Merge pull request #578 from bcgsc/feat/DEVSU-2465-rapid-intersecttmb…

…score [DEVSU-2465] add intersectTMBscore to EditDialog
bcgsc · Jan 7, 2025 · 27eb944 · 27eb944
2 parents 7884233 + f2a934d
commit 27eb944
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Showing 5 changed files with 65 additions and 22 deletions.
diff --git a/app/common.d.ts b/app/common.d.ts
@@ -308,7 +308,6 @@ type TmburType = {
   comments: string;
   genomeSnvTmb: number;
   genomeIndelTmb: number;
-  tmbHidden: boolean;
   kbCategory: string | null;
   kbMatches: KbMatchType[];
   msiScore: number;
@@ -318,6 +317,7 @@ type TmburType = {
   proteinIndelTmb: number;
   proteinSnvs: number;
   proteinSnvTmb: number;
+  tmbHidden: boolean;
   totalGenomeIndels: number;
   totalGenomeSnvs: number;
   tumour: string;

diff --git a/app/components/TumourSummaryEdit/index.scss b/app/components/TumourSummaryEdit/index.scss
@@ -7,6 +7,15 @@
     margin: 12px 0;
   }
 
+  &__number-field {
+    margin: 12px 0;
+    input::-webkit-outer-spin-button,
+    input::-webkit-inner-spin-button {
+      -webkit-appearance: none;
+      margin: 0;
+    }
+  }
+
   &__check-box {
     color: gray;
     margin-top: -12px;

diff --git a/app/components/TumourSummaryEdit/index.tsx b/app/components/TumourSummaryEdit/index.tsx
@@ -92,6 +92,7 @@ const TumourSummaryEdit = ({
         tumourContent: report.tumourContent,
         subtyping: report.subtyping,
         captiv8Score: report.captiv8Score,
+        genomeTmb: report.genomeTmb,
       });
     }
   }, [report]);
@@ -398,7 +399,7 @@ const TumourSummaryEdit = ({
     if (newReportData) {
       const captiv8Section = (
         <TextField
-          className="tumour-dialog__text-field"
+          className="tumour-dialog__number-field"
           label={`${reportType === 'rapid' ? 'Preliminary ' : ''}CAPTIV-8 Score`}
           value={newReportData.captiv8Score}
           name="captiv8Score"
@@ -436,7 +437,21 @@ const TumourSummaryEdit = ({
         );
       }
       if (reportType === 'rapid') {
-        return captiv8Section;
+        return (
+          <>
+            <TextField
+              className="tumour-dialog__number-field"
+              label="Intersect TMB Score"
+              value={newReportData?.genomeTmb ?? ''}
+              name="genomeTmb"
+              onChange={handleReportChange}
+              variant="outlined"
+              fullWidth
+              type="number"
+            />
+            {captiv8Section}
+          </>
+        );
       }
     }
     return null;
@@ -480,7 +495,7 @@ const TumourSummaryEdit = ({
   const tCellCd8DataSection = useMemo(() => (
     <>
       <TextField
-        className="tumour-dialog__text-field"
+        className="tumour-dialog__number-field"
         label="CD8+ T Cell Score"
         value={newTCellCd8Data?.score ?? null}
         name="score"
@@ -490,7 +505,7 @@ const TumourSummaryEdit = ({
         type="number"
       />
       <TextField
-        className="tumour-dialog__text-field"
+        className="tumour-dialog__number-field"
         label="CD8+ T Cell Percentile"
         value={newTCellCd8Data?.percentile ?? null}
         name="percentile"
@@ -521,7 +536,7 @@ const TumourSummaryEdit = ({
         label={<div className="checkbox-label">Show/Hide CD8+ Percentile</div>}
       />
       <TextField
-        className="tumour-dialog__text-field"
+        className="tumour-dialog__number-field"
         label="Pediatric CD8+ T Cell Score"
         value={newTCellCd8Data?.pedsScore ?? null}
         name="pedsScore"
@@ -532,7 +547,7 @@ const TumourSummaryEdit = ({
         type="number"
       />
       <TextField
-        className="tumour-dialog__text-field"
+        className="tumour-dialog__number-field"
         label="Pediatric CD8+ T Cell Percentile"
         value={newTCellCd8Data?.pedsPercentile ?? null}
         name="pedsPercentile"
@@ -560,7 +575,7 @@ const TumourSummaryEdit = ({
   const mutBurDataSection = useMemo(() => (
     <>
       <TextField
-        className="tumour-dialog__text-field"
+        className="tumour-dialog__number-field"
         label="SV Burden (Count)"
         value={newMutationBurdenData?.qualitySvCount ?? null}
         name="qualitySvCount"
@@ -570,7 +585,7 @@ const TumourSummaryEdit = ({
         type="number"
       />
       <TextField
-        className="tumour-dialog__text-field"
+        className="tumour-dialog__number-field"
         label="SV Burden (Percentile)"
         value={newMutationBurdenData?.qualitySvPercentile ?? null}
         name="qualitySvPercentile"
@@ -606,7 +621,7 @@ const TumourSummaryEdit = ({
   const tmburMutBurSection = useMemo(() => (
     <>
       <TextField
-        className="tumour-dialog__text-field"
+        className="tumour-dialog__number-field"
         label="genomeSnvTmb"
         value={newTmburMutData?.genomeSnvTmb ?? null}
         name="genomeSnvTmb"
@@ -616,7 +631,7 @@ const TumourSummaryEdit = ({
         type="number"
       />
       <TextField
-        className="tumour-dialog__text-field"
+        className="tumour-dialog__number-field"
         label="genomeIndelTmb"
         value={newTmburMutData?.genomeIndelTmb ?? null}
         name="genomeIndelTmb"
@@ -626,7 +641,7 @@ const TumourSummaryEdit = ({
         type="number"
       />
       <TextField
-        className="tumour-dialog__text-field"
+        className="tumour-dialog__number-field"
         label="Adjusted TMB"
         value={newTmburMutData?.adjustedTmb ?? null}
         name="adjustedTmb"
@@ -669,7 +684,16 @@ const TumourSummaryEdit = ({
         label={<div className="checkbox-label">Show/Hide TMB Information</div>}
       />
     </>
-  ), [newTmburMutData?.genomeSnvTmb, newTmburMutData?.genomeIndelTmb, newTmburMutData?.adjustedTmb, newTmburMutData?.adjustedTmbComment, newTmburMutData?.tmbHidden, handleTmburChange, handleAdjustedTmbCommentChange, handleAdjustedTmbVisibleChange]);
+  ), [
+    newTmburMutData?.genomeSnvTmb,
+    newTmburMutData?.genomeIndelTmb,
+    newTmburMutData?.adjustedTmb,
+    newTmburMutData?.adjustedTmbComment,
+    newTmburMutData?.tmbHidden,
+    handleTmburChange,
+    handleAdjustedTmbCommentChange,
+    handleAdjustedTmbVisibleChange,
+  ]);
 
   return (
     <Dialog open={isOpen}>

diff --git a/app/context/ReportContext/types.d.ts b/app/context/ReportContext/types.d.ts
@@ -35,14 +35,20 @@ type UserRoleType = {
 
 type ReportType = {
   alternateIdentifier?: string;
-  pediatricIds?: string;
   analysisStartedAt: string | null;
+  appendix?: string;
   biopsyName?: string;
+  captiv8Score: number;
   createdBy?: UserType;
   expression_matrix: string;
+  genomeTmb?: number;
+  kbDiseaseMatch: string;
   kbVersion: string;
+  m1m2Score: number;
+  oncotreeTumourType: string;
   patientId: string;
-  patientInformation: PatientInformationType,
+  patientInformation: PatientInformationType;
+  pediatricIds?: string;
   ploidy: string;
   projects?: ProjectType[];
   reportVersion: string;
@@ -53,11 +59,6 @@ type ReportType = {
   tumourContent?: number;
   type: string;
   users: UserRoleType[];
-  oncotreeTumourType: string;
-  kbDiseaseMatch: string;
-  m1m2Score: number;
-  captiv8Score: number;
-  appendix?: string;
 } & RecordDefaults;
 
 type ReportContextType = {

diff --git a/app/views/ReportView/components/RapidSummary/index.tsx b/app/views/ReportView/components/RapidSummary/index.tsx
@@ -369,13 +369,22 @@ const RapidSummary = ({
         value:
           tmburMutBur?.adjustedTmbComment && !tmburMutBur.tmbHidden ? tmburMutBur.adjustedTmbComment : null,
       },
+      {
+        term: 'Intersect TMB Score',
+        value:
+          report?.genomeTmb ?? null,
+      },
       {
         term: 'MSI Status',
         value: msiStatus,
       },
     ]);
-  }, [microbial, primaryBurden, tmburMutBur, report.m1m2Score, report.sampleInfo, report.tumourContent, tCellCd8?.percentile, tCellCd8?.score, report.captiv8Score,
-    tCellCd8?.percentileHidden, tCellCd8, tCellCd8?.pedsScoreComment, tmburMutBur?.adjustedTmb, tmburMutBur?.tmbHidden, tCellCd8?.pedsScore, tCellCd8?.pedsPercentile]);
+  }, [
+    microbial, primaryBurden, tmburMutBur, tCellCd8,
+    report.m1m2Score, report.sampleInfo, report.tumourContent, report?.genomeTmb, report.captiv8Score,
+    tCellCd8?.percentile, tCellCd8?.score, tCellCd8?.percentileHidden, tCellCd8?.pedsScoreComment, tCellCd8?.pedsScore, tCellCd8?.pedsPercentile,
+    tmburMutBur?.adjustedTmb, tmburMutBur?.tmbHidden,
+  ]);
 
   const handleSign = useCallback(async (signed: boolean, updatedSignature: SignatureType) => {
     setIsSigned(signed);