martinchapman · May 5, 2026 14:16
diff --git a/oncoqwen_sample_data_input.json b/oncoqwen_sample_data_input.json
 [
  {"document_id": "5609cc8b-f83b-443c-9583-364c188b4dc8", "document_content": "Oncology MDT Letter – Outpatient Clinic Date: 14th March 2024 Dear Dr. Patel, Thank you for referring Mrs. Eleanor Hughes, a 58-year-old woman, regarding her known metastatic non-small cell lung carcinoma, initially diagnosed in September 2021. This represents a recurrence of her previously treated early-stage disease. Disease Status & Staging Eleanor's primary tumour is a right upper lobe lung adenocarcinoma, staged at T3N2M1c (Group Stage IVb) at the time of metastatic diagnosis. Molecular profiling revealed an EGFR exon 19 deletion (VAF 34.2%), with PD-L1 expression of 60% positive. KRAS was negative. MSI testing confirmed microsatellite stable (MSS) disease. TMB was 6.2 mutations/Mb (TMB-low). Known sites of spread include bilateral mediastinal lymph nodes, a solitary liver metastasis (segment VI), and leptomeningeal disease confirmed on MRI in January 2024. Scores Performance status is ECOG 1 (\"she remains independently active and working part-time\"). No Gleason or FIGO applicable. Treatment History October 2021: Commenced osimertinib 80mg OD as first-line therapy. She achieved a partial response confirmed on CT chest/abdomen at 3 months. August 2023: Repeat imaging demonstrated radiological progression with enlargement of the liver lesion and two new mediastinal nodes. September 2023: Osimertinib was stopped due to progression and treatment was switched to carboplatin/pemetrexed chemotherapy. She experienced grade 2 nausea and fatigue as treatment-related toxicities, requiring a dose reduction in cycle 3. January 2024: MRI brain/spine confirmed leptomeningeal metastatic progression. Eleanor was considered for the LAURA trial in November 2023 but was not eligible due to prior osimertinib use. Patient Findings Eleanor reports persistent mild dyspnoea on exertion and a 4kg unintentional weight loss over 3 months. She denies haemoptysis. On examination, there is mild cachexia. She is a lifelong non-smoker. Family history is notable for breast cancer in her mother. Psychologically, she is described as deeply anxious about the leptomeningeal diagnosis but engaged with the MDT plan. Comorbidities Known type 2 diabetes mellitus, well-controlled on metformin. Future Plans We plan to commence amivantamab plus lazertinib on a named-patient basis pending funding approval. A repeat LP is planned to reconfirm leptomeningeal disease cytology. We are enrolling Eleanor to the MARIPOSA-2 clinical trial pending consent. Yours sincerely, Dr. A. Rahman, Consultant Medical Oncologist"},
  {"document_id": "25a137f0-803c-4859-a068-031cdc2f8f11", "document_content": "Haematology MDT Note Date: 3rd January 2024Dear Dr. Okonkwo,I reviewed Mr. Samuel Adeyemi, a 45-year-old man, in the haematology clinic today regarding his relapsed acute myeloid leukaemia. His AML was first diagnosed in February 2022 following a 6-week history of fatigue and recurrent infections. Bone marrow biopsy at diagnosis confirmed FLT3-ITD mutation (VAF 42.1%) and NPM1 mutation (VAF 38.6%). Cytogenetics showed normal karyotype.Treatment History March 2022: Commenced intensive induction chemotherapy with daunorubicin and cytarabine (7+3) plus midostaurin given FLT3 positivity. Cycle 1 was complicated by grade 3 febrile neutropenia requiring ITU admission for 4 days — a significant treatment-related complication. June 2022: Bone marrow assessment confirmed complete morphological remission with MRD negativity by flow cytometry. October 2022: Proceeded to allogeneic stem cell transplant from a matched unrelated donor. Post-transplant course was complicated by grade 2 acute graft-versus-host disease affecting skin and gut, managed with systemic steroids with good response. September 2023: Routine surveillance bone marrow biopsy demonstrated morphological relapse with 28% blasts. FLT3-ITD re-confirmed. BCR-ABL1 was negative. Samuel is currently ECOG 2 (\"he is symptomatic and in bed less than 50% of the day but requires assistance with some daily activities\"). He reports significant fatigue and exertional dyspnoea. He denies active bleeding. On examination there is mild hepatosplenomegaly. He is a non-drinker and non-smoker, lives alone in supported housing with a care package in place.Future Plans We plan to commence salvage therapy with gilteritinib monotherapy. He has been referred to the MORPHO trial assessment clinic and is under active consideration for enrolment. A repeat bone marrow trephine is planned in 4 weeks to assess response.Yours sincerely, Dr. F. Mensah, Consultant Haematologist"},
  {"document_id": "74fbef3d-17b9-439d-bae4-12b4fcf9c730", "document_content": "Colorectal MDT Clinic Letter Date: 22nd February 2024 Dear Dr. Clarkson, Thank you for your referral of Mrs. Patricia Doyle, a 67-year-old woman, with confirmed metastatic colorectal adenocarcinoma of the sigmoid colon, initially diagnosed in May 2019 (Dukes Stage C, TNM T3N1M0 at primary resection). Molecular Profile Tumour molecular profiling has demonstrated MSI-high disease, confirmed on both PCR and IHC (MLH1 and PMS2 protein loss). TMB was reported as 48.3 mutations/Mb (TMB-high). KRAS and NRAS are both wild-type. BRAF V600E mutation was identified. PDL1 combined positive score was 12. Disease History & Spread June 2019: She underwent anterior resection with curative intent. Pathology confirmed clear margins. November 2019 – April 2020: Completed adjuvant CAPOX chemotherapy. She tolerated this reasonably well, though experienced grade 1 peripheral neuropathy and grade 2 hand-foot syndrome, the latter requiring a dose reduction in cycle 4. March 2022: CT staging demonstrated new hepatic metastases (segments IV and VII) and peritoneal deposits — confirmed metastatic progression. CA19-9 markedly elevated. April 2022: Commenced first-line FOLFOX plus bevacizumab. Interim CT at 3 months confirmed partial response with >30% reduction in hepatic lesion size. January 2024: Repeat CT demonstrated enlargement of the peritoneal disease and a new omental deposit — radiological evidence of progression. Mrs. Doyle is ECOG 1. She reports worsening abdominal bloating and intermittent altered bowel habit. She denies rectal bleeding. She is an ex-smoker (20 pack-year history, ceased 2015) and drinks approximately 14 units of alcohol per week. Family history is notable for colorectal cancer in her father (diagnosed aged 55) and endometrial cancer in her sister — Lynch syndrome testing has been initiated. Future Plans Given MSI-high and BRAF V600E status, we plan to switch to pembrolizumab plus encorafenib/binimetinib. She has been enrolled to the BREAKWATER trial. A diagnostic laparoscopy is planned to formally assess peritoneal disease burden prior to any surgical consideration. Yours sincerely, Dr. L. Singh, Consultant Medical Oncologist"},
  {"document_id": "e4db4a86-5bc1-477d-b03f-ff12fa70ce08", "document_content": "Breast Cancer Clinic Letter Date: 8th April 2024 Dear Dr. Whitmore, I am writing regarding Ms. Aisha Nkemdirim, a 42-year-old woman, who attended the breast oncology clinic today. She has metastatic breast cancer (ER-positive 8+/8, PR-positive 6+/8, HER2 3+ by IHC confirmed on ISH) with Ki67 of 42%, consistent with a high-proliferation luminal B HER2-positive tumour. PIK3CA H1047R mutation was identified on liquid biopsy. BRCA2 pathogenic germline variant confirmed (BRCA1 negative). ESR1 mutation was not detected. Her primary left breast invasive ductal carcinoma (adenocarcinoma) was diagnosed in August 2020, staged T2N1M0 (Group Stage IIb). This is not a recurrence — she presented de novo with locally advanced disease. Known Sites of Spread Confirmed metastatic sites include: multiple thoracic and lumbar vertebral bone metastases, bilateral axillary lymph nodes, and a single right adrenal deposit identified on most recent PET-CT. Treatment Timeline September 2020: Underwent left mastectomy and axillary node clearance. Pathology confirmed 3 of 14 nodes positive. November 2020 – March 2021: Completed adjuvant docetaxel, carboplatin, trastuzumab and pertuzumab (TCHP). Complicated by grade 3 neutropenic sepsis during cycle 2. April 2021 – July 2022: Completed adjuvant radiotherapy to chest wall and supraclavicular fossa, followed by T-DM1 for 14 cycles. Achieved confirmed radiological remission on CT at completion. February 2023: PET-CT demonstrated new bone metastases — confirmed disease recurrence. March 2023: Commenced trastuzumab deruxtecan (T-DXd). Interim assessment confirmed partial response at 3 months. March 2024: Interval CT demonstrates stable bone disease but new adrenal lesion — mixed/equivocal response. Aisha is ECOG 1 (\"independently active, working part-time from home\"). She reports moderate back pain, scoring 5/10, managed with regular analgesia. She denies neurological symptoms. She is a lifelong non-smoker. She is visibly distressed regarding implications of her BRCA2 status for her two daughters and has been referred to the clinical genetics team. She has a strong family history: mother with breast cancer (age 38) and maternal aunt with ovarian cancer. Future Plans We plan to add tucatinib to her current regimen and enrol her to the HER2CLIMB-02 trial. Genetic counselling appointment arranged. Zoledronic acid infusion planned to continue quarterly. Yours sincerely, Dr. C. Oduya, Consultant Medical Oncologist"},
  {"document_id": "c1c3cdef-cd4d-4bbf-8ffb-4088eb3939ec", "document_content": "Neuro-oncology MDT Note Date: 19th March 2024 Dear Dr. Harrington, I am writing with a brief update regarding Mr. Thomas Grenville, a 71-year-old man, with IDH-wildtype glioblastoma (GBM), WHO Grade 4. Diagnosis was confirmed histologically following craniotomy in April 2023. MGMT promoter methylation was confirmed present. IDH1 and IDH2 were both wild-type. EGFR amplification was identified. TERT promoter mutation confirmed. The primary tumour was located in the right temporal lobe with involvement of the insula. TNM staging is not formally applied; FIGO and Gleason are not applicable. Breslow and Clark staging are similarly not relevant. Treatment History May 2023: Commenced standard Stupp protocol — concurrent temozolomide with radiotherapy (60Gy in 30 fractions to the right temporal lobe). He tolerated this reasonably well with grade 1 fatigue and grade 1 radiation dermatitis only. August 2023: Following completion of concurrent phase, commenced adjuvant temozolomide. Interim MRI at cycle 3 demonstrated increased T1 enhancement — assessed as likely pseudoprogression given early timing and MGMT methylation status. Decision made to continue. November 2023: Repeat MRI brain confirmed true radiological progression with significant enlargement of the right temporal enhancing lesion and new mass effect, with midline shift of 6mm. December 2023: Commenced bevacizumab monotherapy as second-line. Performance status at this point had declined to ECOG 3 (\"spends more than 50% of the day in bed, limited self-care\"). January 2024: He was considered for the REGN2810 trial but was excluded due to prior bevacizumab use and declining performance status. Mr. Grenville was increasingly confused and disorientated at the time of his last clinic attendance in February 2024, consistent with disease-related cognitive impairment. His wife reported that he had become bedbound at home. He denied pain but was unable to reliably report symptoms. A social care package had been urgently escalated and he was transferred to a local hospice for symptom management. It is with great regret that I must inform you that Mr. Grenville passed away on 14th March 2024, approximately 11 months from his initial diagnosis. Yours sincerely, Dr. M. Tran, Consultant Neuro-oncologist"}
 ]
diff --git a/oncoqwen_sample_data_output.json b/oncoqwen_sample_data_output.json
 {"document_id":"25a137f0-803c-4859-a068-031cdc2f8f11","document_source":"{}","document_inference":"{\"document_has_primary_cancer_flag\":true,\"primary_cancer_confirmed_flag\":true,\"primary_cancer\":{\"primary_cancer_facts\":{\"topography\":\"haematological\",\"topography_name_desc\":null,\"morphology\":\"acute_myeloid_leukaemia\",\"morphology_name_desc\":\"acute myeloid leukaemia\",\"is_recurrence\":true,\"diagnosis_year\":2022,\"diagnosis_month\":2,\"tnm_stage\":null,\"numeric_group_stage\":null},\"primary_cancer_tumour_facts\":{\"msi_status\":null,\"msi_desc\":null,\"tmb_status\":null,\"tmb_numeric_value\":null,\"tmb_desc\":null,\"molecular_biomarker_profiles\":[{\"biomarker\":\"flt3\",\"biomarker_name_desc\":\"FLT3-ITD\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":\"ITD\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":42.1,\"biomarker_vaf_desc\":\"VAF 42.1%\",\"biomarker_desc\":\"FLT3-ITD mutation (VAF 42.1%)\"},{\"biomarker\":\"npm1\",\"biomarker_name_desc\":\"NPM1\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":null,\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":38.6,\"biomarker_vaf_desc\":\"VAF 38.6%\",\"biomarker_desc\":\"NPM1 mutation (VAF 38.6%)\"},{\"biomarker\":\"bcr_abl1\",\"biomarker_name_desc\":\"BCR-ABL1\",\"biomarker_status\":\"negative\",\"biomarker_alteration\":null,\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"BCR-ABL1 was negative.\"}]},\"primary_cancer_scores\":null,\"primary_cancer_spread\":null,\"primary_cancer_timeline_events\":[{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2022,\"event_month\":3,\"event_summary\":\"Commenced intensive induction chemotherapy with daunorubicin and cytarabine (7+3) plus midostaurin\",\"event_desc\":\"Commenced intensive induction chemotherapy with daunorubicin and cytarabine (7+3) plus midostaurin given FLT3 positivity.\"},{\"event_type\":\"experienced_toxicity_or_complication_related_to_treatment\",\"event_year\":2022,\"event_month\":3,\"event_summary\":\"Grade 3 febrile neutropenia requiring ITU admission for 4 days\",\"event_desc\":\"Cycle 1 was complicated by grade 3 febrile neutropenia requiring ITU admission for 4 days – a significant treatment-related complication.\"},{\"event_type\":\"experienced_disease_remission\",\"event_year\":2022,\"event_month\":6,\"event_summary\":\"Complete morphological remission with MRD negativity\",\"event_desc\":\"Bone marrow assessment confirmed complete morphological remission with MRD negativity by flow cytometry.\"},{\"event_type\":\"had_surgical_treatment_performed\",\"event_year\":2022,\"event_month\":10,\"event_summary\":\"Allogeneic stem cell transplant from a matched unrelated donor\",\"event_desc\":\"Proceeded to allogeneic stem cell transplant from a matched unrelated donor.\"},{\"event_type\":\"experienced_toxicity_or_complication_related_to_treatment\",\"event_year\":2022,\"event_month\":10,\"event_summary\":\"Grade 2 acute graft-versus-host disease affecting skin and gut\",\"event_desc\":\"Post-transplant course was complicated by grade 2 acute graft-versus-host disease affecting skin and gut, managed with systemic steroids with good response.\"},{\"event_type\":\"experienced_disease_recurrence\",\"event_year\":2023,\"event_month\":9,\"event_summary\":\"Morphological relapse with 28% blasts\",\"event_desc\":\"Routine surveillance bone marrow biopsy demonstrated morphological relapse with 28% blasts.\"}]},\"performance_status\":{\"ps_scale\":\"ECOG\",\"ps_score_value\":\"2\",\"ps_desc\":\"ECOG 2 (“He is symptomatic and in bed less than 50% of the day but requires assistance with some daily activities”)\"},\"other_cancers\":null,\"patient_findings\":[{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"fatigue\",\"patient_finding_desc\":\"He reports significant fatigue\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"exertional dyspnoea\",\"patient_finding_desc\":\"He reports significant fatigue and exertional dyspnoea.\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"active bleeding\",\"patient_finding_desc\":\"He denies active bleeding.\",\"patient_finding_status\":\"is_not_present\"},{\"patient_finding_type\":\"physical_examination_finding\",\"patient_finding_name_desc\":\"mild hepatosplenomegaly\",\"patient_finding_desc\":\"On examination there is mild hepatosplenomegaly.\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"non-drinker\",\"patient_finding_desc\":\"He is a non-drinker\",\"patient_finding_status\":\"is_not_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"non-smoker\",\"patient_finding_desc\":\"and non-smoker\",\"patient_finding_status\":\"is_not_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"supported housing with a care package\",\"patient_finding_desc\":\"lives alone in supported housing with a care package in place.\",\"patient_finding_status\":\"is_present\"}],\"future_plans\":[{\"future_plan_type\":\"planned_systemic_or_radiotherapy_treatment\",\"future_plan_summary\":\"Commence salvage therapy with gilteritinib monotherapy\",\"future_plan_desc\":\"We plan to commence salvage therapy with gilteritinib monotherapy.\"},{\"future_plan_type\":\"planned_clinical_trial_involvement\",\"future_plan_summary\":\"Referral to MORPHO trial assessment clinic and under active consideration for enrolment\",\"future_plan_desc\":\"He has been referred to the MORPHO trial assessment clinic and is under active consideration for enrolment.\"},{\"future_plan_type\":\"planned_investigation\",\"future_plan_summary\":\"Repeat bone marrow trephine in 4 weeks to assess response\",\"future_plan_desc\":\"A repeat bone marrow trephine is planned in 4 weeks to assess response.\"}],\"context_summary\":{\"doc_context\":\"Haematology MDT Note\",\"doc_summary\":\"Patient with relapsed acute myeloid leukaemia, FLT3-ITD/NPM1 positive, post-allogeneic transplant, now with morphological relapse. Planned for salvage therapy with gilteritinib and consideration for MORPHO trial.\"}}","metadata":"{\"inference\": {\"failed_output\": null, \"inference_error\": null, \"schema_package_name\": \"londonaicentre-oncoschema\", \"schema_package_version\": \"2.0.1\", \"inference_metadata\": \"2026-04-29 13:41:30.419147\"}, \"model\": {\"model_name\": \"oncoqwen_1_0_0\", \"model_version\": \"1.0\", \"trained_schema_name\": \"londonaicentre-oncoschema\", \"trained_schema_version\": \"2.0.1\"}}","is_valid":true}
 {"document_id":"c1c3cdef-cd4d-4bbf-8ffb-4088eb3939ec","document_source":"{}","document_inference":"{\"document_has_primary_cancer_flag\":true,\"primary_cancer_confirmed_flag\":true,\"primary_cancer\":{\"primary_cancer_facts\":{\"topography\":\"brain\",\"topography_name_desc\":\"right temporal lobe with involvement of the insula\",\"morphology\":\"glioblastoma\",\"morphology_name_desc\":\"glioblastoma (GBM), WHO Grade 4\",\"is_recurrence\":false,\"diagnosis_year\":2023,\"diagnosis_month\":4,\"tnm_stage\":null,\"numeric_group_stage\":null},\"primary_cancer_tumour_facts\":{\"msi_status\":null,\"msi_desc\":null,\"tmb_status\":null,\"tmb_numeric_value\":null,\"tmb_desc\":null,\"molecular_biomarker_profiles\":[{\"biomarker\":\"mgmt\",\"biomarker_name_desc\":\"MGMT promoter\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":\"methylation\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"MGMT promoter methylation was confirmed present.\"},{\"biomarker\":\"idh1\",\"biomarker_name_desc\":\"IDH1\",\"biomarker_status\":\"negative\",\"biomarker_alteration\":\"wild-type\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"IDH1 and IDH2 were both wild-type.\"},{\"biomarker\":\"idh2\",\"biomarker_name_desc\":\"IDH2\",\"biomarker_status\":\"negative\",\"biomarker_alteration\":\"wild-type\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"IDH1 and IDH2 were both wild-type.\"},{\"biomarker\":\"egfr\",\"biomarker_name_desc\":\"EGFR\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":\"amplification\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"EGFR amplification was identified.\"},{\"biomarker\":\"other\",\"biomarker_name_desc\":\"TERT promoter\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":\"mutation\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"TERT promoter mutation confirmed.\"}]},\"primary_cancer_scores\":[{\"score\":\"pathological_grade\",\"score_name_desc\":\"WHO Grade\",\"score_value\":\"4\",\"score_value_desc\":\"WHO Grade 4\"}],\"primary_cancer_spread\":null,\"primary_cancer_timeline_events\":[{\"event_type\":\"had_surgical_treatment_performed\",\"event_year\":2023,\"event_month\":4,\"event_summary\":\"Craniotomy performed for diagnosis.\",\"event_desc\":\"Diagnosis was confirmed histologically following craniotomy in April 2023.\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2023,\"event_month\":5,\"event_summary\":\"Commenced standard Stupp protocol (concurrent temozolomide with radiotherapy 60Gy in 30 fractions).\",\"event_desc\":\"Commenced standard Stupp protocol – concurrent temozolomide with radiotherapy (60Gy in 30 fractions to the right temporal lobe).\"},{\"event_type\":\"experienced_toxicity_or_complication_related_to_treatment\",\"event_year\":2023,\"event_month\":5,\"event_summary\":\"Experienced grade 1 fatigue and grade 1 radiation dermatitis during Stupp protocol.\",\"event_desc\":\"He tolerated this reasonably well with grade 1 fatigue and grade 1 radiation dermatitis only.\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2023,\"event_month\":8,\"event_summary\":\"Commenced adjuvant temozolomide.\",\"event_desc\":\"Following completion of concurrent phase, commenced adjuvant temozolomide.\"},{\"event_type\":\"radiology_evidence_of_disease_progression\",\"event_year\":2023,\"event_month\":8,\"event_summary\":\"Interim MRI at cycle 3 demonstrated increased T1 enhancement, assessed as likely pseudoprogression.\",\"event_desc\":\"Interim MRI at cycle 3 demonstrated increased T1 enhancement – assessed as likely pseudoprogression given early timing and MGMT methylation status.\"},{\"event_type\":\"radiology_evidence_of_disease_progression\",\"event_year\":2023,\"event_month\":11,\"event_summary\":\"Repeat MRI confirmed true radiological progression with significant enlargement of the right temporal enhancing lesion and new mass effect (midline shift 6mm).\",\"event_desc\":\"Repeat MRI brain confirmed true radiological progression with significant enlargement of the right temporal enhancing lesion and new mass effect, with midline shift of 6mm.\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2023,\"event_month\":12,\"event_summary\":\"Commenced bevacizumab monotherapy as second-line.\",\"event_desc\":\"Commenced bevacizumab monotherapy as second-line.\"},{\"event_type\":\"considered_for_clinical_trial\",\"event_year\":2024,\"event_month\":1,\"event_summary\":\"Considered for the REGN2810 trial but was excluded due to prior bevacizumab use and declining performance status.\",\"event_desc\":\"He was considered for the REGN2810 trial but was excluded due to prior bevacizumab use and declining performance status.\"},{\"event_type\":\"patient_died\",\"event_year\":2024,\"event_month\":3,\"event_summary\":\"Patient passed away on 14th March 2024, approximately 11 months from initial diagnosis.\",\"event_desc\":\"It is with great regret that I must inform you that Mr. Grenville passed away on 14th March 2024, approximately 11 months from his initial diagnosis.\"}]},\"performance_status\":{\"ps_scale\":\"ECOG\",\"ps_score_value\":\"3\",\"ps_desc\":\"Performance status at this point had declined to ECOG 3 (“spends more than 50% of the day in bed, limited self-care”).\"},\"other_cancers\":null,\"patient_findings\":[{\"patient_finding_type\":\"functional_finding\",\"patient_finding_name_desc\":\"Declining performance status (ECOG 3)\",\"patient_finding_desc\":\"Performance status at this point had declined to ECOG 3 (“spends more than 50% of the day in bed, limited self-care”).\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"Pain denial\",\"patient_finding_desc\":\"He denied pain\",\"patient_finding_status\":\"is_not_present\"},{\"patient_finding_type\":\"mental_state_finding\",\"patient_finding_name_desc\":\"Increasingly confused and disorientated\",\"patient_finding_desc\":\"Mr. Grenville was increasingly confused and disorientated at the time of his last clinic attendance in February 2024, consistent with disease-related cognitive impairment.\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"functional_finding\",\"patient_finding_name_desc\":\"Bedbound\",\"patient_finding_desc\":\"His wife reported that he had become bedbound at home.\",\"patient_finding_status\":\"is_present\"}],\"future_plans\":null,\"context_summary\":{\"doc_context\":\"Neuro-oncology MDT Note\",\"doc_summary\":\"Patient with IDH-wildtype Glioblastoma (WHO Grade 4) diagnosed April 2023, progressed after Stupp protocol and adjuvant temozolomide, commenced bevacizumab, and subsequently died in March 2024.\"}}","metadata":"{\"inference\": {\"failed_output\": null, \"inference_error\": null, \"schema_package_name\": \"londonaicentre-oncoschema\", \"schema_package_version\": \"2.0.1\", \"inference_metadata\": \"2026-04-29 13:41:35.178452\"}, \"model\": {\"model_name\": \"oncoqwen_1_0_0\", \"model_version\": \"1.0\", \"trained_schema_name\": \"londonaicentre-oncoschema\", \"trained_schema_version\": \"2.0.1\"}}","is_valid":true}
 {"document_id":"74fbef3d-17b9-439d-bae4-12b4fcf9c730","document_source":"{}","document_inference":"{\"document_has_primary_cancer_flag\":true,\"primary_cancer_confirmed_flag\":true,\"primary_cancer\":{\"primary_cancer_facts\":{\"topography\":\"colon\",\"topography_name_desc\":\"sigmoid colon\",\"morphology\":\"adenocarcinoma\",\"morphology_name_desc\":\"adenocarcinoma\",\"is_recurrence\":false,\"diagnosis_year\":2019,\"diagnosis_month\":5,\"tnm_stage\":\"T3N1M0\",\"numeric_group_stage\":null},\"primary_cancer_tumour_facts\":{\"msi_status\":\"msi_high\",\"msi_desc\":\"MSI-high disease, confirmed on both PCR and IHC (MLH1 and PMS2 protein loss)\",\"tmb_status\":\"tmb_high\",\"tmb_numeric_value\":48.3,\"tmb_desc\":\"TMB was reported as 48.3 mutations/Mb (TMB-high)\",\"molecular_biomarker_profiles\":[{\"biomarker\":\"kras\",\"biomarker_name_desc\":\"KRAS\",\"biomarker_status\":\"negative\",\"biomarker_alteration\":\"wild-type\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"KRAS and NRAS are both wild-type.\"},{\"biomarker\":\"nras\",\"biomarker_name_desc\":\"NRAS\",\"biomarker_status\":\"negative\",\"biomarker_alteration\":\"wild-type\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"KRAS and NRAS are both wild-type.\"},{\"biomarker\":\"braf\",\"biomarker_name_desc\":\"BRAF\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":\"V600E\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"BRAF V600E mutation was identified.\"},{\"biomarker\":\"pdl1\",\"biomarker_name_desc\":\"PDL1\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":null,\"biomarker_expression_level\":\"12\",\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"PDL1 combined positive score was 12.\"}]},\"primary_cancer_scores\":[{\"score\":\"dukes\",\"score_name_desc\":\"Dukes Stage\",\"score_value\":\"C\",\"score_value_desc\":\"C\"}],\"primary_cancer_spread\":[{\"spread_type\":\"liver\",\"spread_site_desc\":\"hepatic metastases (segments IV and VII)\"},{\"spread_type\":\"peritoneum\",\"spread_site_desc\":\"peritoneal deposits\"},{\"spread_type\":\"peritoneum\",\"spread_site_desc\":\"omental deposit\"}],\"primary_cancer_timeline_events\":[{\"event_type\":\"had_surgical_treatment_performed\",\"event_year\":2019,\"event_month\":6,\"event_summary\":\"Anterior resection with curative intent\",\"event_desc\":\"She underwent anterior resection with curative intent.\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2019,\"event_month\":11,\"event_summary\":\"Completed adjuvant CAPOX chemotherapy\",\"event_desc\":\"Completed adjuvant CAPOX chemotherapy.\"},{\"event_type\":\"experienced_toxicity_or_complication_related_to_treatment\",\"event_year\":2020,\"event_month\":4,\"event_summary\":\"Experienced grade 1 peripheral neuropathy and grade 2 hand-foot syndrome during CAPOX, requiring dose reduction\",\"event_desc\":\"experienced grade 1 peripheral neuropathy and grade 2 hand-foot syndrome, the latter requiring a dose reduction in cycle 4.\"},{\"event_type\":\"evidence_of_metastatic_progression\",\"event_year\":2022,\"event_month\":3,\"event_summary\":\"CT staging demonstrated new hepatic metastases and peritoneal deposits\",\"event_desc\":\"CT staging demonstrated new hepatic metastases (segments IV and VII) and peritoneal deposits – confirmed metastatic progression.\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2022,\"event_month\":4,\"event_summary\":\"Commenced first-line FOLFOX plus bevacizumab\",\"event_desc\":\"Commenced first-line FOLFOX plus bevacizumab.\"},{\"event_type\":\"positive_treatment_response_on_assessment\",\"event_year\":2022,\"event_month\":7,\"event_summary\":\"Interim CT confirmed partial response (>30% reduction in hepatic lesion size) to FOLFOX/Bevacizumab\",\"event_desc\":\"Interim CT at 3 months confirmed partial response with >30% reduction in hepatic lesion size.\"},{\"event_type\":\"radiology_evidence_of_disease_progression\",\"event_year\":2024,\"event_month\":1,\"event_summary\":\"Repeat CT demonstrated enlargement of peritoneal disease and a new omental deposit\",\"event_desc\":\"Repeat CT demonstrated enlargement of the peritoneal disease and a new omental deposit – radiological evidence of progression.\"},{\"event_type\":\"enrolled_to_clinical_trial\",\"event_year\":2024,\"event_month\":2,\"event_summary\":\"Enrolled to the BREAKWATER trial\",\"event_desc\":\"She has been enrolled to the BREAKWATER trial.\"}]},\"performance_status\":{\"ps_scale\":\"ECOG\",\"ps_score_value\":\"1\",\"ps_desc\":\"ECOG 1\"},\"other_cancers\":null,\"patient_findings\":[{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"worsening abdominal bloating\",\"patient_finding_desc\":\"She reports worsening abdominal bloating\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"intermittent altered bowel habit\",\"patient_finding_desc\":\"intermittent altered bowel habit\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"rectal bleeding\",\"patient_finding_desc\":\"She denies rectal bleeding.\",\"patient_finding_status\":\"is_not_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"ex-smoker\",\"patient_finding_desc\":\"She is an ex-smoker (20 pack-year history, ceased 2015)\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"alcohol consumption\",\"patient_finding_desc\":\"drinks approximately 14 units of alcohol per week.\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"Family history of colorectal cancer (father)\",\"patient_finding_desc\":\"Family history is notable for colorectal cancer in her father (diagnosed aged 55)\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"Family history of endometrial cancer (sister)\",\"patient_finding_desc\":\"endometrial cancer in her sister\",\"patient_finding_status\":\"is_present\"}],\"future_plans\":[{\"future_plan_type\":\"planned_systemic_or_radiotherapy_treatment\",\"future_plan_summary\":\"Switch to pembrolizumab plus encorafenib/binimetinib\",\"future_plan_desc\":\"Given MSI-high and BRAF V600E status, we plan to switch to pembrolizumab plus encorafenib/binimetinib.\"},{\"future_plan_type\":\"planned_investigation\",\"future_plan_summary\":\"Diagnostic laparoscopy planned to assess peritoneal disease burden\",\"future_plan_desc\":\"A diagnostic laparoscopy is planned to formally assess peritoneal disease burden prior to any surgical consideration.\"}],\"context_summary\":{\"doc_context\":\"Colorectal MDT Clinic Letter\",\"doc_summary\":\"Patient with metastatic colorectal adenocarcinoma (MSI-high, BRAF V600E) progressing on FOLFOX/Bevacizumab. Planned switch to pembrolizumab plus encorafenib/binimetinib and diagnostic laparoscopy.\"}}","metadata":"{\"inference\": {\"failed_output\": null, \"inference_error\": null, \"schema_package_name\": \"londonaicentre-oncoschema\", \"schema_package_version\": \"2.0.1\", \"inference_metadata\": \"2026-04-29 13:41:37.191609\"}, \"model\": {\"model_name\": \"oncoqwen_1_0_0\", \"model_version\": \"1.0\", \"trained_schema_name\": \"londonaicentre-oncoschema\", \"trained_schema_version\": \"2.0.1\"}}","is_valid":true}
 {"document_id":"5609cc8b-f83b-443c-9583-364c188b4dc8","document_source":"{}","document_inference":"{\"document_has_primary_cancer_flag\":true,\"primary_cancer_confirmed_flag\":true,\"primary_cancer\":{\"primary_cancer_facts\":{\"topography\":\"lung\",\"topography_name_desc\":\"lung\",\"morphology\":\"adenocarcinoma\",\"morphology_name_desc\":\"non-small cell lung carcinoma, right upper lobe lung adenocarcinoma\",\"is_recurrence\":true,\"diagnosis_year\":2021,\"diagnosis_month\":9,\"tnm_stage\":\"T3N2M1c\",\"numeric_group_stage\":\"IVb\"},\"primary_cancer_tumour_facts\":{\"msi_status\":\"ms_stable\",\"msi_desc\":\"MSI testing confirmed microsatellite stable (MSS) disease.\",\"tmb_status\":\"tmb_low\",\"tmb_numeric_value\":6.2,\"tmb_desc\":\"TMB was 6.2 mutations/Mb (TMB-low).\",\"molecular_biomarker_profiles\":[{\"biomarker\":\"egfr\",\"biomarker_name_desc\":\"EGFR\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":\"exon 19 deletion\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":34.2,\"biomarker_vaf_desc\":\"VAF 34.2%\",\"biomarker_desc\":\"EGFR exon 19 deletion (VAF 34.2%)\"},{\"biomarker\":\"pdl1\",\"biomarker_name_desc\":\"PD-L1\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":null,\"biomarker_expression_level\":\"60% positive\",\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"PD-L1 expression of 60% positive\"},{\"biomarker\":\"kras\",\"biomarker_name_desc\":\"KRAS\",\"biomarker_status\":\"negative\",\"biomarker_alteration\":null,\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"KRAS was negative\"}]},\"primary_cancer_scores\":null,\"primary_cancer_spread\":[{\"spread_type\":\"lymph_node\",\"spread_site_desc\":\"bilateral mediastinal lymph nodes\"},{\"spread_type\":\"liver\",\"spread_site_desc\":\"solitary liver metastasis (segment VI)\"},{\"spread_type\":\"other_cns\",\"spread_site_desc\":\"leptomeningeal disease\"}],\"primary_cancer_timeline_events\":[{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2021,\"event_month\":10,\"event_summary\":\"Commenced osimertinib 80mg OD as first-line therapy.\",\"event_desc\":\"October 2021: Commenced osimertinib 80mg OD as first-line therapy.\"},{\"event_type\":\"positive_treatment_response_on_assessment\",\"event_year\":2022,\"event_month\":1,\"event_summary\":\"Achieved a partial response confirmed on CT chest/abdomen at 3 months.\",\"event_desc\":\"She achieved a partial response confirmed on CT chest/abdomen at 3 months.\"},{\"event_type\":\"radiology_evidence_of_disease_progression\",\"event_year\":2023,\"event_month\":8,\"event_summary\":\"Repeat imaging demonstrated radiological progression with enlargement of the liver lesion and two new mediastinal nodes.\",\"event_desc\":\"August 2023: Repeat imaging demonstrated radiological progression with enlargement of the liver lesion and two new mediastinal nodes.\"},{\"event_type\":\"experienced_treatment_reduction_or_stop\",\"event_year\":2023,\"event_month\":9,\"event_summary\":\"Osimertinib was stopped due to progression.\",\"event_desc\":\"September 2023: Osimertinib was stopped due to progression\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2023,\"event_month\":9,\"event_summary\":\"Switched to carboplatin/pemetrexed chemotherapy.\",\"event_desc\":\"September 2023: Osimertinib was stopped due to progression and treatment was switched to carboplatin/pemetrexed chemotherapy.\"},{\"event_type\":\"experienced_toxicity_or_complication_related_to_treatment\",\"event_year\":2023,\"event_month\":null,\"event_summary\":\"Experienced grade 2 nausea and fatigue as treatment-related toxicities, requiring a dose reduction in cycle 3.\",\"event_desc\":\"She experienced grade 2 nausea and fatigue as treatment-related toxicities, requiring a dose reduction in cycle 3.\"},{\"event_type\":\"evidence_of_metastatic_progression\",\"event_year\":2024,\"event_month\":1,\"event_summary\":\"MRI brain/spine confirmed leptomeningeal metastatic progression.\",\"event_desc\":\"January 2024: MRI brain/spine confirmed leptomeningeal metastatic progression.\"},{\"event_type\":\"considered_for_clinical_trial\",\"event_year\":2023,\"event_month\":11,\"event_summary\":\"Considered for the LAURA trial but was not eligible due to prior osimertinib use.\",\"event_desc\":\"Eleanor was considered for the LAURA trial in November 2023 but was not eligible due to prior osimertinib use.\"}]},\"performance_status\":{\"ps_scale\":\"ECOG\",\"ps_score_value\":\"1\",\"ps_desc\":\"ECOG 1 (“she remains independently active and working part-time”)\"},\"other_cancers\":null,\"patient_findings\":[{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"persistent mild dyspnoea on exertion\",\"patient_finding_desc\":\"Eleanor reports persistent mild dyspnoea on exertion\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"4kg unintentional weight loss over 3 months\",\"patient_finding_desc\":\"a 4kg unintentional weight loss over 3 months.\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"haemoptysis\",\"patient_finding_desc\":\"She denies haemoptysis.\",\"patient_finding_status\":\"is_not_present\"},{\"patient_finding_type\":\"physical_examination_finding\",\"patient_finding_name_desc\":\"mild cachexia\",\"patient_finding_desc\":\"On examination, there is mild cachexia.\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"lifelong non-smoker\",\"patient_finding_desc\":\"She is a lifelong non-smoker.\",\"patient_finding_status\":\"is_not_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"breast cancer in her mother\",\"patient_finding_desc\":\"Family history is notable for breast cancer in her mother.\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"mental_state_finding\",\"patient_finding_name_desc\":\"deeply anxious about the leptomeningeal diagnosis\",\"patient_finding_desc\":\"Psychologically, she is described as deeply anxious about the leptomeningeal diagnosis\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"comorbidity_finding\",\"patient_finding_name_desc\":\"type 2 diabetes mellitus\",\"patient_finding_desc\":\"Known type 2 diabetes mellitus, well-controlled on metformin.\",\"patient_finding_status\":\"is_present\"}],\"future_plans\":[{\"future_plan_type\":\"planned_systemic_or_radiotherapy_treatment\",\"future_plan_summary\":\"Plan to commence amivantamab plus lazertinib on a named-patient basis pending funding approval.\",\"future_plan_desc\":\"We plan to commence amivantamab plus lazertinib on a named-patient basis pending funding approval.\"},{\"future_plan_type\":\"planned_investigation\",\"future_plan_summary\":\"A repeat LP is planned to reconfirm leptomeningeal disease cytology.\",\"future_plan_desc\":\"A repeat LP is planned to reconfirm leptomeningeal disease cytology.\"},{\"future_plan_type\":\"planned_clinical_trial_involvement\",\"future_plan_summary\":\"Enrolling Eleanor to the MARIPOSA-2 clinical trial pending consent.\",\"future_plan_desc\":\"We are enrolling Eleanor to the MARIPOSA-2 clinical trial pending consent.\"}],\"context_summary\":{\"doc_context\":\"Oncology MDT Letter\",\"doc_summary\":\"Patient with recurrent metastatic EGFR+ NSCLC (T3N2M1c, MSS, TMB-low) with recent leptomeningeal progression. Previous progression on osimertinib and carboplatin/pemetrexed. Current plan involves switching to amivantamab/lazertinib and enrolling in MARIPOSA-2 trial.\"}}","metadata":"{\"inference\": {\"failed_output\": null, \"inference_error\": null, \"schema_package_name\": \"londonaicentre-oncoschema\", \"schema_package_version\": \"2.0.1\", \"inference_metadata\": \"2026-04-29 13:41:39.348983\"}, \"model\": {\"model_name\": \"oncoqwen_1_0_0\", \"model_version\": \"1.0\", \"trained_schema_name\": \"londonaicentre-oncoschema\", \"trained_schema_version\": \"2.0.1\"}}","is_valid":true}
 {"document_id":"e4db4a86-5bc1-477d-b03f-ff12fa70ce08","document_source":"{}","document_inference":"{\"document_has_primary_cancer_flag\":true,\"primary_cancer_confirmed_flag\":true,\"primary_cancer\":{\"primary_cancer_facts\":{\"topography\":\"breast\",\"topography_name_desc\":\"left breast\",\"morphology\":\"adenocarcinoma\",\"morphology_name_desc\":\"invasive ductal carcinoma (adenocarcinoma)\",\"is_recurrence\":false,\"diagnosis_year\":2020,\"diagnosis_month\":8,\"tnm_stage\":\"T2N1M0\",\"numeric_group_stage\":\"IIb\"},\"primary_cancer_tumour_facts\":{\"msi_status\":null,\"msi_desc\":null,\"tmb_status\":null,\"tmb_numeric_value\":null,\"tmb_desc\":null,\"molecular_biomarker_profiles\":[{\"biomarker\":\"esr1_er\",\"biomarker_name_desc\":\"ER\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":null,\"biomarker_expression_level\":\"8+/8\",\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"ER-positive 8+/8\"},{\"biomarker\":\"pgr_pr\",\"biomarker_name_desc\":\"PR\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":null,\"biomarker_expression_level\":\"6+/8\",\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"PR-positive 6+/8\"},{\"biomarker\":\"erbb2_her2\",\"biomarker_name_desc\":\"HER2\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":null,\"biomarker_expression_level\":\"3+\",\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"HER2 3+ by IHC confirmed on ISH\"},{\"biomarker\":\"ki_67\",\"biomarker_name_desc\":\"Ki67\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":null,\"biomarker_expression_level\":\"42%\",\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"Ki67 of 42%\"},{\"biomarker\":\"pik3ca\",\"biomarker_name_desc\":\"PIK3CA\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":\"H1047R\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"PIK3CA H1047R mutation was identified on liquid biopsy.\"},{\"biomarker\":\"brca2\",\"biomarker_name_desc\":\"BRCA2\",\"biomarker_status\":\"altered\",\"biomarker_alteration\":\"pathogenic germline variant\",\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"BRCA2 pathogenic germline variant confirmed (BRCA1 negative).\"},{\"biomarker\":\"esr1_er\",\"biomarker_name_desc\":\"ESR1\",\"biomarker_status\":\"negative\",\"biomarker_alteration\":null,\"biomarker_expression_level\":null,\"biomarker_vaf_numeric_value\":null,\"biomarker_vaf_desc\":null,\"biomarker_desc\":\"ESR1 mutation was not detected.\"}]},\"primary_cancer_scores\":[{\"score\":\"pathological_grade\",\"score_name_desc\":\"luminal B HER2-positive tumour\",\"score_value\":null,\"score_value_desc\":\"high-proliferation luminal B HER2-positive tumour\"}],\"primary_cancer_spread\":[{\"spread_type\":\"spine\",\"spread_site_desc\":\"multiple thoracic and lumbar vertebral bone metastases\"},{\"spread_type\":\"lymph_node\",\"spread_site_desc\":\"bilateral axillary lymph nodes\"},{\"spread_type\":\"adrenal\",\"spread_site_desc\":\"single right adrenal deposit\"}],\"primary_cancer_timeline_events\":[{\"event_type\":\"had_surgical_treatment_performed\",\"event_year\":2020,\"event_month\":9,\"event_summary\":\"Left mastectomy and axillary node clearance performed.\",\"event_desc\":\"Underwent left mastectomy and axillary node clearance. Pathology confirmed 3 of 14 nodes positive.\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2020,\"event_month\":11,\"event_summary\":\"Completed adjuvant docetaxel, carboplatin, trastuzumab and pertuzumab (TCHP).\",\"event_desc\":\"Completed adjuvant docetaxel, carboplatin, trastuzumab and pertuzumab (TCHP).\"},{\"event_type\":\"experienced_toxicity_or_complication_related_to_treatment\",\"event_year\":2020,\"event_month\":11,\"event_summary\":\"Experienced grade 3 neutropenic sepsis during cycle 2 of TCHP.\",\"event_desc\":\"Complicated by grade 3 neutropenic sepsis during cycle 2.\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2021,\"event_month\":4,\"event_summary\":\"Completed adjuvant radiotherapy to chest wall and supraclavicular fossa.\",\"event_desc\":\"Completed adjuvant radiotherapy to chest wall and supraclavicular fossa\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2021,\"event_month\":7,\"event_summary\":\"Received T-DM1 for 14 cycles.\",\"event_desc\":\"followed by T-DM1 for 14 cycles.\"},{\"event_type\":\"experienced_disease_remission\",\"event_year\":2022,\"event_month\":7,\"event_summary\":\"Achieved confirmed radiological remission on CT at completion of T-DM1.\",\"event_desc\":\"Achieved confirmed radiological remission on CT at completion.\"},{\"event_type\":\"evidence_of_metastatic_progression\",\"event_year\":2023,\"event_month\":2,\"event_summary\":\"PET-CT demonstrated new bone metastases, confirmed disease recurrence.\",\"event_desc\":\"PET-CT demonstrated new bone metastases – confirmed disease recurrence.\"},{\"event_type\":\"had_systemic_or_radiotherapy_treatment\",\"event_year\":2023,\"event_month\":3,\"event_summary\":\"Commenced trastuzumab deruxtecan (T-DXd).\",\"event_desc\":\"Commenced trastuzumab deruxtecan (T-DXd).\"},{\"event_type\":\"positive_treatment_response_on_assessment\",\"event_year\":2023,\"event_month\":3,\"event_summary\":\"Interim assessment confirmed partial response at 3 months on T-DXd.\",\"event_desc\":\"Interim assessment confirmed partial response at 3 months.\"},{\"event_type\":\"radiology_evidence_of_disease_progression\",\"event_year\":2024,\"event_month\":3,\"event_summary\":\"Interval CT demonstrates stable bone disease but new adrenal lesion, resulting in mixed/equivocal response.\",\"event_desc\":\"Interval CT demonstrates stable bone disease but new adrenal lesion – mixed/equivocal response.\"}]},\"performance_status\":{\"ps_scale\":\"ECOG\",\"ps_score_value\":\"1\",\"ps_desc\":\"ECOG 1 (“independently active, working part-time from home”)\"},\"other_cancers\":null,\"patient_findings\":[{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"moderate back pain\",\"patient_finding_desc\":\"She reports moderate back pain, scoring 5/10, managed with regular analgesia.\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"symptom_finding\",\"patient_finding_name_desc\":\"neurological symptoms\",\"patient_finding_desc\":\"She denies neurological symptoms.\",\"patient_finding_status\":\"is_not_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"lifelong non-smoker\",\"patient_finding_desc\":\"She is a lifelong non-smoker.\",\"patient_finding_status\":\"is_not_present\"},{\"patient_finding_type\":\"mental_state_finding\",\"patient_finding_name_desc\":\"visibly distressed\",\"patient_finding_desc\":\"She is visibly distressed regarding implications of her BRCA2 status for her two daughters\",\"patient_finding_status\":\"is_present\"},{\"patient_finding_type\":\"social_or_family_finding\",\"patient_finding_name_desc\":\"strong family history of breast and ovarian cancer\",\"patient_finding_desc\":\"She has a strong family history: mother with breast cancer (age 38) and maternal aunt with ovarian cancer.\",\"patient_finding_status\":\"is_present\"}],\"future_plans\":[{\"future_plan_type\":\"planned_systemic_or_radiotherapy_treatment\",\"future_plan_summary\":\"Add tucatinib to current regimen.\",\"future_plan_desc\":\"We plan to add tucatinib to her current regimen\"},{\"future_plan_type\":\"planned_clinical_trial_involvement\",\"future_plan_summary\":\"Enrol in HER2CLIMB-02 trial.\",\"future_plan_desc\":\"and enrol her to the HER2CLIMB-02 trial.\"},{\"future_plan_type\":\"planned_investigation\",\"future_plan_summary\":\"Genetic counselling appointment arranged.\",\"future_plan_desc\":\"Genetic counselling appointment arranged.\"},{\"future_plan_type\":\"planned_systemic_or_radiotherapy_treatment\",\"future_plan_summary\":\"Continue quarterly Zoledronic acid infusion.\",\"future_plan_desc\":\"Zoledronic acid infusion planned to continue quarterly.\"}],\"context_summary\":{\"doc_context\":\"Breast Cancer Clinic Letter\",\"doc_summary\":\"Patient with metastatic ER+/PR+/HER2+ breast cancer (PIK3CA altered, BRCA2 germline altered) currently on T-DXd, showing mixed response. Plans include adding tucatinib and enrolling in the HER2CLIMB-02 trial.\"}}","metadata":"{\"inference\": {\"failed_output\": null, \"inference_error\": null, \"schema_package_name\": \"londonaicentre-oncoschema\", \"schema_package_version\": \"2.0.1\", \"inference_metadata\": \"2026-04-29 13:41:45.886377\"}, \"model\": {\"model_name\": \"oncoqwen_1_0_0\", \"model_version\": \"1.0\", \"trained_schema_name\": \"londonaicentre-oncoschema\", \"trained_schema_version\": \"2.0.1\"}}","is_valid":true}
	[
	{"document_id": "5609cc8b-f83b-443c-9583-364c188b4dc8", "document_content": "Oncology MDT Letter – Outpatient Clinic Date: 14th March 2024 Dear Dr. Patel, Thank you for referring Mrs. Eleanor Hughes, a 58-year-old woman, regarding her known metastatic non-small cell lung carcinoma, initially diagnosed in September 2021. This represents a recurrence of her previously treated early-stage disease. Disease Status & Staging Eleanor's primary tumour is a right upper lobe lung adenocarcinoma, staged at T3N2M1c (Group Stage IVb) at the time of metastatic diagnosis. Molecular profiling revealed an EGFR exon 19 deletion (VAF 34.2%), with PD-L1 expression of 60% positive. KRAS was negative. MSI testing confirmed microsatellite stable (MSS) disease. TMB was 6.2 mutations/Mb (TMB-low). Known sites of spread include bilateral mediastinal lymph nodes, a solitary liver metastasis (segment VI), and leptomeningeal disease confirmed on MRI in January 2024. Scores Performance status is ECOG 1 (\"she remains independently active and working part-time\"). No Gleason or FIGO applicable. Treatment History October 2021: Commenced osimertinib 80mg OD as first-line therapy. She achieved a partial response confirmed on CT chest/abdomen at 3 months. August 2023: Repeat imaging demonstrated radiological progression with enlargement of the liver lesion and two new mediastinal nodes. September 2023: Osimertinib was stopped due to progression and treatment was switched to carboplatin/pemetrexed chemotherapy. She experienced grade 2 nausea and fatigue as treatment-related toxicities, requiring a dose reduction in cycle 3. January 2024: MRI brain/spine confirmed leptomeningeal metastatic progression. Eleanor was considered for the LAURA trial in November 2023 but was not eligible due to prior osimertinib use. Patient Findings Eleanor reports persistent mild dyspnoea on exertion and a 4kg unintentional weight loss over 3 months. She denies haemoptysis. On examination, there is mild cachexia. She is a lifelong non-smoker. Family history is notable for breast cancer in her mother. Psychologically, she is described as deeply anxious about the leptomeningeal diagnosis but engaged with the MDT plan. Comorbidities Known type 2 diabetes mellitus, well-controlled on metformin. Future Plans We plan to commence amivantamab plus lazertinib on a named-patient basis pending funding approval. A repeat LP is planned to reconfirm leptomeningeal disease cytology. We are enrolling Eleanor to the MARIPOSA-2 clinical trial pending consent. Yours sincerely, Dr. A. Rahman, Consultant Medical Oncologist"},
	{"document_id": "25a137f0-803c-4859-a068-031cdc2f8f11", "document_content": "Haematology MDT Note Date: 3rd January 2024Dear Dr. Okonkwo,I reviewed Mr. Samuel Adeyemi, a 45-year-old man, in the haematology clinic today regarding his relapsed acute myeloid leukaemia. His AML was first diagnosed in February 2022 following a 6-week history of fatigue and recurrent infections. Bone marrow biopsy at diagnosis confirmed FLT3-ITD mutation (VAF 42.1%) and NPM1 mutation (VAF 38.6%). Cytogenetics showed normal karyotype.Treatment History March 2022: Commenced intensive induction chemotherapy with daunorubicin and cytarabine (7+3) plus midostaurin given FLT3 positivity. Cycle 1 was complicated by grade 3 febrile neutropenia requiring ITU admission for 4 days — a significant treatment-related complication. June 2022: Bone marrow assessment confirmed complete morphological remission with MRD negativity by flow cytometry. October 2022: Proceeded to allogeneic stem cell transplant from a matched unrelated donor. Post-transplant course was complicated by grade 2 acute graft-versus-host disease affecting skin and gut, managed with systemic steroids with good response. September 2023: Routine surveillance bone marrow biopsy demonstrated morphological relapse with 28% blasts. FLT3-ITD re-confirmed. BCR-ABL1 was negative. Samuel is currently ECOG 2 (\"he is symptomatic and in bed less than 50% of the day but requires assistance with some daily activities\"). He reports significant fatigue and exertional dyspnoea. He denies active bleeding. On examination there is mild hepatosplenomegaly. He is a non-drinker and non-smoker, lives alone in supported housing with a care package in place.Future Plans We plan to commence salvage therapy with gilteritinib monotherapy. He has been referred to the MORPHO trial assessment clinic and is under active consideration for enrolment. A repeat bone marrow trephine is planned in 4 weeks to assess response.Yours sincerely, Dr. F. Mensah, Consultant Haematologist"},
	{"document_id": "74fbef3d-17b9-439d-bae4-12b4fcf9c730", "document_content": "Colorectal MDT Clinic Letter Date: 22nd February 2024 Dear Dr. Clarkson, Thank you for your referral of Mrs. Patricia Doyle, a 67-year-old woman, with confirmed metastatic colorectal adenocarcinoma of the sigmoid colon, initially diagnosed in May 2019 (Dukes Stage C, TNM T3N1M0 at primary resection). Molecular Profile Tumour molecular profiling has demonstrated MSI-high disease, confirmed on both PCR and IHC (MLH1 and PMS2 protein loss). TMB was reported as 48.3 mutations/Mb (TMB-high). KRAS and NRAS are both wild-type. BRAF V600E mutation was identified. PDL1 combined positive score was 12. Disease History & Spread June 2019: She underwent anterior resection with curative intent. Pathology confirmed clear margins. November 2019 – April 2020: Completed adjuvant CAPOX chemotherapy. She tolerated this reasonably well, though experienced grade 1 peripheral neuropathy and grade 2 hand-foot syndrome, the latter requiring a dose reduction in cycle 4. March 2022: CT staging demonstrated new hepatic metastases (segments IV and VII) and peritoneal deposits — confirmed metastatic progression. CA19-9 markedly elevated. April 2022: Commenced first-line FOLFOX plus bevacizumab. Interim CT at 3 months confirmed partial response with >30% reduction in hepatic lesion size. January 2024: Repeat CT demonstrated enlargement of the peritoneal disease and a new omental deposit — radiological evidence of progression. Mrs. Doyle is ECOG 1. She reports worsening abdominal bloating and intermittent altered bowel habit. She denies rectal bleeding. She is an ex-smoker (20 pack-year history, ceased 2015) and drinks approximately 14 units of alcohol per week. Family history is notable for colorectal cancer in her father (diagnosed aged 55) and endometrial cancer in her sister — Lynch syndrome testing has been initiated. Future Plans Given MSI-high and BRAF V600E status, we plan to switch to pembrolizumab plus encorafenib/binimetinib. She has been enrolled to the BREAKWATER trial. A diagnostic laparoscopy is planned to formally assess peritoneal disease burden prior to any surgical consideration. Yours sincerely, Dr. L. Singh, Consultant Medical Oncologist"},
	{"document_id": "e4db4a86-5bc1-477d-b03f-ff12fa70ce08", "document_content": "Breast Cancer Clinic Letter Date: 8th April 2024 Dear Dr. Whitmore, I am writing regarding Ms. Aisha Nkemdirim, a 42-year-old woman, who attended the breast oncology clinic today. She has metastatic breast cancer (ER-positive 8+/8, PR-positive 6+/8, HER2 3+ by IHC confirmed on ISH) with Ki67 of 42%, consistent with a high-proliferation luminal B HER2-positive tumour. PIK3CA H1047R mutation was identified on liquid biopsy. BRCA2 pathogenic germline variant confirmed (BRCA1 negative). ESR1 mutation was not detected. Her primary left breast invasive ductal carcinoma (adenocarcinoma) was diagnosed in August 2020, staged T2N1M0 (Group Stage IIb). This is not a recurrence — she presented de novo with locally advanced disease. Known Sites of Spread Confirmed metastatic sites include: multiple thoracic and lumbar vertebral bone metastases, bilateral axillary lymph nodes, and a single right adrenal deposit identified on most recent PET-CT. Treatment Timeline September 2020: Underwent left mastectomy and axillary node clearance. Pathology confirmed 3 of 14 nodes positive. November 2020 – March 2021: Completed adjuvant docetaxel, carboplatin, trastuzumab and pertuzumab (TCHP). Complicated by grade 3 neutropenic sepsis during cycle 2. April 2021 – July 2022: Completed adjuvant radiotherapy to chest wall and supraclavicular fossa, followed by T-DM1 for 14 cycles. Achieved confirmed radiological remission on CT at completion. February 2023: PET-CT demonstrated new bone metastases — confirmed disease recurrence. March 2023: Commenced trastuzumab deruxtecan (T-DXd). Interim assessment confirmed partial response at 3 months. March 2024: Interval CT demonstrates stable bone disease but new adrenal lesion — mixed/equivocal response. Aisha is ECOG 1 (\"independently active, working part-time from home\"). She reports moderate back pain, scoring 5/10, managed with regular analgesia. She denies neurological symptoms. She is a lifelong non-smoker. She is visibly distressed regarding implications of her BRCA2 status for her two daughters and has been referred to the clinical genetics team. She has a strong family history: mother with breast cancer (age 38) and maternal aunt with ovarian cancer. Future Plans We plan to add tucatinib to her current regimen and enrol her to the HER2CLIMB-02 trial. Genetic counselling appointment arranged. Zoledronic acid infusion planned to continue quarterly. Yours sincerely, Dr. C. Oduya, Consultant Medical Oncologist"},
	{"document_id": "c1c3cdef-cd4d-4bbf-8ffb-4088eb3939ec", "document_content": "Neuro-oncology MDT Note Date: 19th March 2024 Dear Dr. Harrington, I am writing with a brief update regarding Mr. Thomas Grenville, a 71-year-old man, with IDH-wildtype glioblastoma (GBM), WHO Grade 4. Diagnosis was confirmed histologically following craniotomy in April 2023. MGMT promoter methylation was confirmed present. IDH1 and IDH2 were both wild-type. EGFR amplification was identified. TERT promoter mutation confirmed. The primary tumour was located in the right temporal lobe with involvement of the insula. TNM staging is not formally applied; FIGO and Gleason are not applicable. Breslow and Clark staging are similarly not relevant. Treatment History May 2023: Commenced standard Stupp protocol — concurrent temozolomide with radiotherapy (60Gy in 30 fractions to the right temporal lobe). He tolerated this reasonably well with grade 1 fatigue and grade 1 radiation dermatitis only. August 2023: Following completion of concurrent phase, commenced adjuvant temozolomide. Interim MRI at cycle 3 demonstrated increased T1 enhancement — assessed as likely pseudoprogression given early timing and MGMT methylation status. Decision made to continue. November 2023: Repeat MRI brain confirmed true radiological progression with significant enlargement of the right temporal enhancing lesion and new mass effect, with midline shift of 6mm. December 2023: Commenced bevacizumab monotherapy as second-line. Performance status at this point had declined to ECOG 3 (\"spends more than 50% of the day in bed, limited self-care\"). January 2024: He was considered for the REGN2810 trial but was excluded due to prior bevacizumab use and declining performance status. Mr. Grenville was increasingly confused and disorientated at the time of his last clinic attendance in February 2024, consistent with disease-related cognitive impairment. His wife reported that he had become bedbound at home. He denied pain but was unable to reliably report symptoms. A social care package had been urgently escalated and he was transferred to a local hospice for symptom management. It is with great regret that I must inform you that Mr. Grenville passed away on 14th March 2024, approximately 11 months from his initial diagnosis. Yours sincerely, Dr. M. Tran, Consultant Neuro-oncologist"}
	]
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