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Update news for v4.15 (#1095)
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‎src/main/webapp/app/config/constants.tsx

+1
Original file line numberDiff line numberDiff line change
@@ -793,6 +793,7 @@ export type DataRelease = {
793793
};
794794

795795
export const DATA_RELEASES: DataRelease[] = [
796+
{ date: '03212024', version: 'v4.15' },
796797
{ date: '02082024', version: 'v4.14' },
797798
{ date: '12212023', version: 'v4.13' },
798799
{ date: '12062023', version: 'v4.12' },

‎src/main/webapp/app/pages/newsPage/ChangedAnnotatonListItem.tsx

+23
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,8 @@ import {
66
GENE,
77
MUTATION,
88
CHANGED_ANNOTATION_DRUG_REMOVAL_COLUMNS,
9+
CHANGED_ANNOTATION_LEVEL_WITH_EVIDENCE_COLUMNS,
10+
CHANGED_ANNOTATION_SENSITIVITY_LEVEL_COLUMNS,
911
} from 'app/pages/newsPage/NewsPageContent';
1012
import { SimpleTable, SimpleTableRow } from 'app/components/SimpleTable';
1113
import { Row } from 'react-bootstrap';
@@ -25,7 +27,10 @@ export enum AnnotationColumnHeaderType {
2527
DRUG,
2628
ADDITIONAL_SAME_LEVEL_DRUG,
2729
ADDITIONAL_DIFF_LEVEL_DRUG,
30+
ADDITIONAL_SENSITIVITY_LEVEL_DRUG,
2831
DRUG_REMOVAL,
32+
DEMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE,
33+
PROMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE,
2934
}
3035

3136
export const ChangedAnnotationListItem = (props: {
@@ -57,12 +62,30 @@ export const ChangedAnnotationListItem = (props: {
5762
useOneLineRowClass = false;
5863
defaultTitle = 'Changed Annotation';
5964
break;
65+
case AnnotationColumnHeaderType.ADDITIONAL_SENSITIVITY_LEVEL_DRUG:
66+
annotationColumnHeader = CHANGED_ANNOTATION_SENSITIVITY_LEVEL_COLUMNS;
67+
useOneLineRowClass = false;
68+
defaultTitle =
69+
'Updated therapeutic implications - Addition of sensitivity-associated therapy(s) for an alteration(s) with a tumor type-specific resistance level of evidence';
70+
break;
6071
case AnnotationColumnHeaderType.DRUG_REMOVAL:
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annotationColumnHeader = CHANGED_ANNOTATION_DRUG_REMOVAL_COLUMNS;
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useOneLineRowClass = false;
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defaultTitle =
6475
'Updated therapeutic implications - Removal of therapie(s) and changed tumor type-specific level of evidence for an alteration(s)';
6576
break;
77+
case AnnotationColumnHeaderType.PROMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE:
78+
annotationColumnHeader = CHANGED_ANNOTATION_LEVEL_WITH_EVIDENCE_COLUMNS;
79+
useOneLineRowClass = false;
80+
defaultTitle =
81+
'Updated therapeutic implications - Promotion of tumor type-specific level of evidence for an alteration(s)';
82+
break;
83+
case AnnotationColumnHeaderType.DEMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE:
84+
annotationColumnHeader = CHANGED_ANNOTATION_LEVEL_WITH_EVIDENCE_COLUMNS;
85+
useOneLineRowClass = false;
86+
defaultTitle =
87+
'Updated therapeutic implications - Demotion of tumor type-specific level of evidence for an alteration(s)';
88+
break;
6689
case AnnotationColumnHeaderType.LEVEL:
6790
default:
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annotationColumnHeader = CHANGED_ANNOTATION_LEVEL_COLUMNS;

‎src/main/webapp/app/pages/newsPage/NewsPage.tsx

+1
Original file line numberDiff line numberDiff line change
@@ -91,6 +91,7 @@ export default class NewsPage extends React.Component<{
9191
<CitationText />
9292
</div>
9393
<div className="mt-2">
94+
<NewsList date={'03212024'} />
9495
<NewsList date={'02082024'} />
9596
<NewsList date={'01172024'} />
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<NewsList date={'12212023'} />

‎src/main/webapp/app/pages/newsPage/NewsPageContent.tsx

+262
Original file line numberDiff line numberDiff line change
@@ -67,6 +67,7 @@ export const MUTATION = 'Mutation';
6767
export const CANCER_TYPE = 'Cancer Type';
6868
export const DRUG = 'Drug';
6969
export const LEVEL = 'Level';
70+
export const LEVELS = 'Level(s)';
7071
export const DRUGS = 'Drug(s)';
7172
export const EVIDENCE = 'Evidence';
7273
export const PREVIOUS_LEVEL = 'Previous Level';
@@ -80,6 +81,10 @@ export const PREVIOUS_LEVEL_OF_EVIDENCE = 'Previous Level of Evidence';
8081
export const DRUGS_ADDED_TO_ONCOKB = `Drug(s) added to ${ONCOKB_TM}`;
8182
export const DRUGS_CURRENTLY_IN_ONCOKB = `Drug(s) currently in ${ONCOKB_TM}`;
8283
export const DRUGS_REMOVED_FROM_ONCOKB = `Drug(s) removed from ${ONCOKB_TM}`;
84+
export const DRUGS_DEMOTED_IN_ONCOKB = `Drug(s) demoted in ${ONCOKB_TM}`;
85+
export const DRUGS_PROMOTED_IN_ONCOKB = `Drug(s) promoted in ${ONCOKB_TM}`;
86+
export const CURRENT_SENSITIVITY_LEVEL = 'Current Sensitivity Level';
87+
export const CURRENT_RESISTANCE_LEVEL = 'Current Resistance Level';
8388
export const PREVIOUS_BIOMARKER_ASSOCIATION = 'Previous Biomarker Association';
8489
export const CURRENT_BIOMARKER_ASSOCIATION = 'Current Biomarker Association';
8590

@@ -114,6 +119,16 @@ export const CHANGED_ANNOTATION_LEVEL_COLUMNS = [
114119
{ name: REASON },
115120
];
116121

122+
export const CHANGED_ANNOTATION_LEVEL_WITH_EVIDENCE_COLUMNS = [
123+
{ name: GENE },
124+
{ name: MUTATION },
125+
{ name: CANCER_TYPE },
126+
{ name: DRUGS },
127+
{ name: PREVIOUS_LEVEL },
128+
{ name: CURRENT_LEVEL },
129+
{ name: EVIDENCE },
130+
];
131+
117132
export const CHANGED_ANNOTATION_DRUG_COLUMNS = [
118133
{ name: LEVEL },
119134
{ name: GENE },
@@ -156,6 +171,17 @@ export const CHANGED_ANNOTATION_DRUG_REMOVAL_COLUMNS = [
156171
{ name: EVIDENCE },
157172
];
158173

174+
export const CHANGED_ANNOTATION_SENSITIVITY_LEVEL_COLUMNS = [
175+
{ name: GENE },
176+
{ name: MUTATION },
177+
{ name: CANCER_TYPE },
178+
{ name: DRUGS_CURRENTLY_IN_ONCOKB },
179+
{ name: DRUGS_ADDED_TO_ONCOKB },
180+
{ name: CURRENT_SENSITIVITY_LEVEL },
181+
{ name: CURRENT_RESISTANCE_LEVEL },
182+
{ name: EVIDENCE },
183+
];
184+
159185
export const CDX_COLUMNS = [
160186
{ name: LEVEL },
161187
{ name: GENE },
@@ -212,6 +238,242 @@ const EVIDENCE_COLUMN_SEPARATOR = '; ';
212238
// https://stackoverflow.com/questions/41947168/is-it-possible-to-use-keyof-operator-on-literals-instead-of-interfaces
213239

214240
export const NEWS_BY_DATE: { [date: string]: NewsData } = {
241+
'03212024': {
242+
priorityNews: [
243+
<span>
244+
Updated therapeutic implications - New alteration(s) with a tumor
245+
type-specific level of evidence
246+
<Row className={'overflow-auto'}>
247+
<table className="table">
248+
<thead>
249+
<tr>
250+
<th>{LEVELS}</th>
251+
<th>{GENE}</th>
252+
<th>{MUTATION}</th>
253+
<th>{CANCER_TYPE}</th>
254+
<th>{DRUGS}</th>
255+
<th>{EVIDENCE}</th>
256+
</tr>
257+
</thead>
258+
<tbody>
259+
<tr>
260+
<td>3A</td>
261+
<td rowSpan={2}>
262+
<GenePageLink hugoSymbol="EGFR" />
263+
</td>
264+
<td rowSpan={2}>
265+
<AlterationPageLink hugoSymbol="EGFR" alteration="L718Q" />
266+
</td>
267+
<td rowSpan={2}>Non-Small Cell Lung Cancer</td>
268+
<td>Afatinib</td>
269+
<td>
270+
<PMIDLink pmids="32146032, 32193290, 31315676" wrapText />
271+
</td>
272+
</tr>
273+
<tr>
274+
<td>R2</td>
275+
<td>Osimertinib</td>
276+
<td>
277+
<PMIDLink
278+
pmids="27257132, 29506987, 33937055, 31205925, 34926262, 31315676, 32146032"
279+
wrapText
280+
/>
281+
</td>
282+
</tr>
283+
<tr>
284+
<td>R2</td>
285+
<td>
286+
<GenePageLink hugoSymbol="EGFR" />
287+
</td>
288+
<td>
289+
<AlterationPageLink hugoSymbol="EGFR" alteration="L792F" />
290+
</td>
291+
<td>Non-Small Cell Lung Cancer</td>
292+
<td>Osimertinib</td>
293+
<td>
294+
<PMIDLink
295+
pmids="35932642, 28093244, 29506987, 35422503"
296+
wrapText
297+
/>
298+
</td>
299+
</tr>
300+
</tbody>
301+
</table>
302+
</Row>
303+
</span>,
304+
],
305+
changedAnnotations: [
306+
{
307+
columnHeaderType:
308+
AnnotationColumnHeaderType.ADDITIONAL_SENSITIVITY_LEVEL_DRUG,
309+
content: [
310+
[
311+
'EGFR',
312+
'G724S',
313+
'Non-Small Cell Lung Cancer',
314+
'Osimertinib (Level R2)',
315+
'Afatinib (Level 3A)',
316+
'3A',
317+
'R2',
318+
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
319+
<PMIDLink
320+
pmids="32093857, 35979997, 33209641, 34590038, 30405134"
321+
wrapText
322+
/>
323+
</WithSeparator>,
324+
],
325+
],
326+
},
327+
{
328+
columnHeaderType:
329+
AnnotationColumnHeaderType.DEMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE,
330+
title:
331+
'Updated therapeutic implications - Demotion of tumor type-specific level of evidence for an alteration',
332+
content: [
333+
[
334+
'AKT1',
335+
'Oncogenic Mutations (excluding E17K, which remains Level 1)',
336+
'Breast Cancer',
337+
'Capivasertib + Fulvestrant',
338+
'1',
339+
'2',
340+
<span>
341+
To adhere to the{' '}
342+
<Linkout link="https://www.accessdata.fda.gov/drugsatfda_docs/label/2023/218197s000lbl.pdf">
343+
FDA-drug label
344+
</Linkout>{' '}
345+
and{' '}
346+
<Linkout link="https://info.foundationmedicine.com/hubfs/FMI%20Labels/FoundationOne_CDx_Label_Technical_Info.pdf">
347+
CDx
348+
</Linkout>{' '}
349+
for Capivasertib, Level 1 assignment will be only for AKT1 E17K
350+
detected by the FoundationOne CDx test. All other AKT1 oncogenic
351+
mutations are Level 2 per their inclusion in the NCCN Breast
352+
Cancer Guidelines V2.2024
353+
</span>,
354+
],
355+
[
356+
'PIK3CA',
357+
'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)',
358+
'Breast Cancer',
359+
<div>
360+
<div style={{ fontStyle: 'italic' }}>
361+
{DRUGS_CURRENTLY_IN_ONCOKB}:
362+
</div>
363+
<div>
364+
Capivasertib + Fulvestrant (Level 1), Alpelisib + Fulvestrant
365+
(Level 2){' '}
366+
</div>
367+
<br></br>
368+
<div style={{ fontStyle: 'italic' }}>
369+
{DRUGS_DEMOTED_IN_ONCOKB}:
370+
</div>
371+
<div>Capivasertib + Fulvestrant (Level 2)</div>
372+
</div>,
373+
'1',
374+
'2',
375+
<span>
376+
To adhere to the{' '}
377+
<Linkout link="https://www.accessdata.fda.gov/drugsatfda_docs/label/2023/218197s000lbl.pdf">
378+
FDA-drug label
379+
</Linkout>{' '}
380+
and{' '}
381+
<Linkout link="https://info.foundationmedicine.com/hubfs/FMI%20Labels/FoundationOne_CDx_Label_Technical_Info.pdf">
382+
CDx
383+
</Linkout>{' '}
384+
for Capivasertib, Level 1 assignment will be only for the PIK3CA
385+
alterations detected by the FoundationOne CDx test. All other
386+
PIK3CA oncogenic mutations are Level 2 per their inclusion in the
387+
NCCN Breast Cancer Guidelines V2.2024
388+
</span>,
389+
],
390+
[
391+
'FGFR1',
392+
'Amplification',
393+
'Lung Squamous Cell Carcinoma',
394+
'Erdafitinib',
395+
'3A',
396+
'No Level',
397+
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
398+
<span>
399+
Limited response rate to EGFR inhibitors for FGFR1-amplified
400+
lung squamous cell carcinoma; Discontinuation of infigratinib
401+
</span>
402+
<PMIDLink pmids={'37909331, 37606995'} />
403+
</WithSeparator>,
404+
],
405+
],
406+
},
407+
{
408+
columnHeaderType:
409+
AnnotationColumnHeaderType.PROMOTION_TUMOR_TYPE_SPECIFIC_EVIDENCE,
410+
title:
411+
'Updated therapeutic implications - Promotion of tumor type-specific level of evidence for an alteration',
412+
content: [
413+
[
414+
'KRAS',
415+
'G12C',
416+
'Ampullary Cancer',
417+
'Sotorasib, Adagrasib',
418+
'3B',
419+
'2',
420+
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
421+
<span>
422+
Inclusion in NCCN Ampullary Adenocarcinoma Guidelines V1.2024
423+
</span>
424+
<PMIDLink pmids="32955176" />
425+
</WithSeparator>,
426+
],
427+
[
428+
'EGFR',
429+
'L718V',
430+
'Non-Small Cell Lung Cancer',
431+
<div>
432+
<div style={{ fontStyle: 'italic' }}>
433+
{DRUGS_CURRENTLY_IN_ONCOKB}:
434+
</div>
435+
<div>Osimertinib (Level R2), Afatinib (Level 4)</div>
436+
<br></br>
437+
<div style={{ fontStyle: 'italic' }}>
438+
{DRUGS_PROMOTED_IN_ONCOKB}:
439+
</div>
440+
<div>Afatinib (Level 3A)</div>
441+
</div>,
442+
'4',
443+
'3A',
444+
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
445+
<Linkout link="https://www.sciencedirect.com/science/article/pii/S2666621923000133">
446+
Ito, T., et al., Current Prob. in cancer, 2023
447+
</Linkout>
448+
<PMIDLink pmids="35365043, 31757379, 29571986" />
449+
</WithSeparator>,
450+
],
451+
],
452+
},
453+
{
454+
columnHeaderType: AnnotationColumnHeaderType.ADDITIONAL_SAME_LEVEL_DRUG,
455+
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)`,
456+
content: [
457+
[
458+
'EGFR',
459+
'Exon 20 in-frame insertions',
460+
'Non-Small Cell Lung Cancer',
461+
'1',
462+
'Amivantamab, Mobocertinib (Level 1); Erlotinib, Afatinib, Gefitinib (Level R1)',
463+
'Amivantamab + Chemotherapy (Level 1)',
464+
<WithSeparator separator={EVIDENCE_COLUMN_SEPARATOR}>
465+
<FdaApprovalLink
466+
approval="Amivantamab + Carboplatin + Pemetrexed"
467+
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"
468+
/>
469+
<PMIDLink pmids="37870976" />
470+
</WithSeparator>,
471+
],
472+
],
473+
},
474+
],
475+
newlyAddedGenes: ['MAP3K21', 'NQO1', 'POU2F2', 'RPS15'],
476+
},
215477
'02082024': {
216478
news: [
217479
<span>

‎src/main/webapp/app/shared/links/PMIDLink.tsx

+6-6
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
import React from 'react';
2-
import {
3-
getShortenPmidsFromList,
4-
getShortenTextFromList,
5-
} from 'app/shared/utils/Utils';
2+
import { getShortenPmidsFromList } from 'app/shared/utils/Utils';
63

7-
export const PMIDLink: React.FunctionComponent<{ pmids: string }> = props => {
4+
export const PMIDLink: React.FunctionComponent<{
5+
pmids: string;
6+
wrapText?: boolean;
7+
}> = props => {
88
return (
99
<span>
1010
PMID:{' '}
@@ -14,7 +14,7 @@ export const PMIDLink: React.FunctionComponent<{ pmids: string }> = props => {
1414
.join(' ')}`}
1515
target="_blank"
1616
rel="noopener noreferrer"
17-
style={{ whiteSpace: 'nowrap' }}
17+
style={{ whiteSpace: props.wrapText ? 'normal' : 'nowrap' }}
1818
>
1919
{props.pmids}
2020
</a>

‎src/main/webapp/content/images/oncokb_summary.png

-2.79 KB
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