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feat: deprecation warning for PP3_strong + PM1_strong (#324) #341

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merged 2 commits into from
Dec 22, 2023
Merged

feat: deprecation warning for PP3_strong + PM1_strong (#324) #341

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594f8a8
feat: deprecation warning for PP3_strong + PM1_strong (#324)
holtgrewe Dec 22, 2023
db0acbd
wip
holtgrewe Dec 22, 2023
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2 changes: 1 addition & 1 deletion frontend/src/components/CaseInformationCard.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@ watch(
disease genes ranked by their CADA score. Also, you will see the rank in the details
section of each gene.
</p>
<p class="text-body-2 pb-3" v-if="caseStore.storageMode === StorageMode.Local">
<p v-if="caseStore.storageMode === StorageMode.Local" class="text-body-2 pb-3">
As you are not logged in, we will store the case information in the local browser
storage.
</p>
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19 changes: 18 additions & 1 deletion frontend/src/components/SeqvarDetails/ClinsigCard.vue
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Expand Up @@ -17,6 +17,7 @@ import {
ACMG_EVIDENCE_LEVELS_PATHOGENIC,
ALL_ACMG_CRITERIA,
AcmgCriteria,
AcmgEvidenceLevel,
Presence
} from '@/lib/acmgSeqVar'
import { type Seqvar } from '@/lib/genomicVars'
Expand Down Expand Up @@ -100,7 +101,9 @@ enum Conflict {
/** PVS1 vs. PM4. */
Pvs1Pm4 = 'pvs1_pm4',
/** PVS1 vs. PP3. */
Pvs1Pp3 = 'pvs1_pp3'
Pvs1Pp3 = 'pvs1_pp3',
/** PP3_strong vs. PM1_strong. */
Pp3StrongPm1Strong = 'pp3_strong_pm1_strong'
}

/** Currently detected conflicts. */
Expand All @@ -124,6 +127,17 @@ const currentConflicts = computed<Conflict[]>(() => {
) {
result.push(Conflict.Pvs1Pp3)
}
// Check for combination of PP3_strong and PM1_strong which is discouraged by Pejaver et al. (2022).
if (
acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PP3).presence === Presence.Present &&
acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PP3).evidenceLevel ===
AcmgEvidenceLevel.PathogenicStrong &&
acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PM1).presence === Presence.Present &&
acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PM1).evidenceLevel ===
AcmgEvidenceLevel.PathogenicStrong
) {
result.push(Conflict.Pp3StrongPm1Strong)
}
return result
})

Expand Down Expand Up @@ -287,6 +301,9 @@ onMounted(async () => {
<li v-if="currentConflicts.includes(Conflict.Pvs1Pp3)">
PVS1 and PP3 cannot be applied at the same time.
</li>
<li v-if="currentConflicts.includes(Conflict.Pp3StrongPm1Strong)">
PP3_strong and PM1_strong should not be applied at the same time.
</li>
</ul>
</v-alert>
<!-- Actual criteria-->
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2 changes: 2 additions & 0 deletions frontend/src/lib/acmgSeqVar.ts
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Expand Up @@ -6,6 +6,7 @@ export enum AcmgEvidenceLevel {
PathogenicSupporting = 'Pathogenic Supporting',
BenignStandalone = 'Benign Standalone',
BenignStrong = 'Benign Strong',
BenignModerate = 'Benign Moderate',
BenignSupporting = 'Benign Supporting',
NotSet = 'Not Set'
}
Expand All @@ -21,6 +22,7 @@ export const ACMG_EVIDENCE_LEVELS_PATHOGENIC = [
/** Array of benign evidence levels. */
export const ACMG_EVIDENCE_LEVELS_BENIGN = [
AcmgEvidenceLevel.BenignStandalone,
AcmgEvidenceLevel.BenignModerate,
AcmgEvidenceLevel.BenignStrong,
AcmgEvidenceLevel.BenignSupporting
]
Expand Down
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