diff --git a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt index c460da6..072b562 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt @@ -212,7 +212,7 @@ class ExtensionsTest { inner class UsingDnpmV2Datamodel { val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json" - val CLEAN_PATIENT_ID = "aca5a971-28be-4089-8128-0036a4fe6f1a" + val CLEAN_PATIENT_ID = "644bae7a-56f6-4ee8-b02f-c532e65af5b1" private fun fakeMtbFile(): Mtb { val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream diff --git a/src/test/resources/mv64e-mtb-fake-patient.json b/src/test/resources/mv64e-mtb-fake-patient.json index 291f22d..c8b8330 100644 --- a/src/test/resources/mv64e-mtb-fake-patient.json +++ b/src/test/resources/mv64e-mtb-fake-patient.json @@ -1,12 +1,13 @@ { "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "gender": { - "code": "male", - "display": "Männlich", + "code": "female", + "display": "Weiblich", "system": "Gender" }, - "birthDate": "1961-09-01", + "birthDate": "1994-05-25", + "dateOfDeath": "2018-05-25", "healthInsurance": { "type": { "code": "GKV", @@ -24,28 +25,28 @@ "municipalityCode": "12345" }, "age": { - "value": 63, + "value": 24, "unit": "Years" }, "vitalStatus": { - "code": "alive", - "display": "Lebend", + "code": "deceased", + "display": "Verstorben", "system": "dnpm-dip/patient/vital-status" } }, "episodesOfCare": [ { - "id": "5481850f-f266-4d2f-8fbc-6bb790680d8f", + "id": "fc02c478-86f6-4910-9ea1-8a0d1e435c83", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "period": { - "start": "2024-12-24" + "start": "2025-01-04" }, "diagnoses": [ { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", "type": "MTBDiagnosis" } ] @@ -53,12 +54,12 @@ ], "diagnoses": [ { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, - "recordedOn": "2023-03-01", + "recordedOn": "2016-01-25", "type": { "history": [ { @@ -67,35 +68,35 @@ "display": "Hauptdiagnose", "system": "dnpm-dip/mtb/diagnosis/type" }, - "date": "2023-03-01" + "date": "2016-01-25" } ] }, "code": { - "code": "C50.1", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", + "code": "C50.2", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm", "version": "2025" }, "topography": { - "code": "C50.1", - "display": "Zentraler Drüsenkörper der Brust", + "code": "C50.2", + "display": "Oberer innerer Quadrant der Brust", "system": "urn:oid:2.16.840.1.113883.6.43.1", "version": "Zweite Revision" }, "grading": { "history": [ { - "date": "2023-03-01", + "date": "2016-01-25", "codes": [ { - "code": "U", - "display": "U = unbekannt", + "code": "1", + "display": "1 = gut differenziert", "system": "https://www.basisdatensatz.de/feld/161/grading" }, { - "code": "2", - "display": "Diffuse astrocytoma", + "code": "4", + "display": "Glioblastoma", "system": "dnpm-dip/mtb/who-grading-cns-tumors", "version": "2021" } @@ -106,7 +107,7 @@ "staging": { "history": [ { - "date": "2023-03-01", + "date": "2016-01-25", "method": { "code": "clinical", "display": "Klinisch", @@ -114,11 +115,11 @@ }, "tnmClassification": { "tumor": { - "code": "T1", + "code": "T2", "system": "UICC" }, "nodes": { - "code": "N2", + "code": "N1", "system": "UICC" }, "metastasis": { @@ -128,8 +129,8 @@ }, "otherClassifications": [ { - "code": "unknown", - "display": "Unbekannt", + "code": "local", + "display": "Lokal", "system": "dnpm-dip/mtb/diagnosis/kds-tumor-spread" } ] @@ -137,8 +138,8 @@ ] }, "guidelineTreatmentStatus": { - "code": "unknown", - "display": "Unbekannt", + "code": "no-guidelines-available", + "display": "Keine Leitlinien vorhanden", "system": "dnpm-dip/mtb/diagnosis/guideline-treatment-status" }, "notes": [ @@ -148,28 +149,28 @@ ], "familyMemberHistories": [ { - "id": "f982b161-f8a3-4b5b-a390-1ef0d84efc1b", + "id": "ba866f34-5681-4446-b635-6ff90e4d03ab", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "relationship": { - "code": "EXT", - "display": "Verwandter weiteren Grades", + "code": "FAMMEMB", + "display": "Verwandter ersten Grades", "system": "dnpm-dip/mtb/family-meber-history/relationship-type" } } ], "guidelineTherapies": [ { - "id": "0c696b1a-d123-419b-9a6f-e79322392f4e", + "id": "9a89aea6-3305-49f3-94e2-dfe347989dec", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "reason": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", "type": "MTBDiagnosis" }, "therapyLine": 3, @@ -179,11 +180,11 @@ "system": "dnpm-dip/therapy/intent" }, "category": { - "code": "I", - "display": "Intraopterativ", + "code": "O", + "display": "Ohne Bezug zur operativen Therapie", "system": "dnpm-dip/therapy/category" }, - "recordedOn": "2025-06-24", + "recordedOn": "2025-07-04", "status": { "code": "stopped", "display": "Abgebrochen", @@ -195,62 +196,13 @@ "system": "dnpm-dip/therapy/status-reason" }, "period": { - "start": "2024-04-24", - "end": "2024-12-18" + "start": "2024-07-04", + "end": "2024-09-12" }, "medication": [ { - "code": "L01EX02", - "display": "Sorafenib", - "system": "http://fhir.de/CodeSystem/bfarm/atc", - "version": "2025" - } - ], - "notes": [ - "Notes on the therapy..." - ] - }, - { - "id": "da26f4c4-834e-4f6a-86eb-4df13c4a442f", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "reason": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", - "type": "MTBDiagnosis" - }, - "therapyLine": 4, - "intent": { - "code": "X", - "display": "Keine Angabe", - "system": "dnpm-dip/therapy/intent" - }, - "category": { - "code": "A", - "display": "Adjuvant", - "system": "dnpm-dip/therapy/category" - }, - "recordedOn": "2025-06-24", - "status": { - "code": "stopped", - "display": "Abgebrochen", - "system": "dnpm-dip/therapy/status" - }, - "statusReason": { - "code": "progression", - "display": "Progression", - "system": "dnpm-dip/therapy/status-reason" - }, - "period": { - "start": "2024-06-24", - "end": "2025-02-24" - }, - "medication": [ - { - "code": "L01EX13", - "display": "Gilteritinib", + "code": "L01FX26", + "display": "Mirvetuximab soravtansin", "system": "http://fhir.de/CodeSystem/bfarm/atc", "version": "2025" } @@ -262,25 +214,25 @@ ], "guidelineProcedures": [ { - "id": "09ac6bfb-05bb-4c8f-b65a-dae96407939c", + "id": "99831a57-e26e-45f4-a9d2-cf41f6ef6560", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "reason": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", "type": "MTBDiagnosis" }, - "therapyLine": 3, + "therapyLine": 7, "intent": { - "code": "X", - "display": "Keine Angabe", + "code": "K", + "display": "Kurativ", "system": "dnpm-dip/therapy/intent" }, "code": { - "code": "nuclear-medicine", - "display": "Nuklearmedizinische Therapie", + "code": "radio-therapy", + "display": "Strahlen-Therapie", "system": "dnpm-dip/mtb/procedure/type" }, "status": { @@ -293,49 +245,9 @@ "display": "Tod", "system": "dnpm-dip/therapy/status-reason" }, - "recordedOn": "2025-06-24", + "recordedOn": "2025-07-04", "period": { - "start": "2024-12-24" - }, - "notes": [ - "Notes on the therapeutic procedure..." - ] - }, - { - "id": "1d12955f-216f-4731-8a37-e2eca4c2a735", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "reason": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", - "type": "MTBDiagnosis" - }, - "therapyLine": 1, - "intent": { - "code": "S", - "display": "Sonstiges", - "system": "dnpm-dip/therapy/intent" - }, - "code": { - "code": "surgery", - "display": "OP", - "system": "dnpm-dip/mtb/procedure/type" - }, - "status": { - "code": "completed", - "display": "Abgeschlossen", - "system": "dnpm-dip/therapy/status" - }, - "statusReason": { - "code": "progression", - "display": "Progression", - "system": "dnpm-dip/therapy/status-reason" - }, - "recordedOn": "2025-06-24", - "period": { - "start": "2024-12-24" + "start": "2025-01-04" }, "notes": [ "Notes on the therapeutic procedure..." @@ -344,28 +256,28 @@ ], "performanceStatus": [ { - "id": "7cf3d19b-a537-47e4-b7f0-d324e8b1ad70", + "id": "6cc2bd40-4193-4814-aa30-54c6dd1dea7d", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, - "effectiveDate": "2025-06-24", + "effectiveDate": "2025-07-04", "value": { - "code": "1", - "display": "ECOG 1", + "code": "4", + "display": "ECOG 4", "system": "ECOG-Performance-Status" } } ], "specimens": [ { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "diagnosis": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", "type": "MTBDiagnosis" }, "type": { @@ -374,15 +286,15 @@ "system": "dnpm-dip/mtb/tumor-specimen/type" }, "collection": { - "date": "2025-06-24", + "date": "2025-07-04", "method": { - "code": "unknown", - "display": "Unbekannt", + "code": "cytology", + "display": "Zytologie", "system": "dnpm-dip/mtb/tumor-specimen/collection/method" }, "localization": { - "code": "unknown", - "display": "Unbekannt", + "code": "regional-lymph-nodes", + "display": "Regionäre Lymphknoten", "system": "dnpm-dip/mtb/tumor-specimen/collection/localization" } } @@ -390,9 +302,9 @@ ], "priorDiagnosticReports": [ { - "id": "0209a1fa-3948-4bc5-a2f5-988818057544", + "id": "e23f3cc9-19ea-477e-a72e-696618064e91", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "performer": { @@ -400,9 +312,9 @@ "display": "Molekular-Pathologie UKx", "type": "Institute" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, "type": { @@ -417,43 +329,43 @@ ], "histologyReports": [ { - "id": "1c51bb6f-b551-43a4-9923-6db7fe36440c", + "id": "138c56dc-b90a-4737-b89d-0422e9323cac", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "results": { "tumorMorphology": { - "id": "a177e88e-af76-45c8-ba93-e2f2339888a0", + "id": "79d857bc-0726-4f59-8add-995943f93670", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, "value": { - "code": "9719/3", - "display": "Nasales NK/T-Zell-Lymphom", + "code": "9372/3", + "display": "Entdifferenziertes Chordom", "system": "urn:oid:2.16.840.1.113883.6.43.1", "version": "Zweite Revision" }, "note": "Notes..." }, "tumorCellContent": { - "id": "32605a2f-4c5c-4f5a-9909-326955405fe0", + "id": "0fa34021-6083-49da-b176-2be816b77e4f", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, "method": { @@ -461,34 +373,118 @@ "display": "Histologisch", "system": "dnpm-dip/mtb/tumor-cell-content/method" }, - "value": 0.40875903241796807 + "value": 0.639758904015403 } } } ], "ihcReports": [ { - "id": "ced8a836-262e-4067-b272-94c8f9222446", + "id": "678bc235-4a27-4fcd-88ab-8d682184e5c0", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "results": { "proteinExpression": [ { - "id": "07bdd4f4-6df7-4c22-9ef2-2abb86cf4666", + "id": "30e22700-b895-4ee6-8f1e-fee9a82d15a7", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "protein": { - "code": "HGNC:3942", - "display": "MTOR", + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + "value": { + "code": "exp", + "display": "Exprimiert", + "system": "dnpm-dip/mtb/ihc/protein-expression/result" + }, + "tpsScore": 58, + "icScore": { + "code": "3", + "display": ">= 10%", + "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" + }, + "tcScore": { + "code": "4", + "display": ">= 25%", + "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" + } + }, + { + "id": "f465d53e-bfab-4392-bcb9-15ff83c92b11", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "protein": { + "code": "HGNC:5173", + "display": "HRAS", + "system": "https://www.genenames.org/" + }, + "value": { + "code": "exp", + "display": "Exprimiert", + "system": "dnpm-dip/mtb/ihc/protein-expression/result" + }, + "tpsScore": 25, + "icScore": { + "code": "1", + "display": ">= 1%", + "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" + }, + "tcScore": { + "code": "4", + "display": ">= 25%", + "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" + } + }, + { + "id": "0d2acf7d-2a6d-49d3-842b-574684e94f03", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "protein": { + "code": "HGNC:6407", + "display": "KRAS", + "system": "https://www.genenames.org/" + }, + "value": { + "code": "unknown", + "display": "untersucht, kein Ergebnis", + "system": "dnpm-dip/mtb/ihc/protein-expression/result" + }, + "tpsScore": 31, + "icScore": { + "code": "1", + "display": ">= 1%", + "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" + }, + "tcScore": { + "code": "1", + "display": ">= 1%", + "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" + } + }, + { + "id": "71c3c5f9-8859-466c-a086-e05f4d454429", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "protein": { + "code": "HGNC:3689", + "display": "FGFR2", "system": "https://www.genenames.org/" }, "value": { @@ -496,7 +492,7 @@ "display": "Nicht exprimiert", "system": "dnpm-dip/mtb/ihc/protein-expression/result" }, - "tpsScore": 21, + "tpsScore": 65, "icScore": { "code": "1", "display": ">= 1%", @@ -509,42 +505,70 @@ } }, { - "id": "38ac3c86-7d13-4d5d-a85d-7d79846aa85d", + "id": "c8048a54-4e03-489a-ba13-19ed6604a04e", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "protein": { - "code": "HGNC:886", - "display": "ATRX", + "code": "HGNC:21597", + "display": "ACAD10", "system": "https://www.genenames.org/" }, "value": { - "code": "3+", - "display": "3+", + "code": "exp", + "display": "Exprimiert", "system": "dnpm-dip/mtb/ihc/protein-expression/result" }, - "tpsScore": 46, + "tpsScore": 61, "icScore": { - "code": "0", - "display": "< 1%", + "code": "3", + "display": ">= 10%", "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" }, "tcScore": { - "code": "1", - "display": ">= 1%", + "code": "0", + "display": "< 1%", "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" } }, { - "id": "002dd577-7a1e-4e47-ae63-bc84e641565e", + "id": "c3cfac81-5058-490a-a21b-6aa5ca69d560", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "protein": { - "code": "HGNC:34", - "display": "ABCA4", + "code": "HGNC:391", + "display": "AKT1", + "system": "https://www.genenames.org/" + }, + "value": { + "code": "2+", + "display": "2+", + "system": "dnpm-dip/mtb/ihc/protein-expression/result" + }, + "tpsScore": 6, + "icScore": { + "code": "1", + "display": ">= 1%", + "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" + }, + "tcScore": { + "code": "0", + "display": "< 1%", + "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" + } + }, + { + "id": "d95f09ce-d57b-4880-a8eb-8b55caec1dbb", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "protein": { + "code": "HGNC:11998", + "display": "TP53", "system": "https://www.genenames.org/" }, "value": { @@ -552,66 +576,10 @@ "display": "Nicht exprimiert", "system": "dnpm-dip/mtb/ihc/protein-expression/result" }, - "tpsScore": 12, + "tpsScore": 86, "icScore": { - "code": "0", - "display": "< 1%", - "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" - }, - "tcScore": { "code": "1", "display": ">= 1%", - "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" - } - }, - { - "id": "70cfa37b-6a87-4108-a7ea-99c7c2f210dc", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "protein": { - "code": "HGNC:3690", - "display": "FGFR3", - "system": "https://www.genenames.org/" - }, - "value": { - "code": "not-exp", - "display": "Nicht exprimiert", - "system": "dnpm-dip/mtb/ihc/protein-expression/result" - }, - "tpsScore": 29, - "icScore": { - "code": "0", - "display": "< 1%", - "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" - }, - "tcScore": { - "code": "1", - "display": ">= 1%", - "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" - } - }, - { - "id": "cad30474-e6e2-4923-bd05-57bbce01708c", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "protein": { - "code": "HGNC:1753", - "display": "CDH13", - "system": "https://www.genenames.org/" - }, - "value": { - "code": "unknown", - "display": "untersucht, kein Ergebnis", - "system": "dnpm-dip/mtb/ihc/protein-expression/result" - }, - "tpsScore": 51, - "icScore": { - "code": "2", - "display": ">= 5%", "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" }, "tcScore": { @@ -619,34 +587,6 @@ "display": ">= 10%", "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" } - }, - { - "id": "cf0ff1b1-e0db-48f3-aa07-684d626f939f", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "protein": { - "code": "HGNC:1097", - "display": "BRAF", - "system": "https://www.genenames.org/" - }, - "value": { - "code": "not-exp", - "display": "Nicht exprimiert", - "system": "dnpm-dip/mtb/ihc/protein-expression/result" - }, - "tpsScore": 81, - "icScore": { - "code": "2", - "display": ">= 5%", - "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" - }, - "tcScore": { - "code": "2", - "display": ">= 5%", - "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" - } } ], "msiMmr": [] @@ -655,19 +595,19 @@ ], "ngsReports": [ { - "id": "3788004a-2c21-4dfb-92d8-70d1b31e39d7", + "id": "3fc2e1a0-4d9c-487d-9606-ee7b5ca4ca8a", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "type": { - "code": "genome-long-read", - "display": "Genome long-read", + "code": "panel", + "display": "Panel", "system": "dnpm-dip/ngs/type" }, "metadata": [ @@ -675,19 +615,19 @@ "kitType": "Kit Type", "kitManufacturer": "Manufacturer", "sequencer": "Sequencer", - "referenceGenome": "HG19", + "referenceGenome": "GRCh37", "pipeline": "https://github.com/pipeline-project" } ], "results": { "tumorCellContent": { - "id": "26a6f41e-c2a4-4a28-ba62-95453c880579", + "id": "a504691e-c0c9-4d98-bbec-066ee9f2c53d", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, "method": { @@ -695,36 +635,36 @@ "display": "Bioinformatisch", "system": "dnpm-dip/mtb/tumor-cell-content/method" }, - "value": 0.9426267499137174 + "value": 0.8558023090467324 }, "tmb": { - "id": "7357476b-fb64-452f-9f47-28babfc7941a", + "id": "7c06ec00-53d2-48a8-8ddb-956c0a360e39", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, "value": { - "value": 98248, + "value": 389586, "unit": "Mutations per megabase" }, "interpretation": { - "code": "low", - "display": "Niedrig", + "code": "high", + "display": "Hoch", "system": "dnpm-dip/mtb/ngs/tmb/interpretation" } }, "brcaness": { - "id": "4e83ece7-7e39-4e46-aeae-4c8a4a726895", + "id": "069e55af-392a-4438-b9ec-b2173b963c73", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, "value": 0.5, @@ -734,241 +674,45 @@ } }, "hrdScore": { - "id": "09271615-ef4d-46c1-b6c0-527f0f319934", + "id": "aefe7b46-319c-4a18-b8fc-9cda27aa2e29", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, - "value": 0.42630126429719584, + "value": 0.3444428804020617, "components": { - "lst": 0.06218415041578196, - "loh": 0.6133607455178999, - "tai": 0.7189481437278346 + "lst": 0.1942866068404976, + "loh": 0.3642816413155029, + "tai": 0.5703447060970377 }, "interpretation": { - "code": "high", - "display": "Hoch", + "code": "intermediate", + "display": "Mittel", "system": "dnpm-dip/mtb/ngs/hrd-score/interpretation" } }, "simpleVariants": [ { - "id": "e4cb43e6-a81b-48cb-8b88-db384057a771", + "id": "9f0690d3-b033-4bd5-a57f-6d3bff5b7e3a", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "externalIds": [ { - "value": "8e75df42-5a8f-4ffb-8d2e-a0b725d14d29", + "value": "a0b5a199-353c-4d33-83e2-e92afebd7411", "system": "https://www.ncbi.nlm.nih.gov/snp" }, { - "value": "bd219662-7470-4afb-a770-1e8c8ff15b9f", + "value": "54b96348-3ecd-41f4-8930-8ffddf623c39", "system": "https://cancer.sanger.ac.uk/cosmic" } ], - "chromosome": "chr11", - "gene": { - "code": "HGNC:886", - "display": "ATRX", - "system": "https://www.genenames.org/" - }, - "localization": [ - { - "code": "intronic", - "display": "Intronic", - "system": "dnpm-dip/variant/localization" - } - ], - "transcriptId": { - "value": "ad777423-fd8c-42c2-99e5-ee4b3b217e63", - "system": "https://www.ensembl.org" - }, - "exonId": "10", - "position": { - "start": 470 - }, - "altAllele": "T", - "refAllele": "A", - "dnaChange": "c.470A>T", - "proteinChange": "p.Gly12Cys", - "readDepth": 7, - "allelicFrequency": 0.26942267625669825, - "interpretation": { - "code": "1", - "display": "Benign", - "system": "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, - { - "id": "a9487572-a2a5-4074-ba8b-1e73cf92b378", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "externalIds": [ - { - "value": "06722bb8-59d3-40f1-9a83-3e0587d69cbb", - "system": "https://www.ncbi.nlm.nih.gov/snp" - }, - { - "value": "3da84ceb-a88a-4a88-9c4a-cced9011d171", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], - "chromosome": "chr6", - "gene": { - "code": "HGNC:11998", - "display": "TP53", - "system": "https://www.genenames.org/" - }, - "localization": [ - { - "code": "intergenic", - "display": "Intergenic", - "system": "dnpm-dip/variant/localization" - } - ], - "transcriptId": { - "value": "2753c548-08cb-4bb9-8a8f-99f16efe0cf3", - "system": "https://www.ensembl.org" - }, - "exonId": "4", - "position": { - "start": 49 - }, - "altAllele": "T", - "refAllele": "G", - "dnaChange": "c.49G>T", - "proteinChange": "p.Cys28_Lys29delinsTrp", - "readDepth": 14, - "allelicFrequency": 0.07637742193107444, - "interpretation": { - "code": "3", - "display": "Uncertain significance", - "system": "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, - { - "id": "97975db5-6559-4bd5-8c89-ef5a34097f11", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "externalIds": [ - { - "value": "145627c2-bf6c-4cc8-8cbf-ec2816d58142", - "system": "https://www.ncbi.nlm.nih.gov/snp" - }, - { - "value": "ffd8916a-95a7-4750-ab49-a25a576009e1", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], - "chromosome": "chr7", - "gene": { - "code": "HGNC:886", - "display": "ATRX", - "system": "https://www.genenames.org/" - }, - "localization": [ - { - "code": "intergenic", - "display": "Intergenic", - "system": "dnpm-dip/variant/localization" - } - ], - "transcriptId": { - "value": "c92dde51-20b5-4c4b-af2d-f4ea9ab58932", - "system": "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId": "11", - "position": { - "start": 223 - }, - "altAllele": "A", - "refAllele": "T", - "dnaChange": "c.223T>A", - "proteinChange": "p.Cys28delinsTrpVal", - "readDepth": 17, - "allelicFrequency": 0.36264101766053647, - "interpretation": { - "code": "2", - "display": "Likely benign", - "system": "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, - { - "id": "9b1793a8-6f73-44d1-a840-cd0314206cb9", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "externalIds": [ - { - "value": "9cfa6eec-1d3b-4d9f-8b36-ad1d69e4d853", - "system": "https://www.ncbi.nlm.nih.gov/snp" - }, - { - "value": "668d1343-38fc-45bd-b67e-c80b092bc737", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], - "chromosome": "chr19", - "gene": { - "code": "HGNC:11998", - "display": "TP53", - "system": "https://www.genenames.org/" - }, - "localization": [ - { - "code": "intronic", - "display": "Intronic", - "system": "dnpm-dip/variant/localization" - } - ], - "transcriptId": { - "value": "fdf36c25-71a8-4782-bffb-9a03890b1c32", - "system": "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId": "5", - "position": { - "start": 450 - }, - "altAllele": "C", - "refAllele": "G", - "dnaChange": "c.450G>C", - "proteinChange": "p.Gly2_Met46del", - "readDepth": 18, - "allelicFrequency": 0.17830646111898962, - "interpretation": { - "code": "1", - "display": "Benign", - "system": "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, - { - "id": "314a3a51-c9e5-42ab-88b7-15392cc40529", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "externalIds": [ - { - "value": "feb21710-a2b3-4bce-9125-20b554388f58", - "system": "https://www.ncbi.nlm.nih.gov/snp" - }, - { - "value": "2a98ad48-c913-4c0a-acbd-f839ee19d883", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], - "chromosome": "chr9", + "chromosome": "chr15", "gene": { "code": "HGNC:1097", "display": "BRAF", @@ -982,19 +726,19 @@ } ], "transcriptId": { - "value": "ce4872b5-737f-4e9f-9f2f-bde6213cca5d", - "system": "https://www.ncbi.nlm.nih.gov/refseq" + "value": "8793ef38-a5b5-4efb-bacf-9188baa592d3", + "system": "https://www.ensembl.org" }, - "exonId": "3", + "exonId": "6", "position": { - "start": 61 + "start": 308 }, - "altAllele": "A", - "refAllele": "G", - "dnaChange": "c.61G>A", - "proteinChange": "p.Cys28_Lys29delinsTrp", - "readDepth": 21, - "allelicFrequency": 0.9523091015802564, + "altAllele": "C", + "refAllele": "T", + "dnaChange": "c.308T>C", + "proteinChange": "p.(Pro578_Lys579delinsLeuTer)", + "readDepth": 8, + "allelicFrequency": 0.0984818710935953, "interpretation": { "code": "2", "display": "Likely benign", @@ -1002,18 +746,312 @@ } }, { - "id": "47fa0995-b468-4516-ac55-9318830fd616", + "id": "2044fe89-23b3-4ab2-b3b5-e32296251c94", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "externalIds": [ { - "value": "e1a320af-7a9e-4163-8894-bd2c4311bb49", + "value": "6e8d07d7-3600-4680-be08-a010096a0f26", "system": "https://www.ncbi.nlm.nih.gov/snp" }, { - "value": "e53e0494-e897-4272-86d1-5d4614eff405", + "value": "a120aa21-c5cd-446c-bd97-a48747890a6e", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr15", + "gene": { + "code": "HGNC:3236", + "display": "EGFR", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "regulatory-region", + "display": "Regulatory region", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "da8c0f90-3e6f-4e6a-b284-5273a2dd33fd", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "6", + "position": { + "start": 351 + }, + "altAllele": "G", + "refAllele": "C", + "dnaChange": "c.351C>G", + "proteinChange": "p.(Glu125_Ala132delinsGlyLeuHisArgPheIleValLeu)", + "readDepth": 13, + "allelicFrequency": 0.6161393635306036, + "interpretation": { + "code": "1", + "display": "Benign", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "09fb41e5-9e6d-4aaa-a9f4-aaee9b5304bd", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "externalIds": [ + { + "value": "ef10ac27-386c-4eb1-addd-6c49006f6ed1", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "b06d1c1c-08b2-4825-b48a-99defad38171", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chrX", + "gene": { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "a8c6bf2f-336a-4d13-9340-792778496239", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "7", + "position": { + "start": 61 + }, + "altAllele": "C", + "refAllele": "A", + "dnaChange": "c.61A>C", + "proteinChange": "p.(His321Leufs*3)", + "readDepth": 5, + "allelicFrequency": 0.23009427896105705, + "interpretation": { + "code": "4", + "display": "Likely pathogenic", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "0f8e945f-185f-4a59-8a6a-8b4fdb18acb6", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "externalIds": [ + { + "value": "a1b48026-a47b-42aa-af55-743ffac4d883", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "34a4ada1-3544-4fa5-b79b-2f205d85dd72", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr19", + "gene": { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "882e066e-1c08-48d3-82e8-2a46d6bdfd8b", + "system": "https://www.ensembl.org" + }, + "exonId": "9", + "position": { + "start": 122 + }, + "altAllele": "G", + "refAllele": "C", + "dnaChange": "c.122C>G", + "proteinChange": "p.Cys28delinsTrpVal", + "readDepth": 9, + "allelicFrequency": 0.9182372831191241, + "interpretation": { + "code": "2", + "display": "Likely benign", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "87d74d48-0042-4a9a-b934-3f90aa6f95f8", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "externalIds": [ + { + "value": "1dde468c-e5c5-4bde-ba79-e08630459289", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "985f1f23-3bf0-4434-8a91-ce520baa40ba", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr5", + "gene": { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "coding-region", + "display": "Coding region", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "b7ea01a2-ae53-4d3f-9604-42889eafe619", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "9", + "position": { + "start": 225 + }, + "altAllele": "C", + "refAllele": "T", + "dnaChange": "c.225T>C", + "proteinChange": "p.His4_Gln5insAla", + "readDepth": 17, + "allelicFrequency": 0.45086975271662, + "interpretation": { + "code": "1", + "display": "Benign", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "2f7fd69f-6d95-4971-a16e-e73dcf6a8545", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "externalIds": [ + { + "value": "005ce56f-ac0d-4f56-82bc-ecdf2372cc93", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "798a8d54-7a49-476f-b025-d34cd9d14cb8", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr11", + "gene": { + "code": "HGNC:6407", + "display": "KRAS", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "69411b5c-9af8-4866-aafa-4d5d6907e753", + "system": "https://www.ensembl.org" + }, + "exonId": "6", + "position": { + "start": 29 + }, + "altAllele": "C", + "refAllele": "A", + "dnaChange": "c.29A>C", + "proteinChange": "p.Lys2_Gly3insGlnSerLys", + "readDepth": 24, + "allelicFrequency": 0.4411564432251045, + "interpretation": { + "code": "2", + "display": "Likely benign", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "6682b275-a44e-491a-b41b-8024252089c7", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "externalIds": [ + { + "value": "9ae79969-6d79-4409-8504-37b40f0a545e", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "9027f3e0-3e9d-4d96-a640-daf12a1e2e37", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr6", + "gene": { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "regulatory-region", + "display": "Regulatory region", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "581dad04-d0dd-405b-978c-0bad00fec6f4", + "system": "https://www.ensembl.org" + }, + "exonId": "7", + "position": { + "start": 86 + }, + "altAllele": "G", + "refAllele": "C", + "dnaChange": "c.86C>G", + "proteinChange": "p.Lys23_Val25del", + "readDepth": 24, + "allelicFrequency": 0.057677192037024816, + "interpretation": { + "code": "3", + "display": "Uncertain significance", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "1ea92b12-9691-4136-bfe9-e02436085c8e", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "externalIds": [ + { + "value": "e12fb8bc-40f8-4f14-84d8-c4e261b08c17", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "0c948974-aad8-4e3a-89e2-fb96fe1ab249", "system": "https://cancer.sanger.ac.uk/cosmic" } ], @@ -1025,74 +1063,25 @@ }, "localization": [ { - "code": "splicing-region", - "display": "splicing region", + "code": "regulatory-region", + "display": "Regulatory region", "system": "dnpm-dip/variant/localization" } ], "transcriptId": { - "value": "4f365f89-e0e0-4019-b84c-67efb2ca118d", - "system": "https://www.ensembl.org" - }, - "exonId": "2", - "position": { - "start": 577 - }, - "altAllele": "G", - "refAllele": "C", - "dnaChange": "c.577C>G", - "proteinChange": "p.Trp24=/Cys", - "readDepth": 17, - "allelicFrequency": 0.23140283502604808, - "interpretation": { - "code": "2", - "display": "Likely benign", - "system": "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, - { - "id": "828dfee4-37e4-485a-8c6f-49f863903f3f", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "externalIds": [ - { - "value": "a05503d8-3ebc-43e8-a7bd-c6f2893b87fd", - "system": "https://www.ncbi.nlm.nih.gov/snp" - }, - { - "value": "2868dd12-0a79-4d33-b421-8d4fa94a79f2", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], - "chromosome": "chr22", - "gene": { - "code": "HGNC:886", - "display": "ATRX", - "system": "https://www.genenames.org/" - }, - "localization": [ - { - "code": "coding-region", - "display": "Coding region", - "system": "dnpm-dip/variant/localization" - } - ], - "transcriptId": { - "value": "01fbcd0c-6518-4910-801b-bd7a7da9bdf1", + "value": "98e944f6-3f8b-4026-92b8-93f7fb8a6be9", "system": "https://www.ncbi.nlm.nih.gov/refseq" }, - "exonId": "11", + "exonId": "6", "position": { - "start": 535 + "start": 181 }, - "altAllele": "T", - "refAllele": "C", - "dnaChange": "c.535C>T", - "proteinChange": "p.Arg78_Gly79insX[23]", - "readDepth": 23, - "allelicFrequency": 0.6339367647943907, + "altAllele": "A", + "refAllele": "T", + "dnaChange": "c.181T>A", + "proteinChange": "p.Lys23_Val25del", + "readDepth": 24, + "allelicFrequency": 0.19813946708293717, "interpretation": { "code": "2", "display": "Likely benign", @@ -1102,60 +1091,32 @@ ], "copyNumberVariants": [ { - "id": "2a7b4922-3cc0-4504-b5d4-fda8a76fc9ac", + "id": "4c5c377e-930a-4d94-9156-e06fd3f5c459", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, - "chromosome": "chr20", + "chromosome": "chrMT", "localization": [ { - "code": "intronic", - "display": "Intronic", + "code": "splicing-region", + "display": "splicing region", "system": "dnpm-dip/variant/localization" } ], "startRange": { - "start": 47283, - "end": 47325 + "start": 43090, + "end": 43132 }, "endRange": { - "start": 47554, - "end": 47604 + "start": 43267, + "end": 43317 }, - "totalCopyNumber": 3, - "relativeCopyNumber": 0.5183732460975659, - "cnA": 0.4575487225914149, - "cnB": 0.2296504258992984, + "totalCopyNumber": 7, + "relativeCopyNumber": 0.7801775227127494, + "cnA": 0.18361943370784084, + "cnB": 0.5811112581878727, "reportedAffectedGenes": [ - { - "code": "HGNC:5173", - "display": "HRAS", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:3942", - "display": "MTOR", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:1777", - "display": "CDK6", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:76", - "display": "ABL1", - "system": "https://www.genenames.org/" - } - ], - "reportedFocality": "partial q-arm", - "type": { - "code": "low-level-gain", - "display": "Low-level-gain", - "system": "dnpm-dip/mtb/ngs-report/cnv/type" - }, - "copyNumberNeutralLoH": [ { "code": "HGNC:11998", "display": "TP53", @@ -1167,52 +1128,8 @@ "system": "https://www.genenames.org/" }, { - "code": "HGNC:25829", - "display": "ABRAXAS1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:391", - "display": "AKT1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:21298", - "display": "AACS", - "system": "https://www.genenames.org/" - } - ] - }, - { - "id": "da5cc035-4c3a-4178-b8f1-9beb10e26bfa", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "chromosome": "chr12", - "localization": [ - { - "code": "coding-region", - "display": "Coding region", - "system": "dnpm-dip/variant/localization" - } - ], - "startRange": { - "start": 47366, - "end": 47408 - }, - "endRange": { - "start": 47422, - "end": 47472 - }, - "totalCopyNumber": 5, - "relativeCopyNumber": 0.042907471951150966, - "cnA": 0.7031003234003745, - "cnB": 0.45868310119316547, - "reportedAffectedGenes": [ - { - "code": "HGNC:1097", - "display": "BRAF", + "code": "HGNC:76", + "display": "ABL1", "system": "https://www.genenames.org/" }, { @@ -1221,95 +1138,13 @@ "system": "https://www.genenames.org/" }, { - "code": "HGNC:21298", - "display": "AACS", + "code": "HGNC:9967", + "display": "RET", "system": "https://www.genenames.org/" }, { - "code": "HGNC:3689", - "display": "FGFR2", - "system": "https://www.genenames.org/" - } - ], - "reportedFocality": "partial q-arm", - "type": { - "code": "high-level-gain", - "display": "High-level-gain", - "system": "dnpm-dip/mtb/ngs-report/cnv/type" - }, - "copyNumberNeutralLoH": [ - { - "code": "HGNC:3690", - "display": "FGFR3", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:391", - "display": "AKT1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:3689", - "display": "FGFR2", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:21597", - "display": "ACAD10", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:6407", - "display": "KRAS", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:25662", - "display": "AAGAB", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:1100", - "display": "BRCA1", - "system": "https://www.genenames.org/" - } - ] - }, - { - "id": "6d8cfac1-7809-46c3-afcb-cf663de78f7f", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "chromosome": "chr2", - "localization": [ - { - "code": "intergenic", - "display": "Intergenic", - "system": "dnpm-dip/variant/localization" - } - ], - "startRange": { - "start": 21639, - "end": 21681 - }, - "endRange": { - "start": 22558, - "end": 22608 - }, - "totalCopyNumber": 4, - "relativeCopyNumber": 0.0963886754685026, - "cnA": 0.7203179871076737, - "cnB": 0.34976893933294917, - "reportedAffectedGenes": [ - { - "code": "HGNC:33", - "display": "ABCA3", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:25829", - "display": "ABRAXAS1", + "code": "HGNC:1753", + "display": "CDH13", "system": "https://www.genenames.org/" }, { @@ -1317,39 +1152,14 @@ "display": "FGFR3", "system": "https://www.genenames.org/" }, - { - "code": "HGNC:1100", - "display": "BRCA1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:76", - "display": "ABL1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:1777", - "display": "CDK6", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:21298", - "display": "AACS", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:3689", - "display": "FGFR2", - "system": "https://www.genenames.org/" - }, { "code": "HGNC:3942", "display": "MTOR", "system": "https://www.genenames.org/" }, { - "code": "HGNC:3236", - "display": "EGFR", + "code": "HGNC:21597", + "display": "ACAD10", "system": "https://www.genenames.org/" }, { @@ -1370,16 +1180,777 @@ "system": "dnpm-dip/mtb/ngs-report/cnv/type" }, "copyNumberNeutralLoH": [ + { + "code": "HGNC:33", + "display": "ABCA3", + "system": "https://www.genenames.org/" + }, { "code": "HGNC:11998", "display": "TP53", "system": "https://www.genenames.org/" }, + { + "code": "HGNC:5173", + "display": "HRAS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1777", + "display": "CDK6", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3236", + "display": "EGFR", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:6407", + "display": "KRAS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:9967", + "display": "RET", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:21298", + "display": "AACS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + } + ] + }, + { + "id": "b255b3e1-6be6-4e37-a152-442c4b7243ad", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "chromosome": "chr5", + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 4113, + "end": 4155 + }, + "endRange": { + "start": 5035, + "end": 5085 + }, + "totalCopyNumber": 1, + "relativeCopyNumber": 0.3045051611141476, + "cnA": 0.2765509366484754, + "cnB": 0.931529617861302, + "reportedAffectedGenes": [ + { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:21597", + "display": "ACAD10", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:18615", + "display": "BRAFP1", + "system": "https://www.genenames.org/" + } + ], + "reportedFocality": "partial q-arm", + "type": { + "code": "loss", + "display": "Loss", + "system": "dnpm-dip/mtb/ngs-report/cnv/type" + }, + "copyNumberNeutralLoH": [ + { + "code": "HGNC:11998", + "display": "TP53", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:391", + "display": "AKT1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, { "code": "HGNC:1097", "display": "BRAF", "system": "https://www.genenames.org/" }, + { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + } + ] + }, + { + "id": "d418b9c7-3ff9-4fe9-82b6-8a44fa16911d", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "chromosome": "chr17", + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 4752, + "end": 4794 + }, + "endRange": { + "start": 4909, + "end": 4959 + }, + "totalCopyNumber": 6, + "relativeCopyNumber": 0.0640321708138667, + "cnA": 0.8042393647214559, + "cnB": 0.45292087841292294, + "reportedAffectedGenes": [ + { + "code": "HGNC:11998", + "display": "TP53", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:391", + "display": "AKT1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:6407", + "display": "KRAS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:9967", + "display": "RET", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:34", + "display": "ABCA4", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:21597", + "display": "ACAD10", + "system": "https://www.genenames.org/" + } + ], + "reportedFocality": "partial q-arm", + "type": { + "code": "high-level-gain", + "display": "High-level-gain", + "system": "dnpm-dip/mtb/ngs-report/cnv/type" + }, + "copyNumberNeutralLoH": [ + { + "code": "HGNC:33", + "display": "ABCA3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1777", + "display": "CDK6", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:6407", + "display": "KRAS", + "system": "https://www.genenames.org/" + } + ] + }, + { + "id": "6c507be2-f91f-4b82-9661-57e1a42825f9", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "chromosome": "chr15", + "localization": [ + { + "code": "regulatory-region", + "display": "Regulatory region", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 37829, + "end": 37871 + }, + "endRange": { + "start": 38035, + "end": 38085 + }, + "totalCopyNumber": 1, + "relativeCopyNumber": 0.3419552514274993, + "cnA": 0.8209416660797689, + "cnB": 0.4005358195974207, + "reportedAffectedGenes": [ + { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1777", + "display": "CDK6", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:9967", + "display": "RET", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:18615", + "display": "BRAFP1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1097", + "display": "BRAF", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + } + ], + "reportedFocality": "partial q-arm", + "type": { + "code": "loss", + "display": "Loss", + "system": "dnpm-dip/mtb/ngs-report/cnv/type" + }, + "copyNumberNeutralLoH": [ + { + "code": "HGNC:11998", + "display": "TP53", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:5173", + "display": "HRAS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:6973", + "display": "MDM2", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:391", + "display": "AKT1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:21298", + "display": "AACS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:34", + "display": "ABCA4", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:18615", + "display": "BRAFP1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + } + ] + }, + { + "id": "33e7074c-bb98-4193-91c5-2cd28c782b85", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "chromosome": "chrY", + "localization": [ + { + "code": "intergenic", + "display": "Intergenic", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 42004, + "end": 42046 + }, + "endRange": { + "start": 42917, + "end": 42967 + }, + "totalCopyNumber": 7, + "relativeCopyNumber": 0.10209135702990402, + "cnA": 0.4965695668072818, + "cnB": 0.43091760377039057, + "reportedAffectedGenes": [ + { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1777", + "display": "CDK6", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:18615", + "display": "BRAFP1", + "system": "https://www.genenames.org/" + } + ], + "reportedFocality": "partial q-arm", + "type": { + "code": "high-level-gain", + "display": "High-level-gain", + "system": "dnpm-dip/mtb/ngs-report/cnv/type" + }, + "copyNumberNeutralLoH": [ + { + "code": "HGNC:33", + "display": "ABCA3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:11998", + "display": "TP53", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1097", + "display": "BRAF", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:9967", + "display": "RET", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:34", + "display": "ABCA4", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3942", + "display": "MTOR", + "system": "https://www.genenames.org/" + } + ] + }, + { + "id": "466a8ae3-9659-452e-a5cb-682daa3f9dc1", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "chromosome": "chr6", + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 11769, + "end": 11811 + }, + "endRange": { + "start": 12305, + "end": 12355 + }, + "totalCopyNumber": 1, + "relativeCopyNumber": 0.8141058551865318, + "cnA": 0.4194301665138298, + "cnB": 0.9291188790820221, + "reportedAffectedGenes": [ + { + "code": "HGNC:391", + "display": "AKT1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:21597", + "display": "ACAD10", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:9967", + "display": "RET", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:21298", + "display": "AACS", + "system": "https://www.genenames.org/" + } + ], + "reportedFocality": "partial q-arm", + "type": { + "code": "loss", + "display": "Loss", + "system": "dnpm-dip/mtb/ngs-report/cnv/type" + }, + "copyNumberNeutralLoH": [ + { + "code": "HGNC:5173", + "display": "HRAS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1097", + "display": "BRAF", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + } + ] + }, + { + "id": "d88bacd7-4621-44dc-b7c4-6dcdb0059135", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "chromosome": "chr13", + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 37841, + "end": 37883 + }, + "endRange": { + "start": 38208, + "end": 38258 + }, + "totalCopyNumber": 6, + "relativeCopyNumber": 0.3086613954843185, + "cnA": 0.7548268045150922, + "cnB": 0.406626558250323, + "reportedAffectedGenes": [ + { + "code": "HGNC:11998", + "display": "TP53", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:391", + "display": "AKT1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:18615", + "display": "BRAFP1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:34", + "display": "ABCA4", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3236", + "display": "EGFR", + "system": "https://www.genenames.org/" + } + ], + "reportedFocality": "partial q-arm", + "type": { + "code": "high-level-gain", + "display": "High-level-gain", + "system": "dnpm-dip/mtb/ngs-report/cnv/type" + }, + "copyNumberNeutralLoH": [ + { + "code": "HGNC:5173", + "display": "HRAS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:34", + "display": "ABCA4", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:21597", + "display": "ACAD10", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + } + ] + }, + { + "id": "1a5bc7a1-637b-485d-a1bd-746b627b5873", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "chromosome": "chrY", + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 44181, + "end": 44223 + }, + "endRange": { + "start": 44392, + "end": 44442 + }, + "totalCopyNumber": 4, + "relativeCopyNumber": 0.34104993057095634, + "cnA": 0.4377954964659361, + "cnB": 0.44587277411147286, + "reportedAffectedGenes": [ + { + "code": "HGNC:5173", + "display": "HRAS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, { "code": "HGNC:391", "display": "AKT1", @@ -1399,45 +1970,6 @@ "code": "HGNC:3690", "display": "FGFR3", "system": "https://www.genenames.org/" - } - ] - }, - { - "id": "79b1b2f1-eece-469a-bf9d-d742ace3b4f5", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "chromosome": "chr4", - "localization": [ - { - "code": "splicing-region", - "display": "splicing region", - "system": "dnpm-dip/variant/localization" - } - ], - "startRange": { - "start": 10032, - "end": 10074 - }, - "endRange": { - "start": 10429, - "end": 10479 - }, - "totalCopyNumber": 2, - "relativeCopyNumber": 0.43102997556480316, - "cnA": 0.0626602855041446, - "cnB": 0.9272306017862723, - "reportedAffectedGenes": [ - { - "code": "HGNC:3690", - "display": "FGFR3", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:76", - "display": "ABL1", - "system": "https://www.genenames.org/" }, { "code": "HGNC:9967", @@ -1445,126 +1977,19 @@ "system": "https://www.genenames.org/" }, { - "code": "HGNC:6407", - "display": "KRAS", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:1097", - "display": "BRAF", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:25662", - "display": "AAGAB", - "system": "https://www.genenames.org/" - } - ], - "reportedFocality": "partial q-arm", - "type": { - "code": "low-level-gain", - "display": "Low-level-gain", - "system": "dnpm-dip/mtb/ngs-report/cnv/type" - }, - "copyNumberNeutralLoH": [ - { - "code": "HGNC:11998", - "display": "TP53", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:25829", - "display": "ABRAXAS1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:391", - "display": "AKT1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:1777", - "display": "CDK6", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:34", - "display": "ABCA4", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:18615", - "display": "BRAFP1", - "system": "https://www.genenames.org/" - } - ] - }, - { - "id": "7ef061c2-25d3-4ab1-b3b5-415711e74763", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "chromosome": "chr1", - "localization": [ - { - "code": "intronic", - "display": "Intronic", - "system": "dnpm-dip/variant/localization" - } - ], - "startRange": { - "start": 21367, - "end": 21409 - }, - "endRange": { - "start": 22243, - "end": 22293 - }, - "totalCopyNumber": 6, - "relativeCopyNumber": 0.5325580143964234, - "cnA": 0.001090613467988999, - "cnB": 0.796867620835479, - "reportedAffectedGenes": [ - { - "code": "HGNC:11998", - "display": "TP53", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:25829", - "display": "ABRAXAS1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:76", - "display": "ABL1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:6407", - "display": "KRAS", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:1097", - "display": "BRAF", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:1100", - "display": "BRCA1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:34", - "display": "ABCA4", + "code": "HGNC:21298", + "display": "AACS", "system": "https://www.genenames.org/" }, { "code": "HGNC:3942", "display": "MTOR", "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3236", + "display": "EGFR", + "system": "https://www.genenames.org/" } ], "reportedFocality": "partial q-arm", @@ -1580,13 +2005,8 @@ "system": "https://www.genenames.org/" }, { - "code": "HGNC:6973", - "display": "MDM2", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:25662", - "display": "AAGAB", + "code": "HGNC:1753", + "display": "CDH13", "system": "https://www.genenames.org/" }, { @@ -1595,67 +2015,77 @@ "system": "https://www.genenames.org/" }, { - "code": "HGNC:886", - "display": "ATRX", + "code": "HGNC:34", + "display": "ABCA4", "system": "https://www.genenames.org/" }, { - "code": "HGNC:3689", - "display": "FGFR2", + "code": "HGNC:6407", + "display": "KRAS", "system": "https://www.genenames.org/" }, { - "code": "HGNC:3942", - "display": "MTOR", + "code": "HGNC:1097", + "display": "BRAF", "system": "https://www.genenames.org/" }, { - "code": "HGNC:3236", - "display": "EGFR", + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1100", + "display": "BRCA1", "system": "https://www.genenames.org/" } ] }, { - "id": "b6c87ffe-cafa-4017-8304-cc7d5e5ed6ef", + "id": "ad83ceec-57a3-4329-bc0b-f1b77ec37c8b", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, - "chromosome": "chr4", + "chromosome": "chr13", "localization": [ { - "code": "intergenic", - "display": "Intergenic", + "code": "coding-region", + "display": "Coding region", "system": "dnpm-dip/variant/localization" } ], "startRange": { - "start": 28913, - "end": 28955 + "start": 35377, + "end": 35419 }, "endRange": { - "start": 29073, - "end": 29123 + "start": 35543, + "end": 35593 }, - "totalCopyNumber": 5, - "relativeCopyNumber": 0.24079048197395347, - "cnA": 0.8864208860638342, - "cnB": 0.9335254612742215, + "totalCopyNumber": 6, + "relativeCopyNumber": 0.25915585742763414, + "cnA": 0.29394604742259056, + "cnB": 0.4078421656729132, "reportedAffectedGenes": [ { - "code": "HGNC:11998", - "display": "TP53", + "code": "HGNC:33", + "display": "ABCA3", "system": "https://www.genenames.org/" }, { - "code": "HGNC:25829", - "display": "ABRAXAS1", + "code": "HGNC:6973", + "display": "MDM2", "system": "https://www.genenames.org/" }, { - "code": "HGNC:886", - "display": "ATRX", + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:76", + "display": "ABL1", "system": "https://www.genenames.org/" }, { @@ -1664,13 +2094,23 @@ "system": "https://www.genenames.org/" }, { - "code": "HGNC:9967", - "display": "RET", + "code": "HGNC:21298", + "display": "AACS", "system": "https://www.genenames.org/" }, { - "code": "HGNC:3689", - "display": "FGFR2", + "code": "HGNC:18615", + "display": "BRAFP1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1100", + "display": "BRCA1", "system": "https://www.genenames.org/" }, { @@ -1682,16 +2122,6 @@ "code": "HGNC:3942", "display": "MTOR", "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:18615", - "display": "BRAFP1", - "system": "https://www.genenames.org/" - }, - { - "code": "HGNC:6407", - "display": "KRAS", - "system": "https://www.genenames.org/" } ], "reportedFocality": "partial q-arm", @@ -1712,18 +2142,28 @@ "system": "https://www.genenames.org/" }, { - "code": "HGNC:25829", - "display": "ABRAXAS1", + "code": "HGNC:5173", + "display": "HRAS", "system": "https://www.genenames.org/" }, { - "code": "HGNC:21298", - "display": "AACS", + "code": "HGNC:3690", + "display": "FGFR3", "system": "https://www.genenames.org/" }, { - "code": "HGNC:34", - "display": "ABCA4", + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3689", + "display": "FGFR2", "system": "https://www.genenames.org/" }, { @@ -1732,13 +2172,13 @@ "system": "https://www.genenames.org/" }, { - "code": "HGNC:1097", - "display": "BRAF", + "code": "HGNC:3236", + "display": "EGFR", "system": "https://www.genenames.org/" }, { - "code": "HGNC:1100", - "display": "BRCA1", + "code": "HGNC:21597", + "display": "ACAD10", "system": "https://www.genenames.org/" } ] @@ -1746,42 +2186,108 @@ ], "dnaFusions": [ { - "id": "80439a87-61a6-449f-ab0e-ea207336b650", + "id": "302967d8-fd18-4c65-95de-c212aeac9515", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "localization": [ { - "code": "splicing-region", - "display": "splicing region", + "code": "intronic", + "display": "Intronic", "system": "dnpm-dip/variant/localization" } ], "fusionPartner5prime": { - "chromosome": "chr10", + "chromosome": "chr13", "gene": { - "code": "HGNC:1100", - "display": "BRCA1", + "code": "HGNC:21298", + "display": "AACS", "system": "https://www.genenames.org/" }, - "position": 988 + "position": 590 }, "fusionPartner3prime": { - "chromosome": "chr19", + "chromosome": "chr16", "gene": { - "code": "HGNC:1097", - "display": "BRAF", + "code": "HGNC:76", + "display": "ABL1", "system": "https://www.genenames.org/" }, - "position": 337 + "position": 938 }, - "reportedNumReads": 7 + "reportedNumReads": 8 }, { - "id": "9d1e2965-d90a-40f1-b40f-c73de15980cf", + "id": "14415292-2555-4e14-97f6-6debe5a0ee14", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "localization": [ + { + "code": "coding-region", + "display": "Coding region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr5", + "gene": { + "code": "HGNC:9967", + "display": "RET", + "system": "https://www.genenames.org/" + }, + "position": 468 + }, + "fusionPartner3prime": { + "chromosome": "chr14", + "gene": { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + "position": 343 + }, + "reportedNumReads": 4 + }, + { + "id": "2cdbcc31-9bd2-456f-91ec-8a754898b9dd", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "localization": [ + { + "code": "intergenic", + "display": "Intergenic", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chrMT", + "gene": { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + "position": 813 + }, + "fusionPartner3prime": { + "chromosome": "chr5", + "gene": { + "code": "HGNC:21298", + "display": "AACS", + "system": "https://www.genenames.org/" + }, + "position": 825 + }, + "reportedNumReads": 4 + }, + { + "id": "0ecdde1f-11ca-4a2d-b0e5-5a9edda324ec", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "localization": [ @@ -1792,105 +2298,31 @@ } ], "fusionPartner5prime": { - "chromosome": "chr3", + "chromosome": "chr2", "gene": { - "code": "HGNC:6973", - "display": "MDM2", + "code": "HGNC:34", + "display": "ABCA4", "system": "https://www.genenames.org/" }, - "position": 61 + "position": 745 }, "fusionPartner3prime": { - "chromosome": "chrX", - "gene": { - "code": "HGNC:886", - "display": "ATRX", - "system": "https://www.genenames.org/" - }, - "position": 728 - }, - "reportedNumReads": 5 - }, - { - "id": "16efbf55-955f-4044-94db-905b74c67d6e", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "localization": [ - { - "code": "coding-region", - "display": "Coding region", - "system": "dnpm-dip/variant/localization" - } - ], - "fusionPartner5prime": { - "chromosome": "chr3", - "gene": { - "code": "HGNC:391", - "display": "AKT1", - "system": "https://www.genenames.org/" - }, - "position": 307 - }, - "fusionPartner3prime": { - "chromosome": "chr22", - "gene": { - "code": "HGNC:11998", - "display": "TP53", - "system": "https://www.genenames.org/" - }, - "position": 297 - }, - "reportedNumReads": 3 - }, - { - "id": "b184adc5-50e4-4a48-8fc4-16442eadec78", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "localization": [ - { - "code": "splicing-region", - "display": "splicing region", - "system": "dnpm-dip/variant/localization" - } - ], - "fusionPartner5prime": { "chromosome": "chr21", "gene": { - "code": "HGNC:1753", - "display": "CDH13", + "code": "HGNC:1777", + "display": "CDK6", "system": "https://www.genenames.org/" }, - "position": 732 + "position": 783 }, - "fusionPartner3prime": { - "chromosome": "chr14", - "gene": { - "code": "HGNC:3689", - "display": "FGFR2", - "system": "https://www.genenames.org/" - }, - "position": 72 - }, - "reportedNumReads": 5 - } - ], - "rnaFusions": [ + "reportedNumReads": 6 + }, { - "id": "2d813e27-e662-46b6-8bfa-62473c591a68", + "id": "d03b7a66-d9d0-4038-be62-22327425a688", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, - "externalIds": [ - { - "value": "8560bec8-434c-485a-9dcf-357903a668df", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], "localization": [ { "code": "intergenic", @@ -1898,46 +2330,170 @@ "system": "dnpm-dip/variant/localization" } ], + "fusionPartner5prime": { + "chromosome": "chr16", + "gene": { + "code": "HGNC:6973", + "display": "MDM2", + "system": "https://www.genenames.org/" + }, + "position": 396 + }, + "fusionPartner3prime": { + "chromosome": "chr14", + "gene": { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + "position": 997 + }, + "reportedNumReads": 7 + }, + { + "id": "94cf49cb-7d02-496c-b283-82ecbc1763cc", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr11", + "gene": { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + "position": 480 + }, + "fusionPartner3prime": { + "chromosome": "chr3", + "gene": { + "code": "HGNC:33", + "display": "ABCA3", + "system": "https://www.genenames.org/" + }, + "position": 649 + }, + "reportedNumReads": 8 + } + ], + "rnaFusions": [ + { + "id": "ac9757c5-2e65-44c6-bb2c-f40004d10d77", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "externalIds": [ + { + "value": "836989c4-62ca-41b3-b421-d08a098cb509", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], "fusionPartner5prime": { "transcriptId": { - "value": "805a7f31-9fe1-49ed-915d-d219b71a45cd", + "value": "7713b535-7b6a-4c61-a70d-f1f854c78d38", "system": "https://www.ncbi.nlm.nih.gov/refseq" }, - "exonId": "6", + "exonId": "4", "gene": { "code": "HGNC:21298", "display": "AACS", "system": "https://www.genenames.org/" }, - "position": 577, - "strand": "+" + "position": 584, + "strand": "-" }, "fusionPartner3prime": { "transcriptId": { - "value": "2ae47187-95cb-4d8c-95f9-6a914fd928f7", + "value": "31904acd-4c03-45f9-bc59-c4d534d600ed", "system": "https://www.ensembl.org" }, "exonId": "3", "gene": { - "code": "HGNC:391", - "display": "AKT1", + "code": "HGNC:25829", + "display": "ABRAXAS1", "system": "https://www.genenames.org/" }, - "position": 286, + "position": 210, + "strand": "-" + }, + "effect": "Effect", + "reportedNumReads": 8 + }, + { + "id": "b1196574-f32b-4c32-84d4-0034698a99b6", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "externalIds": [ + { + "value": "d9286de1-9938-4683-84ed-e486f16bf363", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "transcriptId": { + "value": "7116faf2-f1e9-4026-878f-ae0dc872c8d2", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "5", + "gene": { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + }, + "position": 648, + "strand": "-" + }, + "fusionPartner3prime": { + "transcriptId": { + "value": "785f85a8-dc83-4f93-ba7c-a157add06294", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "4", + "gene": { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + }, + "position": 717, "strand": "-" }, "effect": "Effect", "reportedNumReads": 6 }, { - "id": "88b337a8-260a-418f-8030-6ce5cd155882", + "id": "75da7cba-5f26-4ef7-9a8c-60fcd1b30399", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "externalIds": [ { - "value": "32d72312-10c9-42ee-be8b-2e84a91750eb", + "value": "d943f58e-fc07-41b3-8e17-89fb5a2a7b14", "system": "https://cancer.sanger.ac.uk/cosmic" } ], @@ -1950,44 +2506,44 @@ ], "fusionPartner5prime": { "transcriptId": { - "value": "82fce546-f37e-4091-b403-68a6c1331f32", - "system": "https://www.ensembl.org" + "value": "8f540990-3a2f-4b8c-83cd-d87ae391b35b", + "system": "https://www.ncbi.nlm.nih.gov/refseq" }, - "exonId": "8", + "exonId": "5", "gene": { - "code": "HGNC:1097", - "display": "BRAF", + "code": "HGNC:21597", + "display": "ACAD10", "system": "https://www.genenames.org/" }, - "position": 215, + "position": 820, "strand": "-" }, "fusionPartner3prime": { "transcriptId": { - "value": "74784723-528c-463b-965a-7b935ef6b892", + "value": "78f1ba5d-5272-4a75-9b91-df2ea355cf01", "system": "https://www.ensembl.org" }, "exonId": "2", "gene": { - "code": "HGNC:34", - "display": "ABCA4", + "code": "HGNC:1100", + "display": "BRCA1", "system": "https://www.genenames.org/" }, - "position": 694, + "position": 708, "strand": "-" }, "effect": "Effect", - "reportedNumReads": 8 + "reportedNumReads": 4 }, { - "id": "139e3749-4ce8-4add-aff8-d50edb63a910", + "id": "03ab7f78-8f11-436a-a1ad-ac458a3d613e", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "externalIds": [ { - "value": "ae45ead3-0e7e-4e7f-9471-80c814cb931b", + "value": "c8ae6b24-8942-4059-9081-6a2b2f843f0d", "system": "https://cancer.sanger.ac.uk/cosmic" } ], @@ -2000,234 +2556,84 @@ ], "fusionPartner5prime": { "transcriptId": { - "value": "aed32d17-6067-4781-9483-cb0c01a8c183", - "system": "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId": "3", - "gene": { - "code": "HGNC:25662", - "display": "AAGAB", - "system": "https://www.genenames.org/" - }, - "position": 122, - "strand": "-" - }, - "fusionPartner3prime": { - "transcriptId": { - "value": "8f459b0b-86b8-431c-9d86-f2454e2806c6", + "value": "4a55b73b-1998-4bbd-b0b4-20ad79c8a33e", "system": "https://www.ensembl.org" }, - "exonId": "11", - "gene": { - "code": "HGNC:5173", - "display": "HRAS", - "system": "https://www.genenames.org/" - }, - "position": 119, - "strand": "+" - }, - "effect": "Effect", - "reportedNumReads": 8 - }, - { - "id": "8e6479b8-5870-42a0-8fa2-be8c33e9c19b", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "externalIds": [ - { - "value": "d40f6710-9923-4e03-8675-46ea7ebc185a", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], - "localization": [ - { - "code": "intergenic", - "display": "Intergenic", - "system": "dnpm-dip/variant/localization" - } - ], - "fusionPartner5prime": { - "transcriptId": { - "value": "958a73f6-3bb0-4491-b916-58cd5a968f35", - "system": "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId": "10", - "gene": { - "code": "HGNC:25662", - "display": "AAGAB", - "system": "https://www.genenames.org/" - }, - "position": 86, - "strand": "-" - }, - "fusionPartner3prime": { - "transcriptId": { - "value": "ef3d8f99-a777-4350-b825-e2895355cc8d", - "system": "https://www.ensembl.org" - }, - "exonId": "11", - "gene": { - "code": "HGNC:1097", - "display": "BRAF", - "system": "https://www.genenames.org/" - }, - "position": 310, - "strand": "+" - }, - "effect": "Effect", - "reportedNumReads": 8 - }, - { - "id": "21613593-fe48-4330-9bf8-d986e885353b", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "externalIds": [ - { - "value": "963a8d60-d1d3-4e4a-904e-4727f4d1604d", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], - "localization": [ - { - "code": "intronic", - "display": "Intronic", - "system": "dnpm-dip/variant/localization" - } - ], - "fusionPartner5prime": { - "transcriptId": { - "value": "23143510-bf67-489a-9bab-c06809780e7e", - "system": "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId": "7", - "gene": { - "code": "HGNC:5173", - "display": "HRAS", - "system": "https://www.genenames.org/" - }, - "position": 107, - "strand": "-" - }, - "fusionPartner3prime": { - "transcriptId": { - "value": "cbcb422a-3201-4b79-893e-95d8c5e75546", - "system": "https://www.ensembl.org" - }, - "exonId": "9", - "gene": { - "code": "HGNC:11998", - "display": "TP53", - "system": "https://www.genenames.org/" - }, - "position": 517, - "strand": "+" - }, - "effect": "Effect", - "reportedNumReads": 7 - }, - { - "id": "ec5cf70d-41cf-4ae6-80c7-f97c762b49bf", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "externalIds": [ - { - "value": "05989288-3ed9-4a9e-b0e8-d71e6b00e486", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], - "localization": [ - { - "code": "splicing-region", - "display": "splicing region", - "system": "dnpm-dip/variant/localization" - } - ], - "fusionPartner5prime": { - "transcriptId": { - "value": "7b5e30e2-2ad0-43ee-a420-c012525ecdc8", - "system": "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId": "8", - "gene": { - "code": "HGNC:3236", - "display": "EGFR", - "system": "https://www.genenames.org/" - }, - "position": 768, - "strand": "-" - }, - "fusionPartner3prime": { - "transcriptId": { - "value": "7bb8a065-afaa-4f70-850f-3b4df9a62f43", - "system": "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId": "3", - "gene": { - "code": "HGNC:9967", - "display": "RET", - "system": "https://www.genenames.org/" - }, - "position": 720, - "strand": "-" - }, - "effect": "Effect", - "reportedNumReads": 4 - }, - { - "id": "b11ccdea-d5ff-4fb0-ba78-4da793e4ffd8", - "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", - "type": "Patient" - }, - "externalIds": [ - { - "value": "5642d5ed-d3ff-47d4-975d-070414c71c60", - "system": "https://cancer.sanger.ac.uk/cosmic" - } - ], - "localization": [ - { - "code": "splicing-region", - "display": "splicing region", - "system": "dnpm-dip/variant/localization" - } - ], - "fusionPartner5prime": { - "transcriptId": { - "value": "04f2a51a-d782-42d2-a313-67e2ea362155", - "system": "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId": "9", + "exonId": "4", "gene": { "code": "HGNC:21597", "display": "ACAD10", "system": "https://www.genenames.org/" }, - "position": 575, - "strand": "-" + "position": 55, + "strand": "+" }, "fusionPartner3prime": { "transcriptId": { - "value": "56e704c3-b889-4768-b33a-f0be5cc3ea4d", - "system": "https://www.ncbi.nlm.nih.gov/refseq" + "value": "1ace9a85-2877-4a8d-b463-58655a1235c4", + "system": "https://www.ensembl.org" }, - "exonId": "6", + "exonId": "4", "gene": { - "code": "HGNC:18615", - "display": "BRAFP1", + "code": "HGNC:76", + "display": "ABL1", "system": "https://www.genenames.org/" }, - "position": 537, + "position": 182, "strand": "-" }, "effect": "Effect", "reportedNumReads": 8 + }, + { + "id": "e3ffd415-79e2-468c-b56c-add78590b55b", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "externalIds": [ + { + "value": "ac1289fa-375c-4a92-8d03-a75b5daad0cf", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "localization": [ + { + "code": "regulatory-region", + "display": "Regulatory region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "transcriptId": { + "value": "a28adcc9-f6d9-4234-9bd9-b9c675cea152", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "8", + "gene": { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + "position": 448, + "strand": "-" + }, + "fusionPartner3prime": { + "transcriptId": { + "value": "57736632-733f-4d7e-9ba0-2d603da2ec12", + "system": "https://www.ensembl.org" + }, + "exonId": "6", + "gene": { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + "position": 932, + "strand": "+" + }, + "effect": "Effect", + "reportedNumReads": 9 } ], "rnaSeqs": [] @@ -2236,24 +2642,24 @@ ], "carePlans": [ { - "id": "75f515ff-44e9-44ef-8de4-20750f160322", + "id": "bbcc3750-cc64-464d-8e46-1bbd45a4cb78", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "reason": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", "type": "MTBDiagnosis" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "geneticCounselingRecommendation": { - "id": "708baa95-c6de-4e1d-9e2c-f40dd1d14a32", + "id": "7b84c55d-d3bc-4fbe-8b78-413382221a2e", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "reason": { "code": "self-anamnesis", "display": "Eigenanamnese", @@ -2262,70 +2668,144 @@ }, "medicationRecommendations": [ { - "id": "1db4d8d9-d6c0-48d1-b135-d040403654f9", + "id": "9900e072-eb7b-4653-a0b5-b34014969bd2", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "reason": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", "type": "MTBDiagnosis" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "priority": { - "code": "4", - "display": "4", + "code": "2", + "display": "2", "system": "dnpm-dip/recommendation/priority" }, "levelOfEvidence": { "grading": { - "code": "m2B", - "display": "m2B", + "code": "m1B", + "display": "m1B", "system": "dnpm-dip/mtb/level-of-evidence/grading" }, "addendums": [ { - "code": "R", - "display": "R", + "code": "iv", + "display": "iv", "system": "dnpm-dip/mtb/level-of-evidence/addendum" } ], "publications": [ { - "id": "1802087682", + "id": "1217003103", "system": "https://pubmed.ncbi.nlm.nih.gov", "type": "Publication" } ] }, - "category": { - "code": "SO", - "display": "Sonstiges", - "system": "dnpm-dip/mtb/recommendation/systemic-therapy/category" - }, + "category": [ + { + "code": "CH", + "display": "Chemotherapie", + "system": "dnpm-dip/mtb/recommendation/systemic-therapy/category" + } + ], "medication": [ { - "code": "L01XX77", - "display": "Adagrasib", + "code": "L01EN02", + "display": "Pemigatinib", "system": "http://fhir.de/CodeSystem/bfarm/atc", "version": "2025" } ], "useType": { - "code": "sec-preventive", - "display": "Sec-preventive", + "code": "in-label", + "display": "In-label Use", "system": "dnpm-dip/mtb/recommendation/systemic-therapy/use-type" }, "supportingVariants": [ { "variant": { - "id": "a9487572-a2a5-4074-ba8b-1e73cf92b378", + "id": "03ab7f78-8f11-436a-a1ad-ac458a3d613e", "type": "Variant" }, "gene": { - "code": "HGNC:11998", - "display": "TP53", + "code": "HGNC:21597", + "display": "ACAD10", + "system": "https://www.genenames.org/" + } + } + ] + }, + { + "id": "49ba8a62-0798-4c4c-88cc-0afba7c2a56e", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "reason": { + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", + "type": "MTBDiagnosis" + }, + "issuedOn": "2025-07-04", + "priority": { + "code": "1", + "display": "1", + "system": "dnpm-dip/recommendation/priority" + }, + "levelOfEvidence": { + "grading": { + "code": "m3", + "display": "m3", + "system": "dnpm-dip/mtb/level-of-evidence/grading" + }, + "addendums": [ + { + "code": "Z", + "display": "Z", + "system": "dnpm-dip/mtb/level-of-evidence/addendum" + } + ], + "publications": [ + { + "id": "1607511973", + "system": "https://pubmed.ncbi.nlm.nih.gov", + "type": "Publication" + } + ] + }, + "category": [ + { + "code": "ZS", + "display": "zielgerichtete Substanzen", + "system": "dnpm-dip/mtb/recommendation/systemic-therapy/category" + } + ], + "medication": [ + { + "code": "L01XA01", + "display": "Cisplatin", + "system": "http://fhir.de/CodeSystem/bfarm/atc", + "version": "2025" + } + ], + "useType": { + "code": "unknown", + "display": "Unknown", + "system": "dnpm-dip/mtb/recommendation/systemic-therapy/use-type" + }, + "supportingVariants": [ + { + "variant": { + "id": "0ecdde1f-11ca-4a2d-b0e5-5a9edda324ec", + "type": "Variant" + }, + "gene": { + "code": "HGNC:34", + "display": "ABCA4", "system": "https://www.genenames.org/" } } @@ -2334,38 +2814,38 @@ ], "procedureRecommendations": [ { - "id": "1f5aebc0-2f32-4fdf-96e3-ba2309a580e3", + "id": "cb384a58-fda2-4dc2-9102-066a45c90834", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "reason": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", "type": "MTBDiagnosis" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "priority": { - "code": "2", - "display": "2", + "code": "3", + "display": "3", "system": "dnpm-dip/recommendation/priority" }, "levelOfEvidence": { "grading": { - "code": "undefined", - "display": "Nicht definiert", + "code": "m2A", + "display": "m2A", "system": "dnpm-dip/mtb/level-of-evidence/grading" }, "addendums": [ { - "code": "R", - "display": "R", + "code": "is", + "display": "is", "system": "dnpm-dip/mtb/level-of-evidence/addendum" } ], "publications": [ { - "id": "519591396", + "id": "102207002", "system": "https://pubmed.ncbi.nlm.nih.gov", "type": "Publication" } @@ -2379,12 +2859,12 @@ "supportingVariants": [ { "variant": { - "id": "828dfee4-37e4-485a-8c6f-49f863903f3f", + "id": "0ecdde1f-11ca-4a2d-b0e5-5a9edda324ec", "type": "Variant" }, "gene": { - "code": "HGNC:886", - "display": "ATRX", + "code": "HGNC:34", + "display": "ABCA4", "system": "https://www.genenames.org/" } } @@ -2393,46 +2873,46 @@ ], "studyEnrollmentRecommendations": [ { - "id": "590cd85f-24b9-435c-bb63-8a719dfa7c8e", + "id": "f0434b14-e96e-4bbe-8566-a54c2eff5a78", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "reason": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", "type": "MTBDiagnosis" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "levelOfEvidence": { "grading": { - "code": "m2B", - "display": "m2B", + "code": "m1B", + "display": "m1B", "system": "dnpm-dip/mtb/level-of-evidence/grading" }, "addendums": [ { - "code": "R", - "display": "R", + "code": "iv", + "display": "iv", "system": "dnpm-dip/mtb/level-of-evidence/addendum" } ], "publications": [ { - "id": "1802087682", + "id": "1217003103", "system": "https://pubmed.ncbi.nlm.nih.gov", "type": "Publication" } ] }, "priority": { - "code": "1", - "display": "1", + "code": "2", + "display": "2", "system": "dnpm-dip/recommendation/priority" }, "study": [ { - "id": "0509-104679-07-52", + "id": "3064-809794-89-39", "system": "Eudra-CT", "type": "Study" } @@ -2440,12 +2920,12 @@ "supportingVariants": [ { "variant": { - "id": "a9487572-a2a5-4074-ba8b-1e73cf92b378", + "id": "03ab7f78-8f11-436a-a1ad-ac458a3d613e", "type": "Variant" }, "gene": { - "code": "HGNC:11998", - "display": "TP53", + "code": "HGNC:21597", + "display": "ACAD10", "system": "https://www.genenames.org/" } } @@ -2454,30 +2934,30 @@ ], "histologyReevaluationRequests": [ { - "id": "38f2133a-f1cf-4af6-b441-c21953e43ed3", + "id": "7e25cc52-876a-416e-968c-2fea1c4a03a9", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "specimen": { - "id": "c3f30fe7-d193-4cde-a3c2-ef8f2497df51", + "id": "6abae7ae-1308-4637-8093-0be6594a5bc4", "type": "TumorSpecimen" }, - "issuedOn": "2025-06-24" + "issuedOn": "2025-07-04" } ], "rebiopsyRequests": [ { - "id": "0860944d-ede1-453b-b7ea-b13ea0fb1d2f", + "id": "b42a28e2-e70c-4655-ad01-627af908c2bc", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "tumorEntity": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", "type": "MTBDiagnosis" }, - "issuedOn": "2025-06-24" + "issuedOn": "2025-07-04" } ], "notes": [ @@ -2487,81 +2967,122 @@ ], "followUps": [ { - "date": "2025-06-03", + "date": "2018-04-20", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, - "lastContactDate": "2025-06-03" + "lastContactDate": "2018-04-20" } ], "claims": [ { - "id": "5ec237d4-4857-475a-9931-0aa374a93634", + "id": "9f09e4a3-c622-4592-88ae-16c54fc2ff4e", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "recommendation": { - "id": "1db4d8d9-d6c0-48d1-b135-d040403654f9", + "id": "9900e072-eb7b-4653-a0b5-b34014969bd2", "type": "MTBMedicationRecommendation" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "stage": { - "code": "unknown", - "display": "Unbekannt", + "code": "follow-up-claim", + "display": "Folgeantrag", + "system": "dnpm-dip/mtb/claim/stage" + } + }, + { + "id": "60dfd2bb-bc0f-47f9-9210-8fe262645888", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "recommendation": { + "id": "49ba8a62-0798-4c4c-88cc-0afba7c2a56e", + "type": "MTBMedicationRecommendation" + }, + "issuedOn": "2025-07-04", + "stage": { + "code": "revocation", + "display": "Widerspruch", "system": "dnpm-dip/mtb/claim/stage" } } ], "claimResponses": [ { - "id": "fed8817e-708a-4230-a7e1-95594b67e5ce", + "id": "277456cc-8214-4d57-89f9-5802a757ac67", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "claim": { - "id": "5ec237d4-4857-475a-9931-0aa374a93634", + "id": "9f09e4a3-c622-4592-88ae-16c54fc2ff4e", "type": "Claim" }, - "issuedOn": "2025-06-24", + "issuedOn": "2025-07-04", "status": { "code": "accepted", "display": "Angenommen", "system": "dnpm-dip/mtb/claim-response/status" } + }, + { + "id": "64b09aaf-7596-4fee-8a12-359ac6b7e802", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "claim": { + "id": "60dfd2bb-bc0f-47f9-9210-8fe262645888", + "type": "Claim" + }, + "issuedOn": "2025-07-04", + "status": { + "code": "rejected", + "display": "Abgelehnt", + "system": "dnpm-dip/mtb/claim-response/status" + }, + "statusReason": [ + { + "code": "insufficient-evidence", + "display": "Nicht ausreichende Evidenz", + "system": "dnpm-dip/mtb/claim-response/status-reason" + } + ] } ], "systemicTherapies": [ { "history": [ { - "id": "0b2347b7-3b85-442d-aa46-e9c5c9ee7802", + "id": "6ac97a41-99a1-4a08-9db4-41a8698c7401", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "reason": { - "id": "c1731d5e-6cca-4f8e-bca6-de233926106e", - "display": "Bösartige Neubildung: Zentraler Drüsenkörper der Brustdrüse", + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", "type": "MTBDiagnosis" }, "intent": { - "code": "P", - "display": "Palliativ", + "code": "S", + "display": "Sonstiges", "system": "dnpm-dip/therapy/intent" }, "category": { - "code": "S", - "display": "Sonstiges", + "code": "A", + "display": "Adjuvant", "system": "dnpm-dip/therapy/category" }, "basedOn": { - "id": "1db4d8d9-d6c0-48d1-b135-d040403654f9", + "id": "9900e072-eb7b-4653-a0b5-b34014969bd2", "type": "MTBMedicationRecommendation" }, - "recordedOn": "2025-06-24", + "recordedOn": "2025-07-04", "status": { "code": "stopped", "display": "Abgebrochen", @@ -2573,8 +3094,8 @@ "system": "dnpm-dip/therapy/status-reason" }, "recommendationFulfillmentStatus": { - "code": "partial", - "display": "Partiell", + "code": "complete", + "display": "Komplett", "system": "dnpm-dip/therapy/recommendation-fulfillment-status" }, "dosage": { @@ -2583,13 +3104,79 @@ "system": "dnpm-dip/therapy/dosage-density" }, "period": { - "start": "2025-03-18", - "end": "2025-06-24" + "start": "2018-02-23", + "end": "2018-05-25" }, "medication": [ { - "code": "L01XX77", - "display": "Adagrasib", + "code": "L01EN02", + "display": "Pemigatinib", + "system": "http://fhir.de/CodeSystem/bfarm/atc", + "version": "2025" + } + ], + "notes": [ + "Notes on the therapy..." + ] + } + ] + }, + { + "history": [ + { + "id": "98847b9b-2e7c-44d2-aa6c-cf9f48e0136e", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "reason": { + "id": "efa999e3-6006-4a76-90f9-32786b5f0531", + "display": "Bösartige Neubildung: Oberer innerer Quadrant der Brustdrüse", + "type": "MTBDiagnosis" + }, + "intent": { + "code": "X", + "display": "Keine Angabe", + "system": "dnpm-dip/therapy/intent" + }, + "category": { + "code": "O", + "display": "Ohne Bezug zur operativen Therapie", + "system": "dnpm-dip/therapy/category" + }, + "basedOn": { + "id": "49ba8a62-0798-4c4c-88cc-0afba7c2a56e", + "type": "MTBMedicationRecommendation" + }, + "recordedOn": "2025-07-04", + "status": { + "code": "stopped", + "display": "Abgebrochen", + "system": "dnpm-dip/therapy/status" + }, + "statusReason": { + "code": "progression", + "display": "Progression", + "system": "dnpm-dip/therapy/status-reason" + }, + "recommendationFulfillmentStatus": { + "code": "complete", + "display": "Komplett", + "system": "dnpm-dip/therapy/recommendation-fulfillment-status" + }, + "dosage": { + "code": "under-50%", + "display": "< 50 %", + "system": "dnpm-dip/therapy/dosage-density" + }, + "period": { + "start": "2017-10-27", + "end": "2018-05-25" + }, + "medication": [ + { + "code": "L01XA01", + "display": "Cisplatin", "system": "http://fhir.de/CodeSystem/bfarm/atc", "version": "2025" } @@ -2603,26 +3190,48 @@ ], "responses": [ { - "id": "70c6b774-ca26-4837-b424-5fc37e9a1548", + "id": "98d80143-3ad2-4cfe-bf29-d04e73d78728", "patient": { - "id": "aca5a971-28be-4089-8128-0036a4fe6f1a", + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", "type": "Patient" }, "therapy": { - "id": "0b2347b7-3b85-442d-aa46-e9c5c9ee7802", + "id": "6ac97a41-99a1-4a08-9db4-41a8698c7401", "type": "MTBSystemicTherapy" }, - "effectiveDate": "2025-06-03", + "effectiveDate": "2018-04-20", + "method": { + "code": "RECIST", + "display": "Nach RECIST-Kriterien", + "system": "dnpm-dip/mtb/response/method" + }, + "value": { + "code": "MR", + "display": "Mixed Response", + "system": "RECIST" + } + }, + { + "id": "f804a75c-d378-4eec-84c3-274fa20416bc", + "patient": { + "id": "644bae7a-56f6-4ee8-b02f-c532e65af5b1", + "type": "Patient" + }, + "therapy": { + "id": "98847b9b-2e7c-44d2-aa6c-cf9f48e0136e", + "type": "MTBSystemicTherapy" + }, + "effectiveDate": "2018-01-19", "method": { "code": "RANO", "display": "Nach RANO-Kriterien", "system": "dnpm-dip/mtb/response/method" }, "value": { - "code": "SD", - "display": "Stable Disease", + "code": "PD", + "display": "Progressive Disease", "system": "RECIST" } } ] -} +} \ No newline at end of file