Author of code and documentation: @kgaonkar6
In this repo, we add molecular subtype for molecular_subtype from all subtyping modules and integrated_diagnosis, short_histology, broad_histology, and Notes from compiled_molecular_subtypes_with_clinical_pathology_feedback.tsv. A column cancer_group is added to provide broader terms derived from harmonized_diagnosis which can be used to generate figures.
bash run-subtyping-integrate.sh01-integrate-subtyping.Rmd integrates results from compiled results in compiled_molecular_subtypes_with_clinical_pathology_feedback.tsv to histologies-base.tsv
| stripped_subtype | cancer_group |
|---|---|
| Abdominal inflammatory myofibroblastic tumor | Other tumor |
| Acute Promyelocytic Leukemia | Acute Myeloid Leukemia |
| Adamantinomatous craniopharyngioma | Adamantinomatous Craniopharyngioma |
| Adenoma | NA |
| Adrenal mass | Other tumor |
| Anaplastic (malignant) meningioma | Meningioma |
| Aneurismal bone cyst (abc) with col1a1-usp6 fusion | Other tumor |
| Aneurysmal bone cyst (abc) | Other tumor |
| Aplastic anemia | NA |
| Arteriovenous malformation | NA |
| Atypical Lymph Node | NA |
| Atypical Neurofibromatous Neoplasm of Uncertain Biologic Potential | Other tumor |
| Atypical Spitz Nevus | Other tumor |
| Atypical Teratoid Rhabdoid Tumor (ATRT) | Atypical Teratoid Rhabdoid Tumor |
| Atypical choroid plexus papilloma | Choroid plexus tumor |
| Atypical lymphoid infiltrate | NA |
| Atypical meningioma | Meningioma |
| Atypical vascular lesion | Other tumor |
| Benign Neoplasm | NA |
| Bone marrow cellularity | Other tumor |
| Bone marrow failure | Other tumor |
| Brain Lower Grade Glioma | Low-grade glioma |
| Brainstem glioma- Diffuse intrinsic pontine glioma | Diffuse intrinsic pontine glioma |
| Cavernoma | NA |
| Cellular Congenital Mesoblastic Nephroma | Other tumor |
| Cerebral ventriculomegaly | Other tumor |
| Childhood Astrocytic Tumor | Other tumor |
| Cholesterol granuloma | NA |
| Chondroma | NA |
| Choroid plexus carcinoma | Choroid plexus tumor |
| Choroid plexus papilloma | Choroid plexus tumor |
| Chronic myeloid leukemia pathway | Other tumor |
| Clear Cell Sarcoma of the Kidney | Clear cell sarcoma of the kidney |
| Clear cell meningioma | Meningioma |
| Congenital Mesoblastic Nephroma | Other tumor |
| Cranial fasciitis | NA |
| Cyst | Other tumor |
| Dermoid cyst | NA |
| Diffuse hemispheric glioma | Astrocytoma |
| Diffuse leptomeningeal glioneuronal tumor | NA |
| Dysembryoplastic neuroepithelial tumor (DNET) | Dysembryoplastic neuroepithelial tumor |
| Dysembryoplastic neuroepithelial tumor (DNET);Dysplasia/Gliosis;Ganglioglioma | NA |
| Dysembryoplastic neuroepithelial tumor (DNET);Ganglioglioma | NA |
| Dysplasia/Gliosis | NA |
| Ependymoma;Metastatic secondary tumors | NA |
| Epidermoid cyst | NA |
| Epilepsy | NA |
| Familial adenomatous polyposis | Other tumor |
| Fibroma | NA |
| Fibromixoid lesion | Fibromyxoid lesion |
| Giant Cell Granuloma | NA |
| Giant cell tumor of bone | NA |
| Glial-neuronal tumor | Glial-neuronal tumor NOS |
| Glioblastoma Multiforme Pathway | NA |
| Glioma | Other tumor |
| Gliomatosis Cerebri;High-grade glioma/astrocytoma (WHO grade III/IV) | NA |
| Gliosis | Other tumor |
| Granular Cell Tumor | Other tumor |
| Hamartoma | NA |
| Hemangioma | NA |
| Hematoma | NA |
| High-grade glioma | Astrocytoma;Oligoastrocytoma |
| High-grade glioma | Glioblastoma |
| High-grade glioma/astrocytoma (WHO grade III/IV) | High-grade glioma |
| High-grade glioma/astrocytoma (WHO grade III/IV);Neurofibroma/Plexiform | NA |
| High-grade glioma/astrocytoma (WHO grade III/IV);Oligodendroglioma | NA |
| Histiocytic Tumor | Histiocytic tumor |
| Hypocellular bone marrow | Other tumor |
| Hypophyseal stalk thickening | Other tumor |
| Inclusion cyst | NA |
| Inflammatory Myofibroblastic Tumor | Other tumor |
| Inflammatory lesion | Other tumor |
| Inflammatory lesion | NA |
| Kidney Chromophobe | Chromophobe renal cell carcinoma |
| Kidney Renal Clear Cell Carcinoma | Renal Clear Cell Carcinoma |
| Kidney Renal Papillary Cell Carcinoma | Renal Papillary Cell Carcinoma |
| Lipoblastoma | NA |
| Lipoma | NA |
| Lipomyelomeningocele | Other tumor |
| Low-grade glioma/astrocytoma (WHO grade I/II) | Low-grade glioma |
| Lymphadenitis | NA |
| Malignant PEComa | Other tumor |
| Malignant peripheral nerve sheath tumor (MPNST) | Malignant peripheral nerve sheath tumor |
| Malignant peripheral nerve sheath tumor (MPNST);Neurofibroma/Plexiform | NA |
| Melanocytoma | Melanocytic tumor |
| Meningioma;Neurofibroma/Plexiform | NA |
| Meningioma;Schwannoma | NA |
| Meningothelial meningioma | Meningioma |
| Microcytic Anemia | NA |
| Mixed Lineage Leukemia | Acute Lymphoblastic Leukemia |
| Monomorphic Post-Transplant Lymphoproliferative Disorder | Other tumor |
| Mucoepidermoid Carcinoma | Other tumor |
| Myelodysplastic syndrome | Other tumor |
| Myofibroblastic tumor | Inflammatory Myofibroblastic Tumor |
| Myofibroma | NA |
| Myxoid spindle cell tumor | Other tumor |
| Myxopapillary ependymoma | Ependymoma |
| Necrotizing myelopathy | NA |
| Neoplasm of unspecified behavior of endocrine glands | Other tumor |
| Neuroblastic tumor | Other tumor |
| Neuroendocrine carcinoma | Other tumor |
| Neuroepithelial neoplasm with EWSR1--PLAG1 fusion | Glial-neuronal tumor |
| Neurofibroma/Plexiform;Schwannoma | NA |
| Neutropenia | Other tumor |
| Nodular fasciitis | Other tumor |
| Non-Cancer Diagnosis | NA |
| Non-cancer diagnosis | NA |
| Non-germinomatous germ cell tumor | NA |
| Non-germinomatous germ cell tumor;Teratoma | NA |
| Nonintractable epilepsy without status epilepticus | NA |
| Noonan syndrome | Other tumor |
| Not Reported | Other tumor |
| Ossifying fibroma | NA |
| Osteoblastoma | NA |
| Osteoma | NA |
| Other | Astroblastoma |
| Papillary Thyroid Carcinoma Pathway | Other tumor |
| Perineuroma | Neurofibroma/Plexiform |
| Pilomatricoma | NA |
| Pleuropulmonary blastoma | Other tumor |
| Portions of white matter with a few reactive astrocytes and rare cells with mild atypia | Other tumor |
| Post-Transplant Lymphoproliferative Disorder | NA |
| Posterior fossa group A (PFA) ependymoma | Ependymoma |
| Posterior fossa group B (PFB) ependymoma | Ependymoma |
| Posterior fossa subependymoma | Ependymoma |
| Primary myelofibrosis | Other tumor |
| Reactive connective tissue | Other tumor |
| Recurrent Acute Leukemia | NA |
| Recurrent Glioma | Other tumor |
| Rosai-dorfman | Rosai-Dorfman disease |
| Shwachman-diamond syndrome | Other tumor |
| Solid pseudopapillary neoplasm of the pancreas | Other tumor |
| Spinal Cord Neoplasm | Other tumor |
| Spinal ependymoma | Ependymoma |
| Spinal subependymoma | Ependymoma |
| Spindle cell neoplasm | Other tumor |
| Spinocerebellar ataxia type 7 | NA |
| Subependymal Giant Cell Astrocytoma (SEGA) | Subependymal Giant Cell Astrocytoma |
| Supratentorial ependymoma | Ependymoma |
| Thrombocytopenia | Other tumor |
| Thrombocytosis | Other tumor |
| Transient Abnormal Myelopoiesis Associated with Down Syndrome | NA |
| Type ii pleuropulmonary blastoma | Other tumor |
| Undifferentiated malignant neoplasm | Other tumor |
| Vascular malformation | Other tumor |