From 594f8a8b9401021616e434cbac68d6fea2a696fa Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Fri, 22 Dec 2023 15:33:37 +0100
Subject: [PATCH 1/2] feat: deprecation warning for PP3_strong + PM1_strong
 (#324)

---
 .../components/SeqvarDetails/ClinsigCard.vue  | 19 ++++++++++++++++++-
 frontend/src/lib/acmgSeqVar.ts                |  2 ++
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/frontend/src/components/SeqvarDetails/ClinsigCard.vue b/frontend/src/components/SeqvarDetails/ClinsigCard.vue
index cb2f53d1..519f3ed6 100644
--- a/frontend/src/components/SeqvarDetails/ClinsigCard.vue
+++ b/frontend/src/components/SeqvarDetails/ClinsigCard.vue
@@ -17,6 +17,7 @@ import {
   ACMG_EVIDENCE_LEVELS_PATHOGENIC,
   ALL_ACMG_CRITERIA,
   AcmgCriteria,
+  AcmgEvidenceLevel,
   Presence
 } from '@/lib/acmgSeqVar'
 import { type Seqvar } from '@/lib/genomicVars'
@@ -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. */
@@ -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.Strong &&
+    acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PM1).presence === Presence.Present &&
+    acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PM1).evidenceLevel ===
+      AcmgEvidenceLevel.Strong
+  ) {
+    result.push(Conflict.Pp3StrongPm1Strong)
+  }
   return result
 })
 
@@ -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-->
diff --git a/frontend/src/lib/acmgSeqVar.ts b/frontend/src/lib/acmgSeqVar.ts
index ddda8c35..d4708457 100644
--- a/frontend/src/lib/acmgSeqVar.ts
+++ b/frontend/src/lib/acmgSeqVar.ts
@@ -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'
 }
@@ -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
 ]

From db0acbdd8a14270a391e467b9da3c27b689c48a6 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Fri, 22 Dec 2023 15:38:42 +0100
Subject: [PATCH 2/2] wip

---
 frontend/src/components/CaseInformationCard.vue       | 2 +-
 frontend/src/components/SeqvarDetails/ClinsigCard.vue | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/frontend/src/components/CaseInformationCard.vue b/frontend/src/components/CaseInformationCard.vue
index ba3b98c6..4b37e026 100644
--- a/frontend/src/components/CaseInformationCard.vue
+++ b/frontend/src/components/CaseInformationCard.vue
@@ -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>
diff --git a/frontend/src/components/SeqvarDetails/ClinsigCard.vue b/frontend/src/components/SeqvarDetails/ClinsigCard.vue
index 519f3ed6..0eb1db90 100644
--- a/frontend/src/components/SeqvarDetails/ClinsigCard.vue
+++ b/frontend/src/components/SeqvarDetails/ClinsigCard.vue
@@ -131,10 +131,10 @@ const currentConflicts = computed<Conflict[]>(() => {
   if (
     acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PP3).presence === Presence.Present &&
     acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PP3).evidenceLevel ===
-      AcmgEvidenceLevel.Strong &&
+      AcmgEvidenceLevel.PathogenicStrong &&
     acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PM1).presence === Presence.Present &&
     acmgRatingStore.acmgRating.getCriteriaState(AcmgCriteria.PM1).evidenceLevel ===
-      AcmgEvidenceLevel.Strong
+      AcmgEvidenceLevel.PathogenicStrong
   ) {
     result.push(Conflict.Pp3StrongPm1Strong)
   }