fix: Drop PP5 and BP6 criteria (#289)

backend/app/schemas/acmgseqvar.py

@@ -37,7 +37,6 @@ class Criteria(str, Enum):
     PP2 = "PP2"
     PP3 = "PP3"
     PP4 = "PP4"
-    PP5 = "PP5"
     BA1 = "BA1"
     BS1 = "BS1"
     BS2 = "BS2"
@@ -48,7 +47,6 @@ class Criteria(str, Enum):
     BP3 = "BP3"
     BP4 = "BP4"
     BP5 = "BP5"
-    BP6 = "BP6"
     BP7 = "BP7"
 
 

frontend/src/components/__tests__/SeqvarDetails/ClinsigCard.spec.ts

@@ -61,7 +61,7 @@ describe.concurrent('AcmgRating', async () => {
     const summarySheet = wrapper.findComponent(SummarySheet)
     expect(summarySheet.exists()).toBe(true)
     const switchers = wrapper.findAllComponents({ name: 'CriterionSwitch' })
-    expect(switchers.length).toBe(56)
+    expect(switchers.length).toBe(52)
 
     // click show failed button
     const btnShowFailed = wrapper.findAll('.show-failed')

frontend/src/lib/__tests__/acmgSeqVar.spec.ts

@@ -19,19 +19,19 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
     expect(AcmgCriteriaState.criteriaStates).toHaveProperty(StateSource.User)
 
     // Check keys of AcmgCriteriaState.criteriaStates[StateSource.Default]
-    expect(Object.keys(AcmgCriteriaState.criteriaStates[StateSource.Default]).length).toEqual(28)
+    expect(Object.keys(AcmgCriteriaState.criteriaStates[StateSource.Default]).length).toEqual(26)
     expect(AcmgCriteriaState.criteriaStates[StateSource.Default]).toHaveProperty(AcmgCriteria.PVS1)
 
     // Check keys of AcmgCriteriaState.criteriaStates[StateSource.InterVar]
-    expect(Object.keys(AcmgCriteriaState.criteriaStates[StateSource.InterVar]).length).toEqual(28)
+    expect(Object.keys(AcmgCriteriaState.criteriaStates[StateSource.InterVar]).length).toEqual(26)
     expect(AcmgCriteriaState.criteriaStates[StateSource.InterVar]).toHaveProperty(AcmgCriteria.PVS1)
 
     // Check keys of AcmgCriteriaState.criteriaStates[StateSource.Server]
-    expect(Object.keys(AcmgCriteriaState.criteriaStates[StateSource.Server]).length).toEqual(28)
+    expect(Object.keys(AcmgCriteriaState.criteriaStates[StateSource.Server]).length).toEqual(26)
     expect(AcmgCriteriaState.criteriaStates[StateSource.Server]).toHaveProperty(AcmgCriteria.PVS1)
 
     // Check keys of AcmgCriteriaState.criteriaStates[StateSource.User]
-    expect(Object.keys(AcmgCriteriaState.criteriaStates[StateSource.User]).length).toEqual(28)
+    expect(Object.keys(AcmgCriteriaState.criteriaStates[StateSource.User]).length).toEqual(26)
     expect(AcmgCriteriaState.criteriaStates[StateSource.User]).toHaveProperty(AcmgCriteria.PVS1)
   })
 
@@ -319,19 +319,19 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
     expect(criteriaStates).toHaveProperty(StateSource.User)
 
     // Check keys of AcmgCriteriaState.criteriaStates[StateSource.Default]
-    expect(Object.keys(criteriaStates[StateSource.Default]).length).toEqual(28)
+    expect(Object.keys(criteriaStates[StateSource.Default]).length).toEqual(26)
     expect(criteriaStates[StateSource.Default]).toHaveProperty(AcmgCriteria.PVS1)
 
     // Check keys of AcmgCriteriaState.criteriaStates[StateSource.InterVar]
-    expect(Object.keys(criteriaStates[StateSource.InterVar]).length).toEqual(28)
+    expect(Object.keys(criteriaStates[StateSource.InterVar]).length).toEqual(26)
     expect(criteriaStates[StateSource.InterVar]).toHaveProperty(AcmgCriteria.PVS1)
 
     // Check keys of AcmgCriteriaState.criteriaStates[StateSource.Server]
-    expect(Object.keys(criteriaStates[StateSource.Server]).length).toEqual(28)
+    expect(Object.keys(criteriaStates[StateSource.Server]).length).toEqual(26)
     expect(criteriaStates[StateSource.Server]).toHaveProperty(AcmgCriteria.PVS1)
 
     // Check keys of AcmgCriteriaState.criteriaStates[StateSource.User]
-    expect(Object.keys(criteriaStates[StateSource.User]).length).toEqual(28)
+    expect(Object.keys(criteriaStates[StateSource.User]).length).toEqual(26)
     expect(criteriaStates[StateSource.User]).toHaveProperty(AcmgCriteria.PVS1)
   })
 

frontend/src/lib/acmgSeqVar.ts

@@ -42,7 +42,6 @@ enum AcmgCriteria {
   PP2 = 'PP2',
   PP3 = 'PP3',
   PP4 = 'PP4',
-  PP5 = 'PP5',
   BA1 = 'BA1',
   BS1 = 'BS1',
   BS2 = 'BS2',
@@ -53,7 +52,6 @@ enum AcmgCriteria {
   BP3 = 'BP3',
   BP4 = 'BP4',
   BP5 = 'BP5',
-  BP6 = 'BP6',
   BP7 = 'BP7'
 }
 
@@ -74,7 +72,6 @@ const ALL_ACMG_CRITERIA = [
   AcmgCriteria.PP2,
   AcmgCriteria.PP3,
   AcmgCriteria.PP4,
-  AcmgCriteria.PP5,
   AcmgCriteria.BA1,
   AcmgCriteria.BS1,
   AcmgCriteria.BS2,
@@ -85,7 +82,6 @@ const ALL_ACMG_CRITERIA = [
   AcmgCriteria.BP3,
   AcmgCriteria.BP4,
   AcmgCriteria.BP5,
-  AcmgCriteria.BP6,
   AcmgCriteria.BP7
 ]
 
@@ -224,15 +220,6 @@ const ACMG_CRITERIA_DEFS: Map<AcmgCriteria, CriteriaDefinition> = new Map(
       description: `Patient's phenotype or family history is highly specific for a disease with a single 
         genetic etiology.`
     },
-    {
-      criteria: AcmgCriteria.PP5,
-      defaultEvidenceLevel: AcmgEvidenceLevel.PathogenicSupporting,
-      label: 'PP5',
-      hint: 'reliable source: pathogenic',
-      description: `Reputable source recently reports variant as pathogenic, but the evidence is not available 
-        to the laboratoryto perform an independent evaluation. Note: Not recommended to use anymore, 
-        use PS3 and PS4 at different levels of evidence.`
-    },
     {
       criteria: AcmgCriteria.BA1,
       defaultEvidenceLevel: AcmgEvidenceLevel.BenignStandalone,
@@ -309,14 +296,6 @@ const ACMG_CRITERIA_DEFS: Map<AcmgCriteria, CriteriaDefinition> = new Map(
       hint: 'different gene in other case',
       description: 'Variant found in a case with an alternate molecular basis for disease'
     },
-    {
-      criteria: AcmgCriteria.BP6,
-      defaultEvidenceLevel: AcmgEvidenceLevel.BenignSupporting,
-      label: 'BP6',
-      hint: 'reputable source: benign',
-      description:
-        'Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation'
-    },
     {
       criteria: AcmgCriteria.BP7,
       defaultEvidenceLevel: AcmgEvidenceLevel.BenignSupporting,
@@ -470,11 +449,6 @@ class MultiSourceAcmgCriteriaState {
         presence: Presence.Unknown,
         evidenceLevel: isDefault ? AcmgEvidenceLevel.PathogenicSupporting : AcmgEvidenceLevel.NotSet
       },
-      PP5: {
-        criteria: AcmgCriteria.PP5,
-        presence: Presence.Unknown,
-        evidenceLevel: isDefault ? AcmgEvidenceLevel.PathogenicSupporting : AcmgEvidenceLevel.NotSet
-      },
       BA1: {
         criteria: AcmgCriteria.BA1,
         presence: Presence.Unknown,
@@ -525,11 +499,6 @@ class MultiSourceAcmgCriteriaState {
         presence: Presence.Unknown,
         evidenceLevel: isDefault ? AcmgEvidenceLevel.BenignSupporting : AcmgEvidenceLevel.NotSet
       },
-      BP6: {
-        criteria: AcmgCriteria.BP6,
-        presence: Presence.Unknown,
-        evidenceLevel: isDefault ? AcmgEvidenceLevel.BenignSupporting : AcmgEvidenceLevel.NotSet
-      },
       BP7: {
         criteria: AcmgCriteria.BP7,
         presence: Presence.Unknown,

frontend/src/stores/__tests__/variantAcmgRating.spec.ts

@@ -37,7 +37,6 @@ const ExampleInterVarResponse = {
   pp2: false,
   pp3: false,
   pp4: false,
-  pp5: false,
   ba1: false,
   bs1: false,
   bs2: false,
@@ -48,7 +47,6 @@ const ExampleInterVarResponse = {
   bp3: false,
   bp4: false,
   bp5: false,
-  bp6: false,
   bp7: false
 }
 

frontend/src/stores/seqVarAcmgRating.ts

@@ -110,6 +110,10 @@ export const useSeqVarAcmgRatingStore = defineStore('seqVarAcmgRating', () => {
       const acmgRatingInterVarData = await response.json()
       // Go through the data and setPresense for each criteria
       for (const [criteriaId, value] of Object.entries(acmgRatingInterVarData)) {
+        // Skip pp5 and bp6 criteria as they are not used anymore
+        if (criteriaId === 'pp5' || criteriaId === 'bp6') {
+          continue
+        }
         const criteriaIdKey = criteriaId.toUpperCase() as keyof typeof AcmgCriteria
         if (value === true) {
           acmgRating.value.setPresence(
@@ -142,7 +146,6 @@ export const useSeqVarAcmgRatingStore = defineStore('seqVarAcmgRating', () => {
       const acmgRatingBackend = await acmgSeqVarClient.fetchAcmgRating(
         seqvar$.chrom + ':' + seqvar$.pos + ':' + seqvar$.del + ':' + seqvar$.ins
       )
-      console.log(acmgRatingBackend)
       if (acmgRatingBackend.acmg_rank?.criterias) {
         acmgRatingStatus.value = true
         // Go through the data and setPresense for each criteria

frontend/src/views/ACMGCriteriaDocs.vue

@@ -149,16 +149,6 @@ const mainBackgroundColor = computed(() => {
                 </p>
                 <p>Hint: Phenotype/pedigree match gene</p>
               </li>
-              <li>
-                <h3>PP5 - Reputable source reports variant as pathogenic</h3>
-                <p>
-                  Description: Reputable source recently reports variant as pathogenic, but the
-                  evidence is not available to the laboratory to perform an independent evaluation.
-                  Note: Not recommended to use anymore, use PS3 and PS4 at different levels of
-                  evidence.
-                </p>
-                <p>Hint: Reliable source: pathogenic</p>
-              </li>
             </ul>
           </div>
 
@@ -241,14 +231,6 @@ const mainBackgroundColor = computed(() => {
                 </p>
                 <p>Hint: Different gene in other case</p>
               </li>
-              <li>
-                <h3>BP6 - Reputable source reports variant as benign</h3>
-                <p>
-                  Description: Reputable source recently reports variant as benign, but the evidence
-                  is not available to the laboratory to perform an independent evaluation
-                </p>
-                <p>Hint: Reputable source: benign</p>
-              </li>
               <li>
                 <h3>BP7 - Synonymous variant with no splicing impact</h3>
                 <p>

frontend/src/views/__tests__/ACMGCriteriaDoc.spec.ts

@@ -40,6 +40,6 @@ describe.concurrent('ACMGCriteriaDocs', async () => {
     expect(mainContent.exists()).toBe(true)
     expect(mainContent.html()).toMatch('PVS1')
     expect(mainContent.html()).toMatch('Benign Criteria')
-    expect(mainContent.html()).toMatch('BP6')
+    expect(mainContent.html()).toMatch('BP1')
   })
 })