Update bundle and processing

src/code_systems/loinc.test.ts

@@ -21,6 +21,7 @@ describe("LOINC", () => {
       classification: getSelectOptions(valueSet.classification),
       inheritance: getSelectOptions(valueSet.inheritance),
       zygosity: getSelectOptions(valueSet.zygosity),
+      reportFinding: getSelectOptions(valueSet.reportFinding),
       followUp: getSelectOptions(valueSet.followUp),
     };
 

src/code_systems/loinc.ts

@@ -21,6 +21,7 @@ export const variantCodes = async () => {
     classification: await getValueSetData("LL4034-6"),
     inheritance: await getValueSetData("LL3731-8"),
     zygosity: await getValueSetData("LL381-5"),
+    reportFinding: await getValueSetData("LL2431-6"),
     followUp: await getValueSetData("LL1037-2"),
   };
 };

src/code_systems/loincCodes.ts

@@ -6,6 +6,7 @@ type LoincCodes = {
   classification: ValueSet;
   inheritance: ValueSet;
   zygosity: ValueSet;
+  reportFinding: ValueSet;
   followUp: ValueSet;
 };
 
@@ -216,6 +217,60 @@ export const loincCodes: LoincCodes = {
       ],
     },
   },
+  reportFinding: {
+    resourceType: "ValueSet",
+    id: "LL2431-6-2.73",
+    meta: {
+      versionId: "1",
+      lastUpdated: "2022-08-08T12:57:53.978+00:00",
+    },
+    url: "http://loinc.org/vs/LL2431-6",
+    identifier: [
+      {
+        system: "urn:ietf:rfc:3986",
+        value: "urn:oid:1.3.6.1.4.1.12009.10.1.1595",
+      },
+    ],
+    version: "Loinc_2.73-2.73",
+    name: "Pos|Neg|Inconcl",
+    status: "active",
+    publisher: "Regenstrief Institute, Inc.",
+    contact: [
+      {
+        name: "Regenstrief Institute, Inc.",
+        telecom: [
+          {
+            system: "url",
+            value: "https://loinc.org",
+          },
+        ],
+      },
+    ],
+    copyright:
+      "This material contains content from LOINC (http://loinc.org). LOINC is copyright ©1995-2022, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.",
+    compose: {
+      include: [
+        {
+          system: "http://loinc.org",
+          version: "2.73",
+          concept: [
+            {
+              code: "LA6576-8",
+              display: "Positive",
+            },
+            {
+              code: "LA6577-6",
+              display: "Negative",
+            },
+            {
+              code: "LA9663-1",
+              display: "Inconclusive",
+            },
+          ],
+        },
+      ],
+    },
+  },
   followUp: {
     resourceType: "ValueSet",
     id: "LL1037-2",
@@ -285,6 +340,7 @@ export const loincSelect = {
   classification: getSelectOptions(loincCodes.classification),
   inheritance: getSelectOptions(loincCodes.inheritance),
   zygosity: getSelectOptions(loincCodes.zygosity),
+  reportFinding: getSelectOptions(loincCodes.reportFinding),
   followUp: getSelectOptions(loincCodes.followUp),
 };
 

src/code_systems/panelappCodes.ts

@@ -0,0 +1,114 @@
+import { RequiredCoding } from "./types";
+
+export const diseases: RequiredCoding[] = [
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R14",
+    display: "Acutely unwell children with a likely monogenic disorder",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R127",
+    display: "Long QT syndrome",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R128",
+    display: "Brugada syndrome and cardiac sodium channel disease",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R129",
+    display: "Catecholaminergic polymorphic VT",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R130",
+    display: "Short QT syndrome",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R131",
+    display: "Hypertrophic cardiomyopathy",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R134",
+    display: "Familial hypercholesterolaemia",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R184",
+    display: "Cystic fibrosis diagnostic test",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R59",
+    display: "Early onset or syndromic epilepsy",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R226",
+    display: "Inherited parathyroid cancer",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R207",
+    display: "Inherited ovarian cancer (without breast cancer)",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R211",
+    display: "Inherited polyposis and early onset colorectal cancer - germline testing",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R215",
+    display: "CDH1-related cancer syndrome",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R404",
+    display: "Testing of unaffected individuals for inherited cancer predisposition syndromes",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R224",
+    display: "Inherited renal cancer",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R364",
+    display: "DICER1-related cancer predisposition",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R367",
+    display: "Inherited pancreatic cancer",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R193",
+    display: "Cystic renal disease",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R173",
+    display: "Polycystic liver disease",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R65",
+    display: "Aminoglycoside exposure posing risk to hearing",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R27",
+    display: "Congenital malformation and dysmorphism syndromes - microarray and sequencing",
+  },
+  {
+    system: "http://panelapp.genomicsengland.co.uk/api/v1/entities",
+    code: "R29",
+    display: "Intellectual disability - microarray and sequencing",
+  },
+];

src/code_systems/snomedCodes.ts

@@ -27,62 +27,3 @@ export const sampleTypes: RequiredCoding[] = [
     display: "Venous blood specimen",
   },
 ];
-
-export const diseases: RequiredCoding[] = [
-  {
-    system: "http://snomed.info/sct",
-    code: "230387008",
-    display: "Benign occipital epilepsy of childhood - early onset variant",
-  },
-  {
-    system: "http://snomed.info/sct",
-    code: "5262007",
-    display: "Spinal muscular atrophy",
-  },
-  {
-    system: "http://snomed.info/sct",
-    code: "73297009",
-    display: "Muscular dystrophy",
-  },
-  {
-    system: "http://snomed.info/sct",
-    code: "190905008",
-    display: "Cystic fibrosis",
-  },
-  {
-    system: "http://snomed.info/sct",
-    code: "398036000",
-    display: "Familial hypercholesterolemia",
-  },
-  // top level SNOMED CT term for cancer
-  {
-    system: "http://snomed.info/sct",
-    code: "363346000",
-    display: "Malignant neoplastic disease",
-  },
-  {
-    system: "http://snomed.info/sct",
-    code: "432328008",
-    display: "Neuroblastoma",
-  },
-  {
-    system: "http://snomed.info/sct",
-    code: "771233008",
-    display: "Inflammatory myofibroblastic tumor",
-  },
-  {
-    system: "http://snomed.info/sct",
-    code: "253062001",
-    display: "Central nervous system tumor morphology",
-  },
-  {
-    system: "http://snomed.info/sct",
-    code: "255032005",
-    display: "Medullary thyroid carcinoma",
-  },
-  {
-    system: "http://snomed.info/sct",
-    code: "702785000",
-    display: "Large cell anaplastic lymphoma T cell and Null cell type",
-  },
-];

src/components/reports/FormDefaults.ts

@@ -11,19 +11,21 @@ export const initialValues: FormValues = {
     postCode: "WC1N 3BH",
   },
   patient: {
-    mrn: "969977",
+    mrn: "40388914",
+    nhsNumber: "8105688202",
+    familyNumber: "Z968769",
     firstName: "Donald",
     lastName: "Duck",
     dateOfBirth: "2012-03-04",
     gender: Patient.GenderEnum.Male,
-    familyNumber: "Z409929",
   },
   sample: {
     specimenCode: "19RG-183G0127",
     specimenType: "122555007",
     collectionDateTime: "04/06/2019 12:00",
     receivedDateTime: "04/06/2019 15:00",
-    reasonForTest: "230387008",
+    authorisedDateTime: "04/06/2019 15:30",
+    reasonForTest: "R59", // epilepsy
     reasonForTestText:
       "Sequence variant screening in Donald Duck because of epilepsy and atypical absences. " +
       "An SLC2A1 variant is suspected.",
@@ -37,7 +39,7 @@ export const initialValues: FormValues = {
         "Clinical features range from severe motor and cognitive impairment with marked choreoathetosis, " +
         "self-injurious behaviour and epileptic encephalopathy, to a milder course with moderate developmental delay, " +
         "complex stereotypies (facial dyskinesia) and mild epilepsy.",
-      genomicHGVS: "c.119G>T",
+      cDnaHgvs: "c.119G>T",
       inheritanceMethod: "LA24640-7", // Autosomal dominant
       classification: "LA26332-9", // Likely Pathogenic
       proteinHGVS: "p.(Gly40Val)",
@@ -71,6 +73,8 @@ export const initialValues: FormValues = {
       "Screening of 82 genes associated with severe delay and seizures " +
       "... Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 Genet Med) " +
       "/ACGS Best Practice guidelines (2019).",
+    genesTested: "ADSL, ALG13, ARHGEF9, ARX, ATP1A3, ATRX, BRAT1",
+    reportFinding: "LA6576-8", // Positive
     clinicalConclusion: "Confirms the diagnosis of Childhood-nset epileptic encephalopathy (EEOC).",
   },
 };
@@ -90,17 +94,19 @@ export const noValues: FormValues = {
   },
   patient: {
     mrn: "",
+    nhsNumber: "",
+    familyNumber: "",
     firstName: "",
     lastName: "",
     dateOfBirth: "",
     gender: undefined,
-    familyNumber: "",
   },
   sample: {
     specimenCode: "",
     specimenType: "",
     collectionDateTime: "",
     receivedDateTime: "",
+    authorisedDateTime: "",
     reasonForTest: "",
     reasonForTestText: "",
   },
@@ -112,11 +118,13 @@ export const noValues: FormValues = {
     followUp: "",
     furtherTesting: "",
     testMethodology: "",
+    genesTested: "",
     authorisingDate: "",
     authorisingScientist: "",
     authorisingScientistTitle: "",
     reportingDate: "",
     reportingScientist: "",
     reportingScientistTitle: "",
+    reportFinding: "",
   },
 };