From b748603c06bd9652da8e042393f6808e2b4326fe Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Sat, 24 May 2025 09:46:20 +0200 Subject: [PATCH 1/3] chore: update Spring Boot (#112) --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index c62029c..c688d6c 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -5,7 +5,7 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage plugins { war - id("org.springframework.boot") version "3.4.5" + id("org.springframework.boot") version "3.4.6" id("io.spring.dependency-management") version "1.1.7" kotlin("jvm") version "1.9.25" kotlin("plugin.spring") version "1.9.25" From 1dd601e8dbeb2e80bf7cb0b24dcf9f99060e09a5 Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Fri, 30 May 2025 22:36:38 +0200 Subject: [PATCH 2/3] chore: update dnpm mtb dto library (#113) --- .../etl/processor/pseudonym/extensions.kt | 7 +- .../output/KafkaMtbFileSenderTest.kt | 40 +- .../output/RestDipMtbFileSenderTest.kt | 42 +- .../etl/processor/pseudonym/ExtensionsTest.kt | 54 +- .../resources/mv64e-mtb-fake-patient.json | 4771 +++++++++-------- 5 files changed, 2643 insertions(+), 2271 deletions(-) diff --git a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt index 111494b..7ce1e0c 100644 --- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt +++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt @@ -279,12 +279,15 @@ infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) { this.responses?.forEach { it.patient.id = patientPseudonym } this.specimens?.forEach { it.patient.id = patientPseudonym } this.priorDiagnosticReports?.forEach { it.patient.id = patientPseudonym } - this.performanceStatus.forEach { it.patient.id = patientPseudonym } - this.systemicTherapies.forEach { + this.performanceStatus?.forEach { it.patient.id = patientPseudonym } + this.systemicTherapies?.forEach { it.history?.forEach { it.patient.id = patientPseudonym } } + this.followUps?.forEach { + it.patient.id = patientPseudonym + } } /** diff --git a/src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt index e5fb925..f1185ef 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSenderTest.kt @@ -44,6 +44,8 @@ import org.springframework.kafka.core.KafkaTemplate import org.springframework.kafka.support.SendResult import org.springframework.retry.policy.SimpleRetryPolicy import org.springframework.retry.support.RetryTemplateBuilder +import java.time.Instant +import java.util.* import java.util.concurrent.CompletableFuture.completedFuture import java.util.concurrent.ExecutionException @@ -309,24 +311,28 @@ class KafkaMtbFileSenderTest { }.build() } - fun dnpmV2MtbFile(): Mtb = Mtb.builder() - .withPatient( - dev.pcvolkmer.mv64e.mtb.Patient.builder() - .withId("PID") - .withBirthDate("2000-08-08") - .withGender(CodingGender.builder().withCode(CodingGender.Code.MALE).build()) - .build() - ) - .withEpisodesOfCare( - listOf( - MTBEpisodeOfCare.builder() - .withId("1") - .withPatient(Reference("PID")) - .withPeriod(PeriodDate.builder().withStart("2023-08-08").build()) - .build() + fun dnpmV2MtbFile(): Mtb { + return Mtb().apply { + this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply { + this.id = "PID" + this.birthDate = Date.from(Instant.now()) + this.gender = GenderCoding().apply { + this.code = GenderCodingCode.MALE + } + } + this.episodesOfCare = listOf( + MtbEpisodeOfCare().apply { + this.id = "1" + this.patient = Reference().apply { + this.id = "PID" + } + this.period = PeriodDate().apply { + this.start = Date.from(Instant.now()) + } + } ) - ) - .build() + } + } fun bwhcV1kafkaRecordData(requestId: RequestId, consentStatus: Consent.Status): MtbRequest { return BwhcV1MtbFileRequest(requestId, bwhcV1MtbFile(consentStatus)) diff --git a/src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt index b35fb47..8395518 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/output/RestDipMtbFileSenderTest.kt @@ -49,6 +49,8 @@ import org.springframework.test.web.client.MockRestServiceServer import org.springframework.test.web.client.match.MockRestRequestMatchers.* import org.springframework.test.web.client.response.MockRestResponseCreators.withStatus import org.springframework.web.client.RestTemplate +import java.time.Instant +import java.util.* class RestDipMtbFileSenderTest { @@ -155,7 +157,7 @@ class RestDipMtbFileSenderTest { withStatus(requestWithResponse.httpStatus).body(requestWithResponse.body).createResponse(it) } - val response = restMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile)) + val response = restMtbFileSender.send(DnpmV2MtbFileRequest(TEST_REQUEST_ID, dnpmV2MtbFile())) assertThat(response.status).isEqualTo(requestWithResponse.response.status) assertThat(response.body).isEqualTo(requestWithResponse.response.body) } @@ -267,24 +269,28 @@ class RestDipMtbFileSenderTest { ) .build() - val dnpmV2MtbFile: Mtb = Mtb.builder() - .withPatient( - dev.pcvolkmer.mv64e.mtb.Patient.builder() - .withId("PID") - .withBirthDate("2000-08-08") - .withGender(CodingGender.builder().withCode(CodingGender.Code.MALE).build()) - .build() - ) - .withEpisodesOfCare( - listOf( - MTBEpisodeOfCare.builder() - .withId("1") - .withPatient(Reference("PID")) - .withPeriod(PeriodDate.builder().withStart("2023-08-08").build()) - .build() + fun dnpmV2MtbFile(): Mtb { + return Mtb().apply { + this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply { + this.id = "PID" + this.birthDate = Date.from(Instant.now()) + this.gender = GenderCoding().apply { + this.code = GenderCodingCode.MALE + } + } + this.episodesOfCare = listOf( + MtbEpisodeOfCare().apply { + this.id = "1" + this.patient = Reference().apply { + this.id = "PID" + } + this.period = PeriodDate().apply { + this.start = Date.from(Instant.now()) + } + } ) - ) - .build() + } + } private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung" 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 d0ccb2b..e30ee73 100644 --- a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt +++ b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt @@ -21,10 +21,8 @@ package dev.dnpm.etl.processor.pseudonym import com.fasterxml.jackson.databind.ObjectMapper import de.ukw.ccc.bwhc.dto.* -import dev.pcvolkmer.mv64e.mtb.MTBEpisodeOfCare -import dev.pcvolkmer.mv64e.mtb.Mtb -import dev.pcvolkmer.mv64e.mtb.PeriodDate -import dev.pcvolkmer.mv64e.mtb.Reference +import de.ukw.ccc.bwhc.dto.Patient +import dev.pcvolkmer.mv64e.mtb.* import org.assertj.core.api.Assertions.assertThat import org.junit.jupiter.api.Nested import org.junit.jupiter.api.Test @@ -36,6 +34,8 @@ import org.mockito.kotlin.anyValueClass import org.mockito.kotlin.doAnswer import org.mockito.kotlin.whenever import org.springframework.core.io.ClassPathResource +import java.time.Instant +import java.util.* @ExtendWith(MockitoExtension::class) class ExtensionsTest { @@ -207,7 +207,7 @@ class ExtensionsTest { inner class UsingDnpmV2Datamodel { val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json" - val CLEAN_PATIENT_ID = "63f8fd7b-8127-4f3c-8843-aa9199e21c29" + val CLEAN_PATIENT_ID = "e14bf9b6-7982-4933-a648-cfdea6484f1c" private fun fakeMtbFile(): Mtb { val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream @@ -244,32 +244,26 @@ class ExtensionsTest { "TESTDOMAIN" }.whenever(pseudonymizeService).prefix() - val mtbFile = Mtb.builder() - .withPatient( - dev.pcvolkmer.mv64e.mtb.Patient.builder() - .withId("1") - .withBirthDate("2000-08-08") - .withGender(null) - .build() + val mtbFile = Mtb().apply { + this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply { + this.id = "PID" + this.birthDate = Date.from(Instant.now()) + this.gender = GenderCoding().apply { + this.code = GenderCodingCode.MALE + } + } + this.episodesOfCare = listOf( + MtbEpisodeOfCare().apply { + this.id = "1" + this.patient = Reference().apply { + this.id = "PID" + } + this.period = PeriodDate().apply { + this.start = Date.from(Instant.now()) + } + } ) - .withEpisodesOfCare( - listOf( - MTBEpisodeOfCare.builder() - .withId("1") - .withPatient(Reference("1")) - .withPeriod(PeriodDate.builder().withStart("2023-08-08").build()) - .build() - ) - ) - .withClaims(null) - .withDiagnoses(null) - .withCarePlans(null) - .withClaimResponses(null) - .withHistologyReports(null) - .withNgsReports(null) - .withResponses(null) - .withSpecimens(null) - .build() + } mtbFile.pseudonymizeWith(pseudonymizeService) mtbFile.anonymizeContentWith(pseudonymizeService) diff --git a/src/test/resources/mv64e-mtb-fake-patient.json b/src/test/resources/mv64e-mtb-fake-patient.json index c82d951..5895be5 100644 --- a/src/test/resources/mv64e-mtb-fake-patient.json +++ b/src/test/resources/mv64e-mtb-fake-patient.json @@ -1,2243 +1,2606 @@ { - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "gender" : { - "code" : "female", - "display" : "Weiblich", - "system" : "Gender" + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "gender": { + "code": "male", + "display": "Männlich", + "system": "Gender" }, - "birthDate" : "1956-02-25", - "dateOfDeath" : "2007-02-25", - "healthInsurance" : { - "type" : { - "code" : "GKV", - "display" : "gesetzliche Krankenversicherung", - "system" : "http://fhir.de/CodeSystem/versicherungsart-de-basis" + "birthDate": "1993-08-01", + "healthInsurance": { + "type": { + "code": "GKV", + "display": "gesetzliche Krankenversicherung", + "system": "http://fhir.de/CodeSystem/versicherungsart-de-basis" }, - "reference" : { - "id" : "1234567890", - "system" : "https://www.dguv.de/arge-ik", - "display" : "AOK", - "type" : "HealthInsurance" + "reference": { + "id": "1234567890", + "system": "https://www.dguv.de/arge-ik", + "display": "AOK", + "type": "HealthInsurance" } }, - "address" : { - "municipalityCode" : "12345" + "address": { + "municipalityCode": "12345" }, - "age" : { - "value" : 51, - "unit" : "Years" + "age": { + "value": 31, + "unit": "Years" }, - "vitalStatus" : { - "code" : "deceased", - "display" : "Verstorben", - "system" : "dnpm-dip/patient/vital-status" + "vitalStatus": { + "code": "alive", + "display": "Lebend", + "system": "dnpm-dip/patient/vital-status" } }, - "episodesOfCare" : [ { - "id" : "a95f44a6-5dbb-4acd-9d52-05db10f8410b", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" + "episodesOfCare": [ + { + "id": "dc4d1b2c-7468-4a4a-8fbd-1b0bb645c082", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "period": { + "start": "2024-11-30" + }, + "diagnoses": [ + { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "type": "MTBDiagnosis" + } + ] + } + ], + "diagnoses": [ + { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "recordedOn": "2022-09-01", + "type": { + "history": [ + { + "value": { + "code": "main", + "display": "Hauptdiagnose", + "system": "dnpm-dip/mtb/diagnosis/type" + }, + "date": "2022-09-01" + } + ] + }, + "code": { + "code": "C57.0", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm", + "version": "2025" + }, + "topography": { + "code": "C57.0", + "display": "Eileiter", + "system": "urn:oid:2.16.840.1.113883.6.43.1", + "version": "Zweite Revision" + }, + "grading": { + "history": [ + { + "date": "2022-09-01", + "codes": [ + { + "code": "4", + "display": "4 = undifferenziert", + "system": "https://www.basisdatensatz.de/feld/161/grading" + }, + { + "code": "1", + "display": "Pilocytic astrocytoma", + "system": "dnpm-dip/mtb/who-grading-cns-tumors", + "version": "2021" + } + ] + } + ] + }, + "staging": { + "history": [ + { + "date": "2022-09-01", + "method": { + "code": "clinical", + "display": "Klinisch", + "system": "dnpm-dip/mtb/tumor-staging/method" + }, + "tnmClassification": { + "tumor": { + "code": "T1", + "system": "UICC" + }, + "nodes": { + "code": "N3", + "system": "UICC" + }, + "metastasis": { + "code": "M0", + "system": "UICC" + } + }, + "otherClassifications": [ + { + "code": "local", + "display": "Lokal", + "system": "dnpm-dip/mtb/diagnosis/kds-tumor-spread" + } + ] + } + ] + }, + "guidelineTreatmentStatus": { + "code": "no-guidelines-available", + "display": "Keine Leitlinien vorhanden", + "system": "dnpm-dip/mtb/diagnosis/guideline-treatment-status" + }, + "notes": [ + "Notes on the tumor diagnosis..." + ] + } + ], + "guidelineTherapies": [ + { + "id": "b63bcd3e-1bbb-425d-bd4f-03820036e249", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "therapyLine": 8, + "intent": { + "code": "X", + "display": "Keine Angabe", + "system": "dnpm-dip/therapy/intent" + }, + "category": { + "code": "S", + "display": "Sonstiges", + "system": "dnpm-dip/therapy/category" + }, + "recordedOn": "2025-05-30", + "status": { + "code": "stopped", + "display": "Abgebrochen", + "system": "dnpm-dip/therapy/status" + }, + "statusReason": { + "code": "progression", + "display": "Progression", + "system": "dnpm-dip/therapy/status-reason" + }, + "period": { + "start": "2024-05-30", + "end": "2024-08-22" + }, + "medication": [ + { + "code": "L01XX57", + "display": "Plitidepsin", + "system": "http://fhir.de/CodeSystem/bfarm/atc", + "version": "2025" + } + ], + "notes": [ + "Notes on the therapy..." + ] }, - "period" : { - "start" : "2024-10-03" - }, - "diagnoses" : [ { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "type" : "MTBDiagnosis" - } ] - } ], - "diagnoses" : [ { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "recordedOn" : "2004-01-25", - "type" : { - "history" : [ { - "value" : { - "code" : "main", - "display" : "Hauptdiagnose", - "system" : "dnpm-dip/mtb/diagnosis/type" + { + "id": "d7de61c1-a5cc-429b-9c6f-e47765828f90", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "therapyLine": 5, + "intent": { + "code": "P", + "display": "Palliativ", + "system": "dnpm-dip/therapy/intent" + }, + "category": { + "code": "S", + "display": "Sonstiges", + "system": "dnpm-dip/therapy/category" + }, + "recordedOn": "2025-05-30", + "status": { + "code": "stopped", + "display": "Abgebrochen", + "system": "dnpm-dip/therapy/status" + }, + "statusReason": { + "code": "progression", + "display": "Progression", + "system": "dnpm-dip/therapy/status-reason" + }, + "period": { + "start": "2024-02-29", + "end": "2024-10-03" + }, + "medication": [ + { + "code": "L01XX29", + "display": "Denileukindiftitox", + "system": "http://fhir.de/CodeSystem/bfarm/atc", + "version": "2025" + } + ], + "notes": [ + "Notes on the therapy..." + ] + } + ], + "guidelineProcedures": [ + { + "id": "960c989f-12f0-4592-96a8-fcb55938cd38", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "therapyLine": 3, + "intent": { + "code": "X", + "display": "Keine Angabe", + "system": "dnpm-dip/therapy/intent" + }, + "code": { + "code": "surgery", + "display": "OP", + "system": "dnpm-dip/mtb/procedure/type" + }, + "status": { + "code": "on-going", + "display": "Laufend", + "system": "dnpm-dip/therapy/status" + }, + "statusReason": { + "code": "payment-pending", + "display": "Kostenübernahme noch ausstehend", + "system": "dnpm-dip/therapy/status-reason" + }, + "recordedOn": "2025-05-30", + "period": { + "start": "2024-11-30" + }, + "notes": [ + "Notes on the therapeutic procedure..." + ] + } + ], + "performanceStatus": [ + { + "id": "2d5108a3-600c-4153-8600-0427ad00d8a9", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "effectiveDate": "2025-05-30", + "value": { + "code": "5", + "display": "ECOG 5", + "system": "ECOG-Performance-Status" + } + } + ], + "specimens": [ + { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "diagnosis": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "type": "MTBDiagnosis" + }, + "type": { + "code": "unknown", + "display": "Unbekannt", + "system": "dnpm-dip/mtb/tumor-specimen/type" + }, + "collection": { + "date": "2025-05-30", + "method": { + "code": "unknown", + "display": "Unbekannt", + "system": "dnpm-dip/mtb/tumor-specimen/collection/method" }, - "date" : "2004-01-25" - } ] - }, - "code" : { - "code" : "C69.0", - "display" : "Bösartige Neubildung: Konjunktiva", - "system" : "http://fhir.de/CodeSystem/bfarm/icd-10-gm", - "version" : "2025" - }, - "topography" : { - "code" : "C69.0", - "display" : "Konjunktiva", - "system" : "urn:oid:2.16.840.1.113883.6.43.1", - "version" : "Zweite Revision" - }, - "grading" : { - "history" : [ { - "date" : "2004-01-25", - "codes" : [ { - "code" : "U", - "display" : "U = unbekannt", - "system" : "https://www.basisdatensatz.de/feld/161/grading" - }, { - "code" : "4", - "display" : "Glioblastoma", - "system" : "dnpm-dip/mtb/who-grading-cns-tumors", - "version" : "2021" - } ] - } ] - }, - "staging" : { - "history" : [ { - "date" : "2004-01-25", - "method" : { - "code" : "clinical", - "display" : "Klinisch", - "system" : "dnpm-dip/mtb/tumor-staging/method" + "localization": { + "code": "primary-tumor", + "display": "Primärtumor", + "system": "dnpm-dip/mtb/tumor-specimen/collection/localization" + } + } + } + ], + "priorDiagnosticReports": [ + { + "id": "c02f0997-c43f-4da0-819e-d7ae7370d78d", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "performer": { + "id": "xyz", + "display": "Molekular-Pathologie UKx", + "type": "Institute" + }, + "issuedOn": "2025-05-30", + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "type": { + "code": "karyotyping", + "display": "Karyotyping", + "system": "dnpm-dip/mtb/molecular-diagnostics/type" + }, + "results": [ + "Result of diagnostics..." + ] + } + ], + "histologyReports": [ + { + "id": "791de8a5-b766-42d5-9454-12fbfe25ad92", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "issuedOn": "2025-05-30", + "results": { + "tumorMorphology": { + "id": "699db4c1-74a1-4c0f-bc20-275f85abfd20", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "value": { + "code": "8891/0", + "display": "Epitheloides Leiomyom", + "system": "urn:oid:2.16.840.1.113883.6.43.1", + "version": "Zweite Revision" + }, + "note": "Notes..." }, - "tnmClassification" : { - "tumor" : { - "code" : "T1", - "system" : "UICC" + "tumorCellContent": { + "id": "5c408779-8f1c-4c44-a3f1-0bee32a0b7f1", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" }, - "nodes" : { - "code" : "N2", - "system" : "UICC" + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" }, - "metastasis" : { - "code" : "Mx", - "system" : "UICC" + "method": { + "code": "histologic", + "display": "Histologisch", + "system": "dnpm-dip/mtb/tumor-cell-content/method" + }, + "value": 0.022777185931090127 + } + } + } + ], + "ihcReports": [ + { + "id": "d913c59b-7788-4931-a24c-5a71995ee77b", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "issuedOn": "2025-05-30", + "journalId": "7f39e2f3-6b0f-486d-b2d2-a1c8c4ec0493", + "blockIds": [ + "a91d53a8-7949-4233-b710-1f1b456ff8c7" + ], + "results": { + "proteinExpression": [ + { + "id": "60538b11-9da7-4248-a878-00dbfe31cf37", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "protein": { + "code": "HGNC:34", + "display": "ABCA4", + "system": "https://www.genenames.org/" + }, + "value": { + "code": "2+", + "display": "2+", + "system": "dnpm-dip/mtb/ihc/protein-expression/result" + }, + "tpsScore": 15, + "icScore": { + "code": "3", + "display": ">= 10%", + "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" + }, + "tcScore": { + "code": "5", + "display": ">= 50%", + "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" + } + }, + { + "id": "32a8c01c-4bd7-4ae9-8835-6ba747fe1991", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "protein": { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + "value": { + "code": "not-exp", + "display": "Nicht exprimiert", + "system": "dnpm-dip/mtb/ihc/protein-expression/result" + }, + "tpsScore": 33, + "icScore": { + "code": "2", + "display": ">= 5%", + "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" + }, + "tcScore": { + "code": "5", + "display": ">= 50%", + "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" + } + }, + { + "id": "edd1cb04-8c1a-49f7-bb88-36ee576ade21", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "protein": { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + "value": { + "code": "3+", + "display": "3+", + "system": "dnpm-dip/mtb/ihc/protein-expression/result" + }, + "tpsScore": 95, + "icScore": { + "code": "2", + "display": ">= 5%", + "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" + }, + "tcScore": { + "code": "1", + "display": ">= 1%", + "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" + } + }, + { + "id": "8e7f8610-2bab-4baa-9567-98a0c71eead4", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "protein": { + "code": "HGNC:33", + "display": "ABCA3", + "system": "https://www.genenames.org/" + }, + "value": { + "code": "not-exp", + "display": "Nicht exprimiert", + "system": "dnpm-dip/mtb/ihc/protein-expression/result" + }, + "tpsScore": 81, + "icScore": { + "code": "3", + "display": ">= 10%", + "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" + }, + "tcScore": { + "code": "1", + "display": ">= 1%", + "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" + } + }, + { + "id": "845b905d-eef9-4a2c-9aff-cde382933968", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "protein": { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + }, + "value": { + "code": "1+", + "display": "1+", + "system": "dnpm-dip/mtb/ihc/protein-expression/result" + }, + "tpsScore": 70, + "icScore": { + "code": "1", + "display": ">= 1%", + "system": "dnpm-dip/mtb/ihc/protein-expression/ic-score" + }, + "tcScore": { + "code": "5", + "display": ">= 50%", + "system": "dnpm-dip/mtb/ihc/protein-expression/tc-score" + } + } + ], + "msiMmr": [] + } + } + ], + "ngsReports": [ + { + "id": "c21b5bdb-47e2-4579-a0d4-7bea8f12a1ae", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "issuedOn": "2025-05-30", + "type": { + "code": "single", + "display": "Single", + "system": "dnpm-dip/ngs/type" + }, + "metadata": [ + { + "kitType": "Kit Type", + "kitManufacturer": "Manufacturer", + "sequencer": "Sequencer", + "referenceGenome": "HG38", + "pipeline": "https://github.com/pipeline-project" + } + ], + "results": { + "tumorCellContent": { + "id": "94927ed9-449d-4b20-b87b-8d30c3262cd8", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "method": { + "code": "bioinformatic", + "display": "Bioinformatisch", + "system": "dnpm-dip/mtb/tumor-cell-content/method" + }, + "value": 0.09638668241172943 + }, + "tmb": { + "id": "b50f37ba-684a-4456-baec-1b852506522e", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "value": { + "value": 111701, + "unit": "Mutations per megabase" + }, + "interpretation": { + "code": "intermediate", + "display": "Mittel", + "system": "dnpm-dip/mtb/ngs/tmb/interpretation" } }, - "otherClassifications" : [ { - "code" : "metastasized", - "display" : "Metastasiert", - "system" : "dnpm-dip/mtb/diagnosis/kds-tumor-spread" - } ] - } ] - }, - "guidelineTreatmentStatus" : { - "code" : "non-exhausted", - "display" : "Leitlinien nicht ausgeschöpft", - "system" : "dnpm-dip/mtb/diagnosis/guideline-treatment-status" - }, - "notes" : [ "Notes on the tumor diagnosis..." ] - } ], - "guidelineTherapies" : [ { - "id" : "a3a6a53f-d531-4f46-8697-9052d98cc9e5", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" - }, - "therapyLine" : 2, - "intent" : { - "code" : "S", - "display" : "Sonstiges", - "system" : "dnpm-dip/therapy/intent" - }, - "category" : { - "code" : "I", - "display" : "Intraopterativ", - "system" : "dnpm-dip/therapy/category" - }, - "recordedOn" : "2025-04-03", - "status" : { - "code" : "stopped", - "display" : "Abgebrochen", - "system" : "dnpm-dip/therapy/status" - }, - "statusReason" : { - "code" : "progression", - "display" : "Progression", - "system" : "dnpm-dip/therapy/status-reason" - }, - "period" : { - "start" : "2023-08-03", - "end" : "2024-01-18" - }, - "medication" : [ { - "code" : "L01EX24", - "display" : "Surufatinib", - "system" : "http://fhir.de/CodeSystem/bfarm/atc", - "version" : "2024" - } ], - "notes" : [ "Notes on the therapy..." ] - } ], - "guidelineProcedures" : [ { - "id" : "ff5148ce-94ab-487f-a2a4-ebc5e1ea8a53", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" - }, - "therapyLine" : 1, - "intent" : { - "code" : "K", - "display" : "Kurativ", - "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" : "chronic-remission", - "display" : "Anhaltende Remission", - "system" : "dnpm-dip/therapy/status-reason" - }, - "recordedOn" : "2025-04-03", - "period" : { - "start" : "2024-10-03" - }, - "notes" : [ "Notes on the therapeutic procedure..." ] - }, { - "id" : "461105eb-c3c6-4fd4-bcd3-799e7eaf281d", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" - }, - "therapyLine" : 8, - "intent" : { - "code" : "K", - "display" : "Kurativ", - "system" : "dnpm-dip/therapy/intent" - }, - "code" : { - "code" : "nuclear-medicine", - "display" : "Nuklearmedizinische Therapie", - "system" : "dnpm-dip/mtb/procedure/type" - }, - "status" : { - "code" : "stopped", - "display" : "Abgebrochen", - "system" : "dnpm-dip/therapy/status" - }, - "statusReason" : { - "code" : "progression", - "display" : "Progression", - "system" : "dnpm-dip/therapy/status-reason" - }, - "recordedOn" : "2025-04-03", - "period" : { - "start" : "2024-10-03" - }, - "notes" : [ "Notes on the therapeutic procedure..." ] - } ], - "performanceStatus" : [ { - "id" : "2b1522a8-9628-4e66-8769-e1f329bf37c5", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "effectiveDate" : "2025-04-03", - "value" : { - "code" : "3", - "display" : "ECOG 3", - "system" : "ECOG-Performance-Status" - } - } ], - "specimens" : [ { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "diagnosis" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "type" : "MTBDiagnosis" - }, - "type" : { - "code" : "FFPE", - "display" : "FFPE", - "system" : "dnpm-dip/mtb/tumor-specimen/type" - }, - "collection" : { - "date" : "2025-04-03", - "method" : { - "code" : "unknown", - "display" : "Unbekannt", - "system" : "dnpm-dip/mtb/tumor-specimen/collection/method" - }, - "localization" : { - "code" : "unknown", - "display" : "Unbekannt", - "system" : "dnpm-dip/mtb/tumor-specimen/collection/localization" + "brcaness": { + "id": "ae6d8152-2ec0-46f3-bc96-a8cdb0354dff", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "value": 0.5, + "confidenceRange": { + "min": 0.4, + "max": 0.6 + } + }, + "hrdScore": { + "id": "09b18803-9465-4cd0-8525-60d7aba52cda", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "value": 0.05766991221140638, + "components": { + "lst": 0.702408484465023, + "loh": 0.9316758294159152, + "tai": 0.27810914785699703 + }, + "interpretation": { + "code": "high", + "display": "Hoch", + "system": "dnpm-dip/mtb/ngs/hrd-score/interpretation" + } + }, + "simpleVariants": [ + { + "id": "d2209570-1391-4035-9365-765e707a7675", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "3ff51b45-bea4-4adf-a652-68e9a8eb9ba0", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "d4ef6e0d-70f3-48af-9815-12add7d405fd", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr4", + "gene": { + "code": "HGNC:18615", + "display": "BRAFP1", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "intergenic", + "display": "Intergenic", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "b0819774-a371-4f25-898e-0e60971a3bba", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "3", + "position": { + "start": 561 + }, + "altAllele": "T", + "refAllele": "C", + "dnaChange": "c.561C>T", + "proteinChange": "p.Trp24=/Cys", + "readDepth": 6, + "allelicFrequency": 0.7168882236398768, + "interpretation": { + "code": "3", + "display": "Uncertain significance", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "0d033c43-d69b-44b3-90f6-b816180829b5", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "e91b92ac-b721-4dfe-a5fc-d39ad54537c9", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "3cc72402-f627-4bbf-9468-fbb566459d81", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr17", + "gene": { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "6512c902-f492-4951-a614-ff4801d2c308", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "2", + "position": { + "start": 193 + }, + "altAllele": "A", + "refAllele": "G", + "dnaChange": "c.193G>A", + "proteinChange": "p.Trp24=/Cys", + "readDepth": 5, + "allelicFrequency": 0.1081527557463462, + "interpretation": { + "code": "2", + "display": "Likely benign", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "ea5a3264-8d84-4312-ba18-7de0da5a89b5", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "29ecbc7d-32bc-41ec-8654-4dbfb76a2333", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "e14e1284-920c-429d-9893-8a027eee414c", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr1", + "gene": { + "code": "HGNC:6407", + "display": "KRAS", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "intergenic", + "display": "Intergenic", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "dd7b0cca-2707-4bf7-a361-37906e36a22c", + "system": "https://www.ensembl.org" + }, + "exonId": "8", + "position": { + "start": 131 + }, + "altAllele": "G", + "refAllele": "T", + "dnaChange": "c.131T>G", + "proteinChange": "p.His4_Gln5insAla", + "readDepth": 24, + "allelicFrequency": 0.7601485607234963, + "interpretation": { + "code": "5", + "display": "Pathogenic", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "5feae8bd-710c-42b6-ba52-e9a33be957b7", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "45515482-873f-46ea-818e-9b2b4dd8d389", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "c49c7e81-c34d-445e-804f-d110718752e1", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr4", + "gene": { + "code": "HGNC:34", + "display": "ABCA4", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "regulatory-region", + "display": "Regulatory region", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "90ed01ce-b09b-44db-87e5-f8b083664838", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "2", + "position": { + "start": 445 + }, + "altAllele": "C", + "refAllele": "A", + "dnaChange": "c.445A>C", + "proteinChange": "p.Gly2_Met46del", + "readDepth": 15, + "allelicFrequency": 0.42158645101228087, + "interpretation": { + "code": "4", + "display": "Likely pathogenic", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "7748dd2f-e547-4412-996b-c8116040a5d4", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "5600f37a-7570-4177-8ca9-43f08f297c1b", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "1c6569e0-a8e6-477a-956a-c95e04097143", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr3", + "gene": { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "coding-region", + "display": "Coding region", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "e97218d5-8e07-4516-980b-9bc3a944f5ed", + "system": "https://www.ensembl.org" + }, + "exonId": "3", + "position": { + "start": 52 + }, + "altAllele": "A", + "refAllele": "T", + "dnaChange": "c.52T>A", + "proteinChange": "p.(Glu125_Ala132delinsGlyLeuHisArgPheIleValLeu)", + "readDepth": 16, + "allelicFrequency": 0.43914773954080655, + "interpretation": { + "code": "2", + "display": "Likely benign", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + }, + { + "id": "c6e4a8ca-9fd5-46d6-b9c3-4fb92fa3ad7f", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "414cfb9c-1a27-49f4-89a7-20fa9b34d4c1", + "system": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "value": "029491a2-a2ec-4153-8f58-0a0643b82c7f", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "chromosome": "chr19", + "gene": { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + }, + "localization": [ + { + "code": "regulatory-region", + "display": "Regulatory region", + "system": "dnpm-dip/variant/localization" + } + ], + "transcriptId": { + "value": "12393377-f07e-468b-bb15-a5dd2498cd31", + "system": "https://www.ensembl.org" + }, + "exonId": "10", + "position": { + "start": 77 + }, + "altAllele": "G", + "refAllele": "C", + "dnaChange": "c.77C>G", + "proteinChange": "p.Lys23_Val25del", + "readDepth": 23, + "allelicFrequency": 0.7263541136743669, + "interpretation": { + "code": "1", + "display": "Benign", + "system": "https://www.ncbi.nlm.nih.gov/clinvar" + } + } + ], + "copyNumberVariants": [ + { + "id": "def11b75-84d6-4910-8f0a-e289326fa14c", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "chromosome": "chr17", + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 49051, + "end": 49093 + }, + "endRange": { + "start": 49114, + "end": 49164 + }, + "totalCopyNumber": 4, + "relativeCopyNumber": 0.951841616210335, + "cnA": 0.4819056712797626, + "cnB": 0.6266734124941649, + "reportedAffectedGenes": [ + { + "code": "HGNC:33", + "display": "ABCA3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:5173", + "display": "HRAS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25662", + "display": "AAGAB", + "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: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/" + }, + { + "code": "HGNC:3942", + "display": "MTOR", + "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:33", + "display": "ABCA3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:5173", + "display": "HRAS", + "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: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:21298", + "display": "AACS", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + } + ] + }, + { + "id": "a8702d47-5520-458e-929f-fdd2bc55fe17", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "chromosome": "chr22", + "localization": [ + { + "code": "intergenic", + "display": "Intergenic", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 48141, + "end": 48183 + }, + "endRange": { + "start": 48711, + "end": 48761 + }, + "totalCopyNumber": 2, + "relativeCopyNumber": 0.5067539649405646, + "cnA": 0.9335404521608939, + "cnB": 0.04708321769922241, + "reportedAffectedGenes": [ + { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1097", + "display": "BRAF", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:18615", + "display": "BRAFP1", + "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:3236", + "display": "EGFR", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:21597", + "display": "ACAD10", + "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: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:1100", + "display": "BRCA1", + "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:3236", + "display": "EGFR", + "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/" + } + ] + }, + { + "id": "e459c5b6-16ab-45ad-be8e-588a466fa42e", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "chromosome": "chr22", + "localization": [ + { + "code": "regulatory-region", + "display": "Regulatory region", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 10844, + "end": 10886 + }, + "endRange": { + "start": 11502, + "end": 11552 + }, + "totalCopyNumber": 3, + "relativeCopyNumber": 0.18257424389770927, + "cnA": 0.6677514703429981, + "cnB": 0.03993481724373449, + "reportedAffectedGenes": [ + { + "code": "HGNC:33", + "display": "ABCA3", + "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/" + } + ], + "reportedFocality": "partial q-arm", + "type": { + "code": "low-level-gain", + "display": "Low-level-gain", + "system": "dnpm-dip/mtb/ngs-report/cnv/type" + }, + "copyNumberNeutralLoH": [ + { + "code": "HGNC:33", + "display": "ABCA3", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1100", + "display": "BRCA1", + "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:3236", + "display": "EGFR", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:6407", + "display": "KRAS", + "system": "https://www.genenames.org/" + } + ] + }, + { + "id": "6050ca03-a0ae-4da7-87b8-76cac7dffa8d", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "chromosome": "chr22", + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], + "startRange": { + "start": 29573, + "end": 29615 + }, + "endRange": { + "start": 30148, + "end": 30198 + }, + "totalCopyNumber": 5, + "relativeCopyNumber": 0.3733910734264396, + "cnA": 0.4299750761842057, + "cnB": 0.20874476574745604, + "reportedAffectedGenes": [ + { + "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:6973", + "display": "MDM2", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:1753", + "display": "CDH13", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:25662", + "display": "AAGAB", + "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:6407", + "display": "KRAS", + "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/" + }, + { + "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:11998", + "display": "TP53", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:6973", + "display": "MDM2", + "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:9967", + "display": "RET", + "system": "https://www.genenames.org/" + }, + { + "code": "HGNC:21597", + "display": "ACAD10", + "system": "https://www.genenames.org/" + } + ] + } + ], + "dnaFusions": [ + { + "id": "1901fef1-f341-49cd-80b3-80af8f6f7bea", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr9", + "gene": { + "code": "HGNC:21597", + "display": "ACAD10", + "system": "https://www.genenames.org/" + }, + "position": 968 + }, + "fusionPartner3prime": { + "chromosome": "chrX", + "gene": { + "code": "HGNC:6407", + "display": "KRAS", + "system": "https://www.genenames.org/" + }, + "position": 61 + }, + "reportedNumReads": 7 + }, + { + "id": "12ca0894-8fe6-4243-aed7-d630df490cac", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr20", + "gene": { + "code": "HGNC:18615", + "display": "BRAFP1", + "system": "https://www.genenames.org/" + }, + "position": 462 + }, + "fusionPartner3prime": { + "chromosome": "chr3", + "gene": { + "code": "HGNC:3942", + "display": "MTOR", + "system": "https://www.genenames.org/" + }, + "position": 984 + }, + "reportedNumReads": 5 + }, + { + "id": "17335f8f-1ac4-43a7-9fdf-5574d8390bf5", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr21", + "gene": { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + }, + "position": 930 + }, + "fusionPartner3prime": { + "chromosome": "chr14", + "gene": { + "code": "HGNC:76", + "display": "ABL1", + "system": "https://www.genenames.org/" + }, + "position": 896 + }, + "reportedNumReads": 7 + }, + { + "id": "a6acd3bb-127b-44f6-8331-dc4b2488ed38", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr8", + "gene": { + "code": "HGNC:1097", + "display": "BRAF", + "system": "https://www.genenames.org/" + }, + "position": 460 + }, + "fusionPartner3prime": { + "chromosome": "chr19", + "gene": { + "code": "HGNC:3236", + "display": "EGFR", + "system": "https://www.genenames.org/" + }, + "position": 577 + }, + "reportedNumReads": 9 + }, + { + "id": "4705fb0d-d429-47d6-8191-c07d06d16c7a", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "localization": [ + { + "code": "regulatory-region", + "display": "Regulatory region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr19", + "gene": { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + "position": 270 + }, + "fusionPartner3prime": { + "chromosome": "chr5", + "gene": { + "code": "HGNC:21298", + "display": "AACS", + "system": "https://www.genenames.org/" + }, + "position": 124 + }, + "reportedNumReads": 3 + }, + { + "id": "9df78e1b-5126-4e72-9d3b-09ddc0fc4d0c", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "localization": [ + { + "code": "intronic", + "display": "Intronic", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr9", + "gene": { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + }, + "position": 658 + }, + "fusionPartner3prime": { + "chromosome": "chr1", + "gene": { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + }, + "position": 805 + }, + "reportedNumReads": 7 + }, + { + "id": "60c7636c-7207-4dbd-bf1f-35fba21137b5", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "localization": [ + { + "code": "coding-region", + "display": "Coding region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr11", + "gene": { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + "position": 146 + }, + "fusionPartner3prime": { + "chromosome": "chr13", + "gene": { + "code": "HGNC:886", + "display": "ATRX", + "system": "https://www.genenames.org/" + }, + "position": 521 + }, + "reportedNumReads": 5 + }, + { + "id": "ade9cd16-516a-4725-b803-51402b8913b2", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "localization": [ + { + "code": "intergenic", + "display": "Intergenic", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "chromosome": "chr13", + "gene": { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + "position": 555 + }, + "fusionPartner3prime": { + "chromosome": "chrY", + "gene": { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + "position": 510 + }, + "reportedNumReads": 9 + } + ], + "rnaFusions": [ + { + "id": "1da6ea65-074a-4850-b2a5-d6c014ba34ec", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "675d80ec-d50b-44ad-8669-a10323550d5a", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "localization": [ + { + "code": "intergenic", + "display": "Intergenic", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "transcriptId": { + "value": "63338877-2207-459b-9700-15bb3794fef4", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "5", + "gene": { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + }, + "position": 844, + "strand": "-" + }, + "fusionPartner3prime": { + "transcriptId": { + "value": "1f43ad86-86f4-4f7c-bc47-893e8ec15584", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "8", + "gene": { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + }, + "position": 280, + "strand": "-" + }, + "effect": "Effect", + "reportedNumReads": 6 + }, + { + "id": "78aaf57f-5e75-47f5-b2ce-284a45f15df3", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "2ac1b8c8-47ec-4465-86c0-0252c9c77fba", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "localization": [ + { + "code": "coding-region", + "display": "Coding region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "transcriptId": { + "value": "c05b0d75-918a-4cde-8ad3-1e72ed88c04c", + "system": "https://www.ensembl.org" + }, + "exonId": "10", + "gene": { + "code": "HGNC:21298", + "display": "AACS", + "system": "https://www.genenames.org/" + }, + "position": 837, + "strand": "-" + }, + "fusionPartner3prime": { + "transcriptId": { + "value": "4e21b4fc-81fb-4e79-a7a7-cff1c9e428ca", + "system": "https://www.ensembl.org" + }, + "exonId": "11", + "gene": { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + "position": 167, + "strand": "-" + }, + "effect": "Effect", + "reportedNumReads": 3 + }, + { + "id": "85ae18ea-3c4b-4990-a983-4d8cdfbc9987", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "3eaec2c4-3a36-466c-9462-46bfd9238c27", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "localization": [ + { + "code": "splicing-region", + "display": "splicing region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "transcriptId": { + "value": "6b4b1249-f90d-4971-85d7-444d39e220eb", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "2", + "gene": { + "code": "HGNC:6973", + "display": "MDM2", + "system": "https://www.genenames.org/" + }, + "position": 252, + "strand": "-" + }, + "fusionPartner3prime": { + "transcriptId": { + "value": "67beabf6-e37e-400b-8861-2706e40e63d0", + "system": "https://www.ensembl.org" + }, + "exonId": "6", + "gene": { + "code": "HGNC:3690", + "display": "FGFR3", + "system": "https://www.genenames.org/" + }, + "position": 755, + "strand": "-" + }, + "effect": "Effect", + "reportedNumReads": 3 + }, + { + "id": "33f12136-e588-4fdb-9a00-d54fd045a8ae", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "f7c89ee5-77fb-40eb-8542-916111cf8b68", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "localization": [ + { + "code": "intergenic", + "display": "Intergenic", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "transcriptId": { + "value": "3a84500a-fbdc-4086-b38e-b7e3454a61a7", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "5", + "gene": { + "code": "HGNC:3689", + "display": "FGFR2", + "system": "https://www.genenames.org/" + }, + "position": 902, + "strand": "-" + }, + "fusionPartner3prime": { + "transcriptId": { + "value": "30c64920-c400-407b-93b5-3bbd8ba3f255", + "system": "https://www.ensembl.org" + }, + "exonId": "7", + "gene": { + "code": "HGNC:21298", + "display": "AACS", + "system": "https://www.genenames.org/" + }, + "position": 254, + "strand": "+" + }, + "effect": "Effect", + "reportedNumReads": 3 + }, + { + "id": "f53c79bf-72e0-4e92-a1fe-b91017602828", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "5b988b8f-54a7-43b7-a001-0feaf31fcfef", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "localization": [ + { + "code": "regulatory-region", + "display": "Regulatory region", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "transcriptId": { + "value": "41d8e247-25d3-426b-b3f7-fddf5cdb558c", + "system": "https://www.ensembl.org" + }, + "exonId": "7", + "gene": { + "code": "HGNC:3236", + "display": "EGFR", + "system": "https://www.genenames.org/" + }, + "position": 376, + "strand": "+" + }, + "fusionPartner3prime": { + "transcriptId": { + "value": "5ec975b9-d2f1-4717-82bd-c7ce4dd2734c", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "10", + "gene": { + "code": "HGNC:1100", + "display": "BRCA1", + "system": "https://www.genenames.org/" + }, + "position": 356, + "strand": "-" + }, + "effect": "Effect", + "reportedNumReads": 4 + }, + { + "id": "7a5955a4-c7d4-4fe8-a529-0a0c01b84743", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "externalIds": [ + { + "value": "032e1ac6-e21f-4311-98a6-ad6a19ee7b35", + "system": "https://cancer.sanger.ac.uk/cosmic" + } + ], + "localization": [ + { + "code": "intergenic", + "display": "Intergenic", + "system": "dnpm-dip/variant/localization" + } + ], + "fusionPartner5prime": { + "transcriptId": { + "value": "6e43eb94-48ca-41e2-a57e-bf964c1d953a", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "5", + "gene": { + "code": "HGNC:391", + "display": "AKT1", + "system": "https://www.genenames.org/" + }, + "position": 714, + "strand": "-" + }, + "fusionPartner3prime": { + "transcriptId": { + "value": "91fb4eaf-c3da-434b-991b-cbaeee330de2", + "system": "https://www.ncbi.nlm.nih.gov/refseq" + }, + "exonId": "11", + "gene": { + "code": "HGNC:34", + "display": "ABCA4", + "system": "https://www.genenames.org/" + }, + "position": 357, + "strand": "-" + }, + "effect": "Effect", + "reportedNumReads": 4 + } + ], + "rnaSeqs": [] } } - } ], - "priorDiagnosticReports" : [ { - "id" : "e3d6eb01-6afb-4cb2-8682-b5f67565a701", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "performer" : { - "id" : "xyz", - "display" : "Molekular-Pathologie UKx", - "type" : "Institute" - }, - "issuedOn" : "2025-04-03", - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "type" : { - "code" : "other", - "display" : "Other", - "system" : "dnpm-dip/mtb/molecular-diagnostics/type" - }, - "results" : [ "Result of diagnostics..." ] - } ], - "histologyReports" : [ { - "id" : "49154f97-84a9-4a8c-8f52-b5dcbf6973ce", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "issuedOn" : "2025-04-03", - "results" : { - "tumorMorphology" : { - "id" : "af23d218-7c03-4950-984c-a5c35295b696", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "value" : { - "code" : "8935/1", - "display" : "Stromatumor o.n.A.", - "system" : "urn:oid:2.16.840.1.113883.6.43.1", - "version" : "Zweite Revision" - }, - "notes" : "Notes..." + ], + "carePlans": [ + { + "id": "01b19e31-f38b-4b69-bb72-01248bb92d11", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" }, - "tumorCellContent" : { - "id" : "f45c7add-f441-4786-aff3-917bad76b140", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "issuedOn": "2025-05-30", + "geneticCounselingRecommendation": { + "id": "f75d972c-f6be-4be9-bd2a-aeef0d492072", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" + "issuedOn": "2025-05-30", + "reason": { + "code": "other", + "display": "Andere", + "system": "dnpm-dip/mtb/recommendation/genetic-counseling/reason" + } + }, + "medicationRecommendations": [ + { + "id": "8c9e7e7f-daea-4b7b-ad72-6ef6be070f95", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "issuedOn": "2025-05-30", + "priority": { + "code": "1", + "display": "1", + "system": "dnpm-dip/recommendation/priority" + }, + "levelOfEvidence": { + "grading": { + "code": "m2A", + "display": "m2A", + "system": "dnpm-dip/mtb/level-of-evidence/grading" + }, + "addendums": [ + { + "code": "iv", + "display": "iv", + "system": "dnpm-dip/mtb/level-of-evidence/addendum" + } + ], + "publications": [ + { + "id": "482370142", + "system": "https://pubmed.ncbi.nlm.nih.gov", + "type": "Publication" + } + ] + }, + "category": { + "code": "HO", + "display": "Hormontherapie", + "system": "dnpm-dip/mtb/recommendation/systemic-therapy/category" + }, + "medication": [ + { + "code": "L01EX01", + "display": "Sunitinib", + "system": "http://fhir.de/CodeSystem/bfarm/atc", + "version": "2025" + } + ], + "useType": { + "code": "in-label", + "display": "In-label Use", + "system": "dnpm-dip/mtb/recommendation/systemic-therapy/use-type" + }, + "supportingVariants": [ + { + "variant": { + "id": "4705fb0d-d429-47d6-8191-c07d06d16c7a", + "type": "Variant" + }, + "gene": { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + } + } + ] }, - "method" : { - "code" : "histologic", - "display" : "Histologisch", - "system" : "dnpm-dip/mtb/tumor-cell-content/method" - }, - "value" : 0.8229387003304868 - } + { + "id": "5adb8293-f9d1-4e65-bdcf-9d4803bd9d1c", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "issuedOn": "2025-05-30", + "priority": { + "code": "2", + "display": "2", + "system": "dnpm-dip/recommendation/priority" + }, + "levelOfEvidence": { + "grading": { + "code": "m4", + "display": "m4", + "system": "dnpm-dip/mtb/level-of-evidence/grading" + }, + "addendums": [ + { + "code": "iv", + "display": "iv", + "system": "dnpm-dip/mtb/level-of-evidence/addendum" + } + ], + "publications": [ + { + "id": "1987640662", + "system": "https://pubmed.ncbi.nlm.nih.gov", + "type": "Publication" + } + ] + }, + "category": { + "code": "HO", + "display": "Hormontherapie", + "system": "dnpm-dip/mtb/recommendation/systemic-therapy/category" + }, + "medication": [ + { + "code": "L01FX01", + "display": "Edrecolomab", + "system": "http://fhir.de/CodeSystem/bfarm/atc", + "version": "2025" + } + ], + "useType": { + "code": "sec-preventive", + "display": "Sec-preventive", + "system": "dnpm-dip/mtb/recommendation/systemic-therapy/use-type" + }, + "supportingVariants": [ + { + "variant": { + "id": "c6e4a8ca-9fd5-46d6-b9c3-4fb92fa3ad7f", + "type": "Variant" + }, + "gene": { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + } + } + ] + } + ], + "procedureRecommendations": [ + { + "id": "7c51af31-3e47-467b-aee6-87a6aee9068a", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "issuedOn": "2025-05-30", + "priority": { + "code": "1", + "display": "1", + "system": "dnpm-dip/recommendation/priority" + }, + "levelOfEvidence": { + "grading": { + "code": "m1A", + "display": "m1A", + "system": "dnpm-dip/mtb/level-of-evidence/grading" + }, + "addendums": [ + { + "code": "iv", + "display": "iv", + "system": "dnpm-dip/mtb/level-of-evidence/addendum" + } + ], + "publications": [ + { + "id": "45577081", + "system": "https://pubmed.ncbi.nlm.nih.gov", + "type": "Publication" + } + ] + }, + "code": { + "code": "WS", + "display": "Wait and see", + "system": "dnpm-dip/mtb/recommendation/procedure/category" + }, + "supportingVariants": [ + { + "variant": { + "id": "7748dd2f-e547-4412-996b-c8116040a5d4", + "type": "Variant" + }, + "gene": { + "code": "HGNC:25829", + "display": "ABRAXAS1", + "system": "https://www.genenames.org/" + } + } + ] + } + ], + "studyEnrollmentRecommendations": [ + { + "id": "3d4c243c-2908-46b7-9faf-d795fd883ac0", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "issuedOn": "2025-05-30", + "levelOfEvidence": { + "grading": { + "code": "m2A", + "display": "m2A", + "system": "dnpm-dip/mtb/level-of-evidence/grading" + }, + "addendums": [ + { + "code": "iv", + "display": "iv", + "system": "dnpm-dip/mtb/level-of-evidence/addendum" + } + ], + "publications": [ + { + "id": "482370142", + "system": "https://pubmed.ncbi.nlm.nih.gov", + "type": "Publication" + } + ] + }, + "priority": { + "code": "4", + "display": "4", + "system": "dnpm-dip/recommendation/priority" + }, + "study": [ + { + "id": "8547-845744-34-56", + "system": "Eudra-CT", + "type": "Study" + } + ], + "supportingVariants": [ + { + "variant": { + "id": "4705fb0d-d429-47d6-8191-c07d06d16c7a", + "type": "Variant" + }, + "gene": { + "code": "HGNC:25662", + "display": "AAGAB", + "system": "https://www.genenames.org/" + } + } + ] + } + ], + "histologyReevaluationRequests": [ + { + "id": "a641f201-fa1e-4650-8fba-adf3665040ed", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "specimen": { + "id": "c59253e3-3c11-40bd-bc35-7c089f734862", + "type": "TumorSpecimen" + }, + "issuedOn": "2025-05-30" + } + ], + "rebiopsyRequests": [ + { + "id": "2501cd78-c360-40c1-9ced-455fa7172191", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "tumorEntity": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "type": "MTBDiagnosis" + }, + "issuedOn": "2025-05-30" + } + ], + "notes": [ + "Protocol of the MTB conference..." + ] } - } ], - "ihcReports" : [ { - "id" : "dfc2429b-4677-4c04-8359-2e8bd68e8006", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "issuedOn" : "2025-04-03", - "journalId" : "9dc66c04-ad2c-4d4c-9e38-b524e4e59c4a", - "blockIds" : [ "34c921a8-d047-414d-a1b6-b0bd24c6b771" ], - "results" : { - "proteinExpression" : [ { - "id" : "ca7b6082-f4ac-4be2-a28f-d1d73ad3eff3", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "protein" : { - "code" : "HGNC:391", - "display" : "AKT1", - "system" : "https://www.genenames.org/" - }, - "value" : { - "code" : "2+", - "display" : "2+", - "system" : "dnpm-dip/mtb/ihc/protein-expression/result" - }, - "tpsScore" : 64, - "icScore" : { - "code" : "3", - "display" : ">= 10%", - "system" : "dnpm-dip/mtb/ihc/protein-expression/ic-score" - }, - "tcScore" : { - "code" : "6", - "display" : ">= 75%", - "system" : "dnpm-dip/mtb/ihc/protein-expression/tc-score" - } - }, { - "id" : "824afa8e-332f-498f-9e98-5e03ba072857", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "protein" : { - "code" : "HGNC:5173", - "display" : "HRAS", - "system" : "https://www.genenames.org/" - }, - "value" : { - "code" : "unknown", - "display" : "untersucht, kein Ergebnis", - "system" : "dnpm-dip/mtb/ihc/protein-expression/result" - }, - "tpsScore" : 67, - "icScore" : { - "code" : "2", - "display" : ">= 5%", - "system" : "dnpm-dip/mtb/ihc/protein-expression/ic-score" - }, - "tcScore" : { - "code" : "4", - "display" : ">= 25%", - "system" : "dnpm-dip/mtb/ihc/protein-expression/tc-score" - } - }, { - "id" : "697544ba-c91b-498c-825d-4768db65f064", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "protein" : { - "code" : "HGNC:21597", - "display" : "ACAD10", - "system" : "https://www.genenames.org/" - }, - "value" : { - "code" : "3+", - "display" : "3+", - "system" : "dnpm-dip/mtb/ihc/protein-expression/result" - }, - "tpsScore" : 99, - "icScore" : { - "code" : "3", - "display" : ">= 10%", - "system" : "dnpm-dip/mtb/ihc/protein-expression/ic-score" - }, - "tcScore" : { - "code" : "1", - "display" : ">= 1%", - "system" : "dnpm-dip/mtb/ihc/protein-expression/tc-score" - } - } ], - "msiMmr" : [ ] + ], + "followUps": [ + { + "date": "2025-02-07", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "lastContactDate": "2025-02-07" } - } ], - "ngsReports" : [ { - "id" : "3a17112d-3dd2-468a-8eb5-d2acd2439b47", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "issuedOn" : "2025-04-03", - "type" : { - "code" : "genome-long-read", - "display" : "Genome long-read", - "system" : "dnpm-dip/ngs/type" - }, - "metadata" : [ { - "kitType" : "Kit Type", - "kitManufacturer" : "Manufacturer", - "sequencer" : "Sequencer", - "referenceGenome" : "HG19", - "pipeline" : "https://github.com/pipeline-project" - } ], - "results" : { - "tumorCellContent" : { - "id" : "1d0df7a7-b298-450d-99f6-be2eaee4c3f2", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "method" : { - "code" : "bioinformatic", - "display" : "Bioinformatisch", - "system" : "dnpm-dip/mtb/tumor-cell-content/method" - }, - "value" : 0.4814437947770913 + ], + "claims": [ + { + "id": "4aa57f09-d47a-4916-852e-c79175a0eca7", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" }, - "tmb" : { - "id" : "e2b42e18-1c99-4d7f-a049-ebf71e3fc2f6", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "value" : { - "value" : 282329, - "unit" : "Mutations per megabase" - }, - "interpretation" : { - "code" : "low", - "display" : "Niedrig", - "system" : "dnpm-dip/mtb/ngs/tmb/interpretation" - } + "recommendation": { + "id": "8c9e7e7f-daea-4b7b-ad72-6ef6be070f95", + "type": "MTBMedicationRecommendation" }, - "brcaness" : { - "id" : "9246f72b-790a-4c6b-aa8d-d00f0cda7a00", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "value" : 0.5, - "confidenceRange" : { - "min" : 0.4, - "max" : 0.6 - } - }, - "hrdScore" : { - "id" : "7a89c96e-f4c3-4f74-b7e7-69676a750ab6", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "value" : 0.7825761496253648, - "components" : { - "lst" : 0.845193455817853, - "loh" : 0.12405816770424238, - "tai" : 0.8345960469445086 - }, - "interpretation" : { - "code" : "high", - "display" : "Hoch", - "system" : "dnpm-dip/mtb/ngs/hrd-score/interpretation" - } - }, - "simpleVariants" : [ { - "id" : "a7a6d971-ccaf-489b-9d6c-3dce0fad63aa", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "aad4cdeb-d085-41d9-a3af-02e4e165ccc1", - "system" : "https://www.ncbi.nlm.nih.gov/snp" - }, { - "value" : "a302ca16-8c98-4697-85c1-6e0a2623ca12", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "chromosome" : "chr22", - "gene" : { - "code" : "HGNC:21597", - "display" : "ACAD10", - "system" : "https://www.genenames.org/" - }, - "localization" : [ { - "code" : "coding-region", - "display" : "Coding region", - "system" : "dnpm-dip/variant/localization" - } ], - "transcriptId" : { - "value" : "468fbe60-ff1f-4151-a8d4-4bd2bd53e9ad", - "system" : "https://www.ensembl.org" - }, - "exonId" : "10", - "position" : { - "start" : 442 - }, - "altAllele" : "G", - "refAllele" : "A", - "dnaChange" : { - "code" : "c.442A>G", - "system" : "https://hgvs-nomenclature.org" - }, - "proteinChange" : { - "code" : "p.Val7del", - "system" : "https://hgvs-nomenclature.org" - }, - "readDepth" : 7, - "allelicFrequency" : 0.05075371444497867, - "interpretation" : { - "code" : "3", - "display" : "Uncertain significance", - "system" : "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, { - "id" : "cfe756be-a9d1-4726-ad1f-16d18c40e1e4", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "3549065d-1a19-4f52-8b5a-7acdc0052981", - "system" : "https://www.ncbi.nlm.nih.gov/snp" - }, { - "value" : "915a64b9-dfd5-4d8f-ba53-5760c452b153", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "chromosome" : "chr19", - "gene" : { - "code" : "HGNC:34", - "display" : "ABCA4", - "system" : "https://www.genenames.org/" - }, - "localization" : [ { - "code" : "regulatory-region", - "display" : "Regulatory region", - "system" : "dnpm-dip/variant/localization" - } ], - "transcriptId" : { - "value" : "30d82280-ce5d-4477-97f8-8dfb33491662", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "5", - "position" : { - "start" : 124 - }, - "altAllele" : "G", - "refAllele" : "A", - "dnaChange" : { - "code" : "c.124A>G", - "system" : "https://hgvs-nomenclature.org" - }, - "proteinChange" : { - "code" : "p.Gly2_Met46del", - "system" : "https://hgvs-nomenclature.org" - }, - "readDepth" : 20, - "allelicFrequency" : 0.623433864043018, - "interpretation" : { - "code" : "1", - "display" : "Benign", - "system" : "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, { - "id" : "d6088d5a-3059-40a3-ae44-22ff4a63fe20", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "59c813ad-f057-4d3e-92f0-f64d198e7a9e", - "system" : "https://www.ncbi.nlm.nih.gov/snp" - }, { - "value" : "f47ba852-77d2-4495-af83-ebbbade46041", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "chromosome" : "chr6", - "gene" : { - "code" : "HGNC:1100", - "display" : "BRCA1", - "system" : "https://www.genenames.org/" - }, - "localization" : [ { - "code" : "splicing-region", - "display" : "splicing region", - "system" : "dnpm-dip/variant/localization" - } ], - "transcriptId" : { - "value" : "7dc56f62-01fe-48de-8425-f2407a5f6797", - "system" : "https://www.ensembl.org" - }, - "exonId" : "9", - "position" : { - "start" : 586 - }, - "altAllele" : "G", - "refAllele" : "C", - "dnaChange" : { - "code" : "c.586C>G", - "system" : "https://hgvs-nomenclature.org" - }, - "proteinChange" : { - "code" : "p.Cys28_Lys29delinsTrp", - "system" : "https://hgvs-nomenclature.org" - }, - "readDepth" : 11, - "allelicFrequency" : 0.7808371811689188, - "interpretation" : { - "code" : "1", - "display" : "Benign", - "system" : "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, { - "id" : "01a40602-1992-44ee-86cf-af4b9f8ede17", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "0c12c379-ec6b-48d2-ab7d-f3ef1e832782", - "system" : "https://www.ncbi.nlm.nih.gov/snp" - }, { - "value" : "e0d20f40-37c8-4203-825c-f8c1c7aabbc9", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "chromosome" : "chr11", - "gene" : { - "code" : "HGNC:25829", - "display" : "ABRAXAS1", - "system" : "https://www.genenames.org/" - }, - "localization" : [ { - "code" : "coding-region", - "display" : "Coding region", - "system" : "dnpm-dip/variant/localization" - } ], - "transcriptId" : { - "value" : "45566daf-2799-45bf-836b-227ad57f1e13", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "11", - "position" : { - "start" : 340 - }, - "altAllele" : "A", - "refAllele" : "G", - "dnaChange" : { - "code" : "c.340G>A", - "system" : "https://hgvs-nomenclature.org" - }, - "proteinChange" : { - "code" : "p.Trp24Cys", - "system" : "https://hgvs-nomenclature.org" - }, - "readDepth" : 23, - "allelicFrequency" : 0.350726510140109, - "interpretation" : { - "code" : "2", - "display" : "Likely benign", - "system" : "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, { - "id" : "b548d991-4270-4b60-96e9-d4d1897e2f3f", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "87a18418-1e1e-4546-9316-c14907c53122", - "system" : "https://www.ncbi.nlm.nih.gov/snp" - }, { - "value" : "7ab23f44-806e-480e-ba8a-2974789b7acc", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "chromosome" : "chr9", - "gene" : { - "code" : "HGNC:1777", - "display" : "CDK6", - "system" : "https://www.genenames.org/" - }, - "localization" : [ { - "code" : "splicing-region", - "display" : "splicing region", - "system" : "dnpm-dip/variant/localization" - } ], - "transcriptId" : { - "value" : "444c908a-a87b-401f-9446-f152b70abff6", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "3", - "position" : { - "start" : 82 - }, - "altAllele" : "C", - "refAllele" : "T", - "dnaChange" : { - "code" : "c.82T>C", - "system" : "https://hgvs-nomenclature.org" - }, - "proteinChange" : { - "code" : "p.Cys28delinsTrpVal", - "system" : "https://hgvs-nomenclature.org" - }, - "readDepth" : 9, - "allelicFrequency" : 0.7308207727279626, - "interpretation" : { - "code" : "1", - "display" : "Benign", - "system" : "https://www.ncbi.nlm.nih.gov/clinvar" - } - }, { - "id" : "b9b37461-cad8-4aa9-ab9a-765cc390ae93", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "c9343e8a-a961-478d-abf7-af8eca753195", - "system" : "https://www.ncbi.nlm.nih.gov/snp" - }, { - "value" : "fe9cf415-da2c-48ee-8239-1c0fff308477", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "chromosome" : "chr22", - "gene" : { - "code" : "HGNC:5173", - "display" : "HRAS", - "system" : "https://www.genenames.org/" - }, - "localization" : [ { - "code" : "coding-region", - "display" : "Coding region", - "system" : "dnpm-dip/variant/localization" - } ], - "transcriptId" : { - "value" : "e089a986-861c-4987-a2d4-4127cd94cfcc", - "system" : "https://www.ensembl.org" - }, - "exonId" : "5", - "position" : { - "start" : 350 - }, - "altAllele" : "A", - "refAllele" : "G", - "dnaChange" : { - "code" : "c.350G>A", - "system" : "https://hgvs-nomenclature.org" - }, - "proteinChange" : { - "code" : "p.Trp24Cys", - "system" : "https://hgvs-nomenclature.org" - }, - "readDepth" : 20, - "allelicFrequency" : 0.6561532201278295, - "interpretation" : { - "code" : "2", - "display" : "Likely benign", - "system" : "https://www.ncbi.nlm.nih.gov/clinvar" - } - } ], - "copyNumberVariants" : [ { - "id" : "674dcb35-ae1f-4c9a-bf96-d718631b0b76", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "chromosome" : "chr13", - "localization" : [ { - "code" : "splicing-region", - "display" : "splicing region", - "system" : "dnpm-dip/variant/localization" - } ], - "startRange" : { - "start" : 7504, - "end" : 7546 - }, - "endRange" : { - "start" : 8028, - "end" : 8078 - }, - "totalCopyNumber" : 7, - "relativeCopyNumber" : 0.11223346698282377, - "cnA" : 0.4978945009603952, - "cnB" : 0.4387588889519498, - "reportedAffectedGenes" : [ { - "code" : "HGNC:5173", - "display" : "HRAS", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:1097", - "display" : "BRAF", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:9967", - "display" : "RET", - "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:25662", - "display" : "AAGAB", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:11998", - "display" : "TP53", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:1753", - "display" : "CDH13", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:5173", - "display" : "HRAS", - "system" : "https://www.genenames.org/" - } ] - }, { - "id" : "0ccc8b6a-7692-405e-afb3-9ba79f6a6dc6", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "chromosome" : "chr4", - "localization" : [ { - "code" : "splicing-region", - "display" : "splicing region", - "system" : "dnpm-dip/variant/localization" - } ], - "startRange" : { - "start" : 29821, - "end" : 29863 - }, - "endRange" : { - "start" : 30310, - "end" : 30360 - }, - "totalCopyNumber" : 2, - "relativeCopyNumber" : 0.004237951938893092, - "cnA" : 0.4120221366346364, - "cnB" : 0.021984357963086842, - "reportedAffectedGenes" : [ { - "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:886", - "display" : "ATRX", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:3942", - "display" : "MTOR", - "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/" - } ], - "reportedFocality" : "partial q-arm", - "type" : { - "code" : "low-level-gain", - "display" : "Low-level-gain", - "system" : "dnpm-dip/mtb/ngs-report/cnv/type" - }, - "copyNumberNeutralLoH" : [ { - "code" : "HGNC:1097", - "display" : "BRAF", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:5173", - "display" : "HRAS", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:3690", - "display" : "FGFR3", - "system" : "https://www.genenames.org/" - } ] - }, { - "id" : "5eec91bc-94e1-462e-8686-df33216192eb", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "chromosome" : "chrX", - "localization" : [ { - "code" : "splicing-region", - "display" : "splicing region", - "system" : "dnpm-dip/variant/localization" - } ], - "startRange" : { - "start" : 18371, - "end" : 18413 - }, - "endRange" : { - "start" : 19283, - "end" : 19333 - }, - "totalCopyNumber" : 3, - "relativeCopyNumber" : 0.795318484180268, - "cnA" : 0.86546686869607, - "cnB" : 0.7216652781170053, - "reportedAffectedGenes" : [ { - "code" : "HGNC:33", - "display" : "ABCA3", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:6973", - "display" : "MDM2", - "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:21298", - "display" : "AACS", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:6407", - "display" : "KRAS", - "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" : "low-level-gain", - "display" : "Low-level-gain", - "system" : "dnpm-dip/mtb/ngs-report/cnv/type" - }, - "copyNumberNeutralLoH" : [ { - "code" : "HGNC:33", - "display" : "ABCA3", - "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:3690", - "display" : "FGFR3", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:25662", - "display" : "AAGAB", - "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:18615", - "display" : "BRAFP1", - "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/" - }, { - "code" : "HGNC:21597", - "display" : "ACAD10", - "system" : "https://www.genenames.org/" - } ] - }, { - "id" : "7a162258-d213-4243-be7e-59244f4561e9", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "chromosome" : "chr9", - "localization" : [ { - "code" : "intronic", - "display" : "Intronic", - "system" : "dnpm-dip/variant/localization" - } ], - "startRange" : { - "start" : 23025, - "end" : 23067 - }, - "endRange" : { - "start" : 23220, - "end" : 23270 - }, - "totalCopyNumber" : 1, - "relativeCopyNumber" : 0.3220959397254798, - "cnA" : 0.11998983501009763, - "cnB" : 0.08203835493839595, - "reportedAffectedGenes" : [ { - "code" : "HGNC:33", - "display" : "ABCA3", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:5173", - "display" : "HRAS", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:3690", - "display" : "FGFR3", - "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:34", - "display" : "ABCA4", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:3236", - "display" : "EGFR", - "system" : "https://www.genenames.org/" - }, { - "code" : "HGNC:21597", - "display" : "ACAD10", - "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: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/" - } ] - } ], - "dnaFusions" : [ { - "id" : "bfbb4eb3-fecf-4be6-a0b6-39ed3ab9f54c", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "localization" : [ { - "code" : "regulatory-region", - "display" : "Regulatory region", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "chromosome" : "chr9", - "gene" : { - "code" : "HGNC:21597", - "display" : "ACAD10", - "system" : "https://www.genenames.org/" - }, - "position" : 788 - }, - "fusionPartner3prime" : { - "chromosome" : "chr19", - "gene" : { - "code" : "HGNC:1753", - "display" : "CDH13", - "system" : "https://www.genenames.org/" - }, - "position" : 384 - }, - "reportedNumReads" : 7 - }, { - "id" : "e99862ce-c098-4aa1-932c-5bfb7de2bb54", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "localization" : [ { - "code" : "splicing-region", - "display" : "splicing region", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "chromosome" : "chr10", - "gene" : { - "code" : "HGNC:1100", - "display" : "BRCA1", - "system" : "https://www.genenames.org/" - }, - "position" : 426 - }, - "fusionPartner3prime" : { - "chromosome" : "chrY", - "gene" : { - "code" : "HGNC:76", - "display" : "ABL1", - "system" : "https://www.genenames.org/" - }, - "position" : 587 - }, - "reportedNumReads" : 8 - }, { - "id" : "362f5786-4521-409a-b63f-69aad335abcb", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "localization" : [ { - "code" : "intronic", - "display" : "Intronic", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "chromosome" : "chrX", - "gene" : { - "code" : "HGNC:1777", - "display" : "CDK6", - "system" : "https://www.genenames.org/" - }, - "position" : 421 - }, - "fusionPartner3prime" : { - "chromosome" : "chr15", - "gene" : { - "code" : "HGNC:3942", - "display" : "MTOR", - "system" : "https://www.genenames.org/" - }, - "position" : 618 - }, - "reportedNumReads" : 3 - }, { - "id" : "d9cc0ae1-1f22-4545-bcfc-3fc93faf1c7b", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "localization" : [ { - "code" : "regulatory-region", - "display" : "Regulatory region", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "chromosome" : "chr16", - "gene" : { - "code" : "HGNC:6407", - "display" : "KRAS", - "system" : "https://www.genenames.org/" - }, - "position" : 727 - }, - "fusionPartner3prime" : { - "chromosome" : "chr22", - "gene" : { - "code" : "HGNC:6973", - "display" : "MDM2", - "system" : "https://www.genenames.org/" - }, - "position" : 955 - }, - "reportedNumReads" : 6 - }, { - "id" : "7acb8b5a-28e5-49e8-9af0-8f0b07dd7928", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "localization" : [ { - "code" : "intergenic", - "display" : "Intergenic", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "chromosome" : "chr8", - "gene" : { - "code" : "HGNC:6407", - "display" : "KRAS", - "system" : "https://www.genenames.org/" - }, - "position" : 910 - }, - "fusionPartner3prime" : { - "chromosome" : "chr6", - "gene" : { - "code" : "HGNC:33", - "display" : "ABCA3", - "system" : "https://www.genenames.org/" - }, - "position" : 567 - }, - "reportedNumReads" : 7 - } ], - "rnaFusions" : [ { - "id" : "809f015f-8e17-45ae-82fe-1d2642a379c0", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "a961e828-b8eb-46a7-b92b-077b188d22eb", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "localization" : [ { - "code" : "regulatory-region", - "display" : "Regulatory region", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "transcriptId" : { - "value" : "7f69ae21-f0ae-4f10-965b-116b5a3a4306", - "system" : "https://www.ensembl.org" - }, - "exonId" : "3", - "gene" : { - "code" : "HGNC:76", - "display" : "ABL1", - "system" : "https://www.genenames.org/" - }, - "position" : 939, - "strand" : "-" - }, - "fusionPartner3prime" : { - "transcriptId" : { - "value" : "3e4978f1-a4e6-4822-bca2-6d65bfa903d0", - "system" : "https://www.ensembl.org" - }, - "exonId" : "5", - "gene" : { - "code" : "HGNC:1097", - "display" : "BRAF", - "system" : "https://www.genenames.org/" - }, - "position" : 898, - "strand" : "+" - }, - "effect" : "Effect", - "reportedNumReads" : 9 - }, { - "id" : "e2686fdf-5aee-4a1c-a9f9-b5117d586a56", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "3530f838-6a51-4f34-84ff-a978182da6a6", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "localization" : [ { - "code" : "intronic", - "display" : "Intronic", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "transcriptId" : { - "value" : "ccf31cee-09ab-4bfc-a92b-f48f5523989e", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "9", - "gene" : { - "code" : "HGNC:21597", - "display" : "ACAD10", - "system" : "https://www.genenames.org/" - }, - "position" : 272, - "strand" : "-" - }, - "fusionPartner3prime" : { - "transcriptId" : { - "value" : "71d1e8fc-9296-4d46-9d1f-a36e1f382d35", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "7", - "gene" : { - "code" : "HGNC:34", - "display" : "ABCA4", - "system" : "https://www.genenames.org/" - }, - "position" : 848, - "strand" : "+" - }, - "effect" : "Effect", - "reportedNumReads" : 8 - }, { - "id" : "139c8db9-edde-4bd0-ac25-4b7b1729f5cc", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "a1324b2a-96de-46a1-86a7-a575fb29b41a", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "localization" : [ { - "code" : "regulatory-region", - "display" : "Regulatory region", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "transcriptId" : { - "value" : "20da1339-f72c-4481-a844-b690a0b950e5", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "6", - "gene" : { - "code" : "HGNC:3689", - "display" : "FGFR2", - "system" : "https://www.genenames.org/" - }, - "position" : 996, - "strand" : "+" - }, - "fusionPartner3prime" : { - "transcriptId" : { - "value" : "96d13df2-6551-41f7-94b5-c7da14dd5ce0", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "6", - "gene" : { - "code" : "HGNC:18615", - "display" : "BRAFP1", - "system" : "https://www.genenames.org/" - }, - "position" : 814, - "strand" : "-" - }, - "effect" : "Effect", - "reportedNumReads" : 7 - }, { - "id" : "bf815c71-c890-40a3-84fb-714f31814c59", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "a6e3dd2f-1d7c-404d-953c-710873f846dd", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "localization" : [ { - "code" : "splicing-region", - "display" : "splicing region", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "transcriptId" : { - "value" : "d7d2344f-6651-4527-aa93-cb5b93f05aee", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "6", - "gene" : { - "code" : "HGNC:5173", - "display" : "HRAS", - "system" : "https://www.genenames.org/" - }, - "position" : 292, - "strand" : "-" - }, - "fusionPartner3prime" : { - "transcriptId" : { - "value" : "4092f456-1d4a-43e0-84a9-f70c3c14cf6b", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "5", - "gene" : { - "code" : "HGNC:6973", - "display" : "MDM2", - "system" : "https://www.genenames.org/" - }, - "position" : 925, - "strand" : "+" - }, - "effect" : "Effect", - "reportedNumReads" : 7 - }, { - "id" : "5436e5f8-db2d-4947-a88a-1ab6b07e5faa", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "b83aa40a-fd2f-49c3-a34f-1411cc32783f", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "localization" : [ { - "code" : "intergenic", - "display" : "Intergenic", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "transcriptId" : { - "value" : "f9481fda-4a3f-442d-ad3f-e6adccfc4e73", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "5", - "gene" : { - "code" : "HGNC:5173", - "display" : "HRAS", - "system" : "https://www.genenames.org/" - }, - "position" : 951, - "strand" : "+" - }, - "fusionPartner3prime" : { - "transcriptId" : { - "value" : "18488fee-209c-4abe-9896-f49007bcc648", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "9", - "gene" : { - "code" : "HGNC:5173", - "display" : "HRAS", - "system" : "https://www.genenames.org/" - }, - "position" : 944, - "strand" : "-" - }, - "effect" : "Effect", - "reportedNumReads" : 6 - }, { - "id" : "a206e483-f18c-4656-924b-0f79969da5ab", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "adae872d-f6a7-4c3f-a7be-c4aad3f57694", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "localization" : [ { - "code" : "regulatory-region", - "display" : "Regulatory region", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "transcriptId" : { - "value" : "1a5c5afe-c41d-4300-b483-9a55a2ca0ac7", - "system" : "https://www.ensembl.org" - }, - "exonId" : "10", - "gene" : { - "code" : "HGNC:3942", - "display" : "MTOR", - "system" : "https://www.genenames.org/" - }, - "position" : 778, - "strand" : "+" - }, - "fusionPartner3prime" : { - "transcriptId" : { - "value" : "16ca230d-78b7-4dfe-9025-616b2d1e0e0e", - "system" : "https://www.ensembl.org" - }, - "exonId" : "10", - "gene" : { - "code" : "HGNC:34", - "display" : "ABCA4", - "system" : "https://www.genenames.org/" - }, - "position" : 216, - "strand" : "+" - }, - "effect" : "Effect", - "reportedNumReads" : 7 - }, { - "id" : "3345abf6-6afa-4069-8b45-390c5ceda24c", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "1b970bcf-766a-472e-a210-4b245c6b697d", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "localization" : [ { - "code" : "intergenic", - "display" : "Intergenic", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "transcriptId" : { - "value" : "030c35d3-eafb-4980-9d26-a6d124e5b411", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "8", - "gene" : { - "code" : "HGNC:33", - "display" : "ABCA3", - "system" : "https://www.genenames.org/" - }, - "position" : 496, - "strand" : "+" - }, - "fusionPartner3prime" : { - "transcriptId" : { - "value" : "4e673024-533a-4931-9ac0-f069d139d0ad", - "system" : "https://www.ensembl.org" - }, - "exonId" : "11", - "gene" : { - "code" : "HGNC:3689", - "display" : "FGFR2", - "system" : "https://www.genenames.org/" - }, - "position" : 525, - "strand" : "+" - }, - "effect" : "Effect", - "reportedNumReads" : 6 - }, { - "id" : "74254963-0987-4123-ba2c-c57e9de9afd7", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "28050793-0c1d-4d3b-abac-3d569d26a154", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "localization" : [ { - "code" : "splicing-region", - "display" : "splicing region", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "transcriptId" : { - "value" : "b6536e66-bc89-4288-812f-436aa4d5a9a2", - "system" : "https://www.ensembl.org" - }, - "exonId" : "10", - "gene" : { - "code" : "HGNC:1100", - "display" : "BRCA1", - "system" : "https://www.genenames.org/" - }, - "position" : 51, - "strand" : "-" - }, - "fusionPartner3prime" : { - "transcriptId" : { - "value" : "1289121c-c6fa-4179-b7fe-5c1f6326c2fa", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "3", - "gene" : { - "code" : "HGNC:21298", - "display" : "AACS", - "system" : "https://www.genenames.org/" - }, - "position" : 905, - "strand" : "-" - }, - "effect" : "Effect", - "reportedNumReads" : 5 - }, { - "id" : "476bf705-ea3e-4a4e-8e9b-29a8fd79446c", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "externalIds" : [ { - "value" : "ed80a31e-8f15-4e4f-8c78-654bc16e56a2", - "system" : "https://cancer.sanger.ac.uk/cosmic" - } ], - "localization" : [ { - "code" : "intronic", - "display" : "Intronic", - "system" : "dnpm-dip/variant/localization" - } ], - "fusionPartner5prime" : { - "transcriptId" : { - "value" : "6ec1314f-0301-4448-adad-da588a340928", - "system" : "https://www.ensembl.org" - }, - "exonId" : "3", - "gene" : { - "code" : "HGNC:21298", - "display" : "AACS", - "system" : "https://www.genenames.org/" - }, - "position" : 335, - "strand" : "+" - }, - "fusionPartner3prime" : { - "transcriptId" : { - "value" : "869e0853-097c-4c03-81f2-5d2b1f702e83", - "system" : "https://www.ncbi.nlm.nih.gov/refseq" - }, - "exonId" : "6", - "gene" : { - "code" : "HGNC:1753", - "display" : "CDH13", - "system" : "https://www.genenames.org/" - }, - "position" : 927, - "strand" : "+" - }, - "effect" : "Effect", - "reportedNumReads" : 5 - } ], - "rnaSeqs" : [ ] - } - } ], - "carePlans" : [ { - "id" : "ddecb45f-d328-4a31-9f0b-504dd74a09bb", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" - }, - "issuedOn" : "2025-04-03", - "statusReason" : { - "code" : "targeted-diagnostics-recommended", - "display" : "Zieldiagnostik empfohlen", - "system" : "dnpm-dip/mtb/careplan/status-reason" - }, - "geneticCounselingRecommendation" : { - "id" : "caee4091-8b35-4be8-954e-e6d7f4d6f8b2", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "issuedOn" : "2025-04-03", - "reason" : { - "code" : "unknown", - "display" : "Unbekannt", - "system" : "dnpm-dip/mtb/recommendation/genetic-counseling/reason" + "issuedOn": "2025-05-30", + "stage": { + "code": "revocation", + "display": "Widerspruch", + "system": "dnpm-dip/mtb/claim/stage" } }, - "medicationRecommendations" : [ { - "id" : "083a04e9-05f3-4b37-9e7d-e0bf703a8c3c", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" + { + "id": "fa9b668c-c39d-42a9-bdb2-410bc3f4a361", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" + "recommendation": { + "id": "5adb8293-f9d1-4e65-bdcf-9d4803bd9d1c", + "type": "MTBMedicationRecommendation" }, - "issuedOn" : "2025-04-03", - "priority" : { - "code" : "2", - "display" : "2", - "system" : "dnpm-dip/recommendation/priority" + "issuedOn": "2025-05-30", + "stage": { + "code": "initial-claim", + "display": "Erstantrag", + "system": "dnpm-dip/mtb/claim/stage" + } + } + ], + "claimResponses": [ + { + "id": "db18a72a-293e-4f2d-bfe5-273776f8286b", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" }, - "levelOfEvidence" : { - "grading" : { - "code" : "m1B", - "display" : "m1B", - "system" : "dnpm-dip/mtb/level-of-evidence/grading" - }, - "addendums" : [ { - "code" : "is", - "display" : "is", - "system" : "dnpm-dip/mtb/level-of-evidence/addendum" - } ], - "publications" : [ { - "id" : "884742948", - "system" : "https://pubmed.ncbi.nlm.nih.gov", - "type" : "Publication" - } ] + "claim": { + "id": "4aa57f09-d47a-4916-852e-c79175a0eca7", + "type": "Claim" }, - "category" : { - "code" : "IM", - "display" : "Immun-/Antikörpertherapie", - "system" : "dnpm-dip/mtb/recommendation/systemic-therapy/category" + "issuedOn": "2025-05-30", + "status": { + "code": "accepted", + "display": "Angenommen", + "system": "dnpm-dip/mtb/claim-response/status" + } + }, + { + "id": "ff5f495e-20c6-4c18-b150-4799343049c4", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" }, - "medication" : [ { - "code" : "L01EN01", - "display" : "Erdafitinib", - "system" : "http://fhir.de/CodeSystem/bfarm/atc", - "version" : "2024" - } ], - "useType" : { - "code" : "in-label", - "display" : "In-label Use", - "system" : "dnpm-dip/mtb/recommendation/systemic-therapy/use-type" + "claim": { + "id": "fa9b668c-c39d-42a9-bdb2-410bc3f4a361", + "type": "Claim" }, - "supportingVariants" : [ { - "variant" : { - "id" : "7acb8b5a-28e5-49e8-9af0-8f0b07dd7928", - "type" : "Variant" - }, - "gene" : { - "code" : "HGNC:6407", - "display" : "KRAS", - "system" : "https://www.genenames.org/" + "issuedOn": "2025-05-30", + "status": { + "code": "accepted", + "display": "Angenommen", + "system": "dnpm-dip/mtb/claim-response/status" + } + } + ], + "systemicTherapies": [ + { + "history": [ + { + "id": "bc0b340d-17ea-4598-ad69-38d309e47182", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "intent": { + "code": "X", + "display": "Keine Angabe", + "system": "dnpm-dip/therapy/intent" + }, + "category": { + "code": "N", + "display": "Neoadjuvant", + "system": "dnpm-dip/therapy/category" + }, + "basedOn": { + "id": "8c9e7e7f-daea-4b7b-ad72-6ef6be070f95", + "type": "MTBMedicationRecommendation" + }, + "recordedOn": "2025-05-30", + "status": { + "code": "on-going", + "display": "Laufend", + "system": "dnpm-dip/therapy/status" + }, + "recommendationFulfillmentStatus": { + "code": "partial", + "display": "Partiell", + "system": "dnpm-dip/therapy/recommendation-fulfillment-status" + }, + "dosage": { + "code": "under-50%", + "display": "< 50 %", + "system": "dnpm-dip/therapy/dosage-density" + }, + "period": { + "start": "2024-11-08", + "end": "2025-05-30" + }, + "medication": [ + { + "code": "L01EX01", + "display": "Sunitinib", + "system": "http://fhir.de/CodeSystem/bfarm/atc", + "version": "2025" + } + ], + "notes": [ + "Notes on the therapy..." + ] } - } ] - }, { - "id" : "5650387b-2f3b-4f77-863c-9af4d02294fb", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" - }, - "issuedOn" : "2025-04-03", - "priority" : { - "code" : "1", - "display" : "1", - "system" : "dnpm-dip/recommendation/priority" - }, - "levelOfEvidence" : { - "grading" : { - "code" : "m2C", - "display" : "m2C", - "system" : "dnpm-dip/mtb/level-of-evidence/grading" - }, - "addendums" : [ { - "code" : "Z", - "display" : "Z", - "system" : "dnpm-dip/mtb/level-of-evidence/addendum" - } ], - "publications" : [ { - "id" : "1566646481", - "system" : "https://pubmed.ncbi.nlm.nih.gov", - "type" : "Publication" - } ] - }, - "category" : { - "code" : "HO", - "display" : "Hormontherapie", - "system" : "dnpm-dip/mtb/recommendation/systemic-therapy/category" - }, - "medication" : [ { - "code" : "L01FX33", - "display" : "Tarlatamab", - "system" : "http://fhir.de/CodeSystem/bfarm/atc", - "version" : "2024" - } ], - "useType" : { - "code" : "off-label", - "display" : "Off-bel Use", - "system" : "dnpm-dip/mtb/recommendation/systemic-therapy/use-type" - }, - "supportingVariants" : [ { - "variant" : { - "id" : "0ccc8b6a-7692-405e-afb3-9ba79f6a6dc6", - "type" : "Variant" - }, - "gene" : { - "code" : "HGNC:11998", - "display" : "TP53", - "system" : "https://www.genenames.org/" + ] + }, + { + "history": [ + { + "id": "e3d4b435-0531-4d75-827c-0da914f054dd", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "reason": { + "id": "53155bb3-39f8-4cd9-aa9b-1675165bfdb8", + "display": "Bösartige Neubildung: Tuba uterina [Falloppio]", + "type": "MTBDiagnosis" + }, + "intent": { + "code": "K", + "display": "Kurativ", + "system": "dnpm-dip/therapy/intent" + }, + "category": { + "code": "A", + "display": "Adjuvant", + "system": "dnpm-dip/therapy/category" + }, + "basedOn": { + "id": "5adb8293-f9d1-4e65-bdcf-9d4803bd9d1c", + "type": "MTBMedicationRecommendation" + }, + "recordedOn": "2025-05-30", + "status": { + "code": "completed", + "display": "Abgeschlossen", + "system": "dnpm-dip/therapy/status" + }, + "recommendationFulfillmentStatus": { + "code": "complete", + "display": "Komplett", + "system": "dnpm-dip/therapy/recommendation-fulfillment-status" + }, + "dosage": { + "code": "over-50%", + "display": ">= 50 %", + "system": "dnpm-dip/therapy/dosage-density" + }, + "period": { + "start": "2024-10-25", + "end": "2025-05-30" + }, + "medication": [ + { + "code": "L01FX01", + "display": "Edrecolomab", + "system": "http://fhir.de/CodeSystem/bfarm/atc", + "version": "2025" + } + ], + "notes": [ + "Notes on the therapy..." + ] } - } ] - } ], - "procedureRecommendations" : [ { - "id" : "1e76d94c-a57a-4b3f-9d6b-4af303c05199", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" - }, - "issuedOn" : "2025-04-03", - "priority" : { - "code" : "3", - "display" : "3", - "system" : "dnpm-dip/recommendation/priority" - }, - "levelOfEvidence" : { - "grading" : { - "code" : "m2C", - "display" : "m2C", - "system" : "dnpm-dip/mtb/level-of-evidence/grading" - }, - "addendums" : [ { - "code" : "iv", - "display" : "iv", - "system" : "dnpm-dip/mtb/level-of-evidence/addendum" - } ], - "publications" : [ { - "id" : "9936302", - "system" : "https://pubmed.ncbi.nlm.nih.gov", - "type" : "Publication" - } ] - }, - "code" : { - "code" : "SO", - "display" : "Sonstiges", - "system" : "dnpm-dip/mtb/recommendation/procedure/category" - }, - "supportingVariants" : [ { - "variant" : { - "id" : "01a40602-1992-44ee-86cf-af4b9f8ede17", - "type" : "Variant" - }, - "gene" : { - "code" : "HGNC:25829", - "display" : "ABRAXAS1", - "system" : "https://www.genenames.org/" - } - } ] - } ], - "studyEnrollmentRecommendations" : [ { - "id" : "c617652e-d118-4033-9678-ea8eade11abb", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" - }, - "issuedOn" : "2025-04-03", - "levelOfEvidence" : { - "code" : "m1B", - "display" : "m1B", - "system" : "dnpm-dip/mtb/level-of-evidence/grading" - }, - "priority" : { - "code" : "1", - "display" : "1", - "system" : "dnpm-dip/recommendation/priority" - }, - "study" : [ { - "id" : "fe066270-e69e-4fc7-95b1-59a3e8456a11", - "system" : "EUDAMED", - "type" : "Study" - } ], - "supportingVariants" : [ { - "variant" : { - "id" : "7acb8b5a-28e5-49e8-9af0-8f0b07dd7928", - "type" : "Variant" - }, - "gene" : { - "code" : "HGNC:6407", - "display" : "KRAS", - "system" : "https://www.genenames.org/" - } - } ] - } ], - "histologyReevaluationRequests" : [ { - "id" : "d9565325-726d-4fc8-bfa9-0fa4c0b53d7b", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "specimen" : { - "id" : "b0557dde-6e54-4d01-8982-7ff88313adaa", - "type" : "TumorSpecimen" - }, - "issuedOn" : "2025-04-03" - } ], - "rebiopsyRequests" : [ { - "id" : "858ce32e-3dea-4cdf-b85a-ae9fa84d113b", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "tumorEntity" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "type" : "MTBDiagnosis" - }, - "issuedOn" : "2025-04-03" - } ], - "notes" : [ "Protocol of the MTB conference..." ] - } ], - "followUps" : [ { - "date" : "2006-12-10" - } ], - "claims" : [ { - "id" : "d7afc9e8-5342-443d-9e13-0a88b4dd6037", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "recommendation" : { - "id" : "083a04e9-05f3-4b37-9e7d-e0bf703a8c3c", - "type" : "MTBMedicationRecommendation" - }, - "issuedOn" : "2025-04-03", - "stage" : { - "code" : "initial-claim", - "display" : "Erstantrag", - "system" : "dnpm-dip/mtb/claim/stage" + ] } - }, { - "id" : "2ef6b3c7-ce7e-4415-8a43-bd7a3a67be95", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" + ], + "responses": [ + { + "id": "1bcd9695-739f-451b-a403-7def6fa43614", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "therapy": { + "id": "bc0b340d-17ea-4598-ad69-38d309e47182", + "type": "MTBSystemicTherapy" + }, + "effectiveDate": "2025-02-07", + "method": { + "code": "RANO", + "display": "Nach RANO-Kriterien", + "system": "dnpm-dip/mtb/response/method" + }, + "value": { + "code": "PR", + "display": "Partial Response", + "system": "RECIST" + } }, - "recommendation" : { - "id" : "5650387b-2f3b-4f77-863c-9af4d02294fb", - "type" : "MTBMedicationRecommendation" - }, - "issuedOn" : "2025-04-03", - "stage" : { - "code" : "revocation", - "display" : "Widerspruch", - "system" : "dnpm-dip/mtb/claim/stage" + { + "id": "89f6c606-0ec6-4b1e-a316-56a16eb52ea2", + "patient": { + "id": "e14bf9b6-7982-4933-a648-cfdea6484f1c", + "type": "Patient" + }, + "therapy": { + "id": "e3d4b435-0531-4d75-827c-0da914f054dd", + "type": "MTBSystemicTherapy" + }, + "effectiveDate": "2024-12-27", + "method": { + "code": "RECIST", + "display": "Nach RECIST-Kriterien", + "system": "dnpm-dip/mtb/response/method" + }, + "value": { + "code": "SD", + "display": "Stable Disease", + "system": "RECIST" + } } - } ], - "claimResponses" : [ { - "id" : "d9085718-77f6-4ace-b6da-c9358c853ff0", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "claim" : { - "id" : "d7afc9e8-5342-443d-9e13-0a88b4dd6037", - "type" : "Claim" - }, - "issuedOn" : "2025-04-03", - "status" : { - "code" : "rejected", - "display" : "Abgelehnt", - "system" : "dnpm-dip/mtb/claim-response/status" - }, - "statusReason" : { - "code" : "unknown", - "display" : "Unbekant", - "system" : "dnpm-dip/mtb/claim-response/status-reason" - } - }, { - "id" : "d93a0943-628d-47c6-9eda-4fba38df42be", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "claim" : { - "id" : "2ef6b3c7-ce7e-4415-8a43-bd7a3a67be95", - "type" : "Claim" - }, - "issuedOn" : "2025-04-03", - "status" : { - "code" : "rejected", - "display" : "Abgelehnt", - "system" : "dnpm-dip/mtb/claim-response/status" - }, - "statusReason" : { - "code" : "approval-revocation", - "display" : "Rücknahme der Zulassung", - "system" : "dnpm-dip/mtb/claim-response/status-reason" - } - } ], - "systemicTherapies" : [ { - "history" : [ { - "id" : "6b150d30-1c82-4663-833f-6a12ac582ca4", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" - }, - "intent" : { - "code" : "S", - "display" : "Sonstiges", - "system" : "dnpm-dip/therapy/intent" - }, - "category" : { - "code" : "I", - "display" : "Intraopterativ", - "system" : "dnpm-dip/therapy/category" - }, - "basedOn" : { - "id" : "083a04e9-05f3-4b37-9e7d-e0bf703a8c3c", - "type" : "MTBMedicationRecommendation" - }, - "recordedOn" : "2025-04-03", - "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" - }, - "period" : { - "start" : "2006-10-15", - "end" : "2007-02-25" - }, - "medication" : [ { - "code" : "L01EN01", - "display" : "Erdafitinib", - "system" : "http://fhir.de/CodeSystem/bfarm/atc", - "version" : "2024" - } ], - "notes" : [ "Notes on the therapy..." ] - } ] - }, { - "history" : [ { - "id" : "27b6eddc-1a4f-4d68-a027-190a2c38754b", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "reason" : { - "id" : "744bf622-ba4b-4e64-867c-0807847d9da4", - "display" : "Bösartige Neubildung: Konjunktiva", - "type" : "MTBDiagnosis" - }, - "intent" : { - "code" : "X", - "display" : "Keine Angabe", - "system" : "dnpm-dip/therapy/intent" - }, - "category" : { - "code" : "A", - "display" : "Adjuvant", - "system" : "dnpm-dip/therapy/category" - }, - "basedOn" : { - "id" : "5650387b-2f3b-4f77-863c-9af4d02294fb", - "type" : "MTBMedicationRecommendation" - }, - "recordedOn" : "2025-04-03", - "status" : { - "code" : "stopped", - "display" : "Abgebrochen", - "system" : "dnpm-dip/therapy/status" - }, - "statusReason" : { - "code" : "progression", - "display" : "Progression", - "system" : "dnpm-dip/therapy/status-reason" - }, - "recommendationFulfillmentStatus" : { - "code" : "partial", - "display" : "Partiell", - "system" : "dnpm-dip/therapy/recommendation-fulfillment-status" - }, - "period" : { - "start" : "2006-10-29", - "end" : "2007-02-25" - }, - "medication" : [ { - "code" : "L01FX33", - "display" : "Tarlatamab", - "system" : "http://fhir.de/CodeSystem/bfarm/atc", - "version" : "2024" - } ], - "notes" : [ "Notes on the therapy..." ] - } ] - } ], - "responses" : [ { - "id" : "bbbbbaaf-8486-454c-ba59-28593519342c", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "therapy" : { - "id" : "6b150d30-1c82-4663-833f-6a12ac582ca4", - "type" : "MTBSystemicTherapy" - }, - "effectiveDate" : "2006-12-10", - "method" : { - "code" : "RECIST", - "display" : "Nach RECIST-Kriterien", - "system" : "dnpm-dip/mtb/response/method" - }, - "value" : { - "code" : "SD", - "display" : "Stable Disease", - "system" : "RECIST" - } - }, { - "id" : "6b93b820-4d03-4883-af96-cf504fa6798e", - "patient" : { - "id" : "63f8fd7b-8127-4f3c-8843-aa9199e21c29", - "type" : "Patient" - }, - "therapy" : { - "id" : "27b6eddc-1a4f-4d68-a027-190a2c38754b", - "type" : "MTBSystemicTherapy" - }, - "effectiveDate" : "2007-02-11", - "method" : { - "code" : "RECIST", - "display" : "Nach RECIST-Kriterien", - "system" : "dnpm-dip/mtb/response/method" - }, - "value" : { - "code" : "PD", - "display" : "Progressive Disease", - "system" : "RECIST" - } - } ] + ] } From 17f4dc3512c922091041beb7c7bb84d467253e7c Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Sun, 8 Jun 2025 20:02:16 +0200 Subject: [PATCH 3/3] chore: update to Spring Boot 3.5.0 (#115) --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index c688d6c..ad92d42 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -5,7 +5,7 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage plugins { war - id("org.springframework.boot") version "3.4.6" + id("org.springframework.boot") version "3.5.0" id("io.spring.dependency-management") version "1.1.7" kotlin("jvm") version "1.9.25" kotlin("plugin.spring") version "1.9.25"