overflow-auto'}>
<table className="table">
<thead>
<tr>
<th>{LEVELS}</th>
<th>{GENE}</th>
<th>{MUTATION}</th>
<th>{CANCER_TYPE}</th>
<th>{DRUGS}</th>
<th>{EVIDENCE}</th>
</tr>
</thead>
<tbody>
<tr>
<td>3A</td>
<td rowSpan={2}>
<GenePageLink hugoSymbol="EGFR" />
</td>
<td rowSpan={2}>
<AlterationPageLink hugoSymbol="EGFR" alteration="L718Q" />
</td>
<td rowSpan={2}>Non-Small Cell Lung Cancer</td>
<td>Afatinib</td>
<td>
<PMIDLink pmids="32146032, 32193290, 31315676" wrapText />
</td>
</tr>
<tr>
<td>R2</td>
<td>Osimertinib</td>
<td>
<PMIDLink
pmids="27257132, 29506987, 33937055, 31205925, 34926262, 31315676, 32146032"
wrapText
/>
</td>
</tr>
<tr>
<td>R2</td>
<td>
<GenePageLink hugoSymbol="EGFR" />
</td>
<td>
<AlterationPageLink hugoSymbol="EGFR" alteration="L792F" />
</td>
<td>Non-Small Cell Lung Cancer</td>
<td>Osimertinib</td>
<td>
<PMIDLink
pmids="35932642, 28093244, 29506987, 35422503"
wrapText
/>
</td>
</tr>
</tbody>
</table>
</Row>
</span>,
],
changedAnnotations: [
{
columnHeaderType:
AnnotationColumnHeaderType.ADDITIONAL_SENSITIVITY_LEVEL_DRUG,
content: [
[
'EGFR',
'G724S',
'Non-Small Cell Lung Cancer',
'Osimertinib (Level R2)',
'Afatinib (Level 3A)',
'3A',
'R2',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<PMIDLink
pmids="32093857, 35979997, 33209641, 34590038, 30405134"
wrapText
/>
</WithSeparator>,
],
],
},
{
columnHeaderType:
AnnotationColumnHeaderType.DEMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE,
title:
'Updated therapeutic implications - Demotion of tumor type-specific level of evidence for an alteration',
content: [
[
'AKT1',
'Oncogenic Mutations (excluding E17K, which remains Level 1)',
'Breast Cancer',
'Capivasertib + Fulvestrant',
'1',
'2',
<span>
To adhere to the{' '}
<Linkout link="https://www.accessdata.fda.gov/drugsatfda_docs/label/2023/218197s000lbl.pdf">
FDA-drug label
</Linkout>{' '}
and{' '}
<Linkout link="https://info.foundationmedicine.com/hubfs/FMI%20Labels/FoundationOne_CDx_Label_Technical_Info.pdf">
CDx
</Linkout>{' '}
for Capivasertib, Level 1 assignment will be only for AKT1 E17K
detected by the FoundationOne CDx test. All other AKT1 oncogenic
mutations are Level 2 per their inclusion in the NCCN Breast
Cancer Guidelines V2.2024
</span>,
],
[
'PIK3CA',
'Oncogenic Mutations (excluding R88Q, N345K, C420R, E542K, E545A, E545D, E545Q, E545K, E545G, Q546E, Q546K, Q546R, Q546P, M1043V, M1043I, H1047Y, H1047R, H1047L and G1049R, which remain Level 1)',
'Breast Cancer',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
</div>
<div>
Capivasertib + Fulvestrant (Level 1), Alpelisib + Fulvestrant
(Level 2){' '}
</div>
<br></br>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_DEMOTED_IN_ONCOKB}:
</div>
<div>Capivasertib + Fulvestrant (Level 2)</div>
</div>,
'1',
'2',
<span>
To adhere to the{' '}
<Linkout link="https://www.accessdata.fda.gov/drugsatfda_docs/label/2023/218197s000lbl.pdf">
FDA-drug label
</Linkout>{' '}
and{' '}
<Linkout link="https://info.foundationmedicine.com/hubfs/FMI%20Labels/FoundationOne_CDx_Label_Technical_Info.pdf">
CDx
</Linkout>{' '}
for Capivasertib, Level 1 assignment will be only for the PIK3CA
alterations detected by the FoundationOne CDx test. All other
PIK3CA oncogenic mutations are Level 2 per their inclusion in the
NCCN Breast Cancer Guidelines V2.2024
</span>,
],
[
'FGFR1',
'Amplification',
'Lung Squamous Cell Carcinoma',
'Erdafitinib',
'3A',
'No Level',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<span>
Limited response rate to EGFR inhibitors for FGFR1-amplified
lung squamous cell carcinoma; Discontinuation of infigratinib
</span>
<PMIDLink pmids={'37909331, 37606995'} />
</WithSeparator>,
],
],
},
{
columnHeaderType:
AnnotationColumnHeaderType.PROMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE,
title:
'Updated therapeutic implications - Promotion of tumor type-specific level of evidence for an alteration',
content: [
[
'KRAS',
'G12C',
'Ampullary Cancer',
'Sotorasib, Adagrasib',
'3B',
'2',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<span>
Inclusion in NCCN Ampullary Adenocarcinoma Guidelines V1.2024
</span>
<PMIDLink pmids="32955176" />
</WithSeparator>,
],
[
'EGFR',
'L718V',
'Non-Small Cell Lung Cancer',
<div>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_CURRENTLY_IN_ONCOKB}:
</div>
<div>Osimertinib (Level R2), Afatinib (Level 4)</div>
<br></br>
<div style={{ fontStyle: 'italic' }}>
{DRUGS_PROMOTED_IN_ONCOKB}:
</div>
<div>Afatinib (Level 3A)</div>
</div>,
'4',
'3A',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<Linkout link="https://www.sciencedirect.com/science/article/pii/S2666621923000133">
Ito, T., et al., Current Prob. in cancer, 2023
</Linkout>
<PMIDLink pmids="35365043, 31757379, 29571986" />
</WithSeparator>,
],
],
},
{
columnHeaderType: AnnotationColumnHeaderType.ADDITIONAL_SAME_LEVEL_DRUG,
title: `Updated therapeutic implications - Addition of therapy(s) associated with a tumor type-specific leveled alteration(s) (without changing the alteration's highest level of evidence)`,
content: [
[
'EGFR',
'Exon 20 in-frame insertions',
'Non-Small Cell Lung Cancer',
'1',
'Amivantamab, Mobocertinib (Level 1); Erlotinib, Afatinib, Gefitinib (Level R1)',
'Amivantamab + Chemotherapy (Level 1)',
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
<FdaApprovalLink
approval="Amivantamab + Carboplatin + Pemetrexed"
link="https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-amivantamab-vmjw-egfr-exon-20-insertion-mutated-non-small-cell-lung-cancer-indications"
/>
<PMIDLink pmids="37870976" />
</WithSeparator>,
],
],
},
],
newlyAddedGenes: ['MAP3K21', 'NQO1', 'POU2F2', 'RPS15'],
},
'02082024': {
news: [
<span>
Expand Down
12 changes: 6 additions & 6 deletions src/main/webapp/app/shared/links/PMIDLink.tsx
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
import React from 'react';
import {
getShortenPmidsFromList,
getShortenTextFromList,
} from 'app/shared/utils/Utils';
import { getShortenPmidsFromList } from 'app/shared/utils/Utils';

export const PMIDLink: React.FunctionComponent<{ pmids: string }> = props => {
export const PMIDLink: React.FunctionComponent<{
pmids: string;
wrapText?: boolean;
}> = props => {
return (
<span>
PMID:{' '}
Expand All @@ -14,7 +14,7 @@ export const PMIDLink: React.FunctionComponent<{ pmids: string }> = props => {
.join(' ')}`}
target="_blank"
rel="noopener noreferrer"
style={{ whiteSpace: 'nowrap' }}
style={{ whiteSpace: props.wrapText ? 'normal' : 'nowrap' }}
>
{props.pmids}
</a>
Expand Down
Binary file modified src/main/webapp/content/images/oncokb_summary.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading

0 comments on commit 68e1695

Please sign in to comment.