CIViC disease requests

[kkrysiak]

Hepatocellular Mixed Fibrolamellar Carcinoma (rare subtype of HCC with mixed conventional and fibrolamellar features, not in NCI)

The following would benefit from review of the WHO classification for myeloid neoplasms (http://www.bloodjournal.org/content/127/20/2391): Chronic Neutrophilic Leukemia (C3179) Chronic Myelomonocytic Leukemia (C3178)

There are more but I wanted to get this started.

[kkrysiak]

epithelioid hemangioendothelioma (C3800)

[kkrysiak]

PTEN hamartoma tumor syndrome. This one will require some work and likely some consultation with experts that know much more than I do. This is the paper where this term was derived for CIViC EID1935.

[lschriml]

Thank you for these cancer terms from CIViC:

[DONE] (1) Hepatocellular Mixed Fibrolamellar Carcinoma I edited the parent term: Hepatocellular Mixed Fibrolamellar Carcinoma, updated it's name to:
fibrolamellar carcinoma --> I added the mixed hepatocellular fibrolamellar carcinoma (this is how the disease was referred to in several articles).

[In progress, examining myeloproliferative neoplasm, revisions for this area of DO]

(2) Chronic Neutrophilic Leukemia (C3179) NCI: lists this as a child of 'chronic leukemia' or 'myeloproliferative neoplasm' A rare chronic myeloproliferative neoplasm characterized by neutrophilic leukocytosis. There is no detectable Philadelphia chromosome or BCR/ABL fusion gene. A disease in which too many neutrophils (a type of white blood cell) are found in the blood. The extra neutrophils may cause the spleen and liver to become enlarged.

https://en.wikipedia.org/wiki/Chronic_neutrophilic_leukemia

(3) Chronic Myelomonocytic Leukemia (C3178)

[lschriml]

Adding to DO, as children of chronic leukemia: (1) chronic neutrophilic leukemia (C3179) (2) chronic nyelomonocytic leukemia (C3178)

--> looking at epithelioid hemangioendothelioma (C3800) --> http://www.rare-cancer.org/info/hemangioendothelioma.php

--> created a new malignant hemangioma parent for; (3) malignant epithelioid hemangioendothelioma

--> added as a syndrome (4) PTEN hamartoma tumor syndrome

[kkrysiak]

@lschriml can these be added to the cancer DO subset? We still can't use them in CIViC.

[lschriml]

yes, can add these terms to the DO cancer subset this week. Apologies, I added the terms to the DO, but not the subset.

To double check, the terms you want added are: mixed hepatocellular fibrolamellar carcinoma chronic neutrophilic leukemia chronic myelonocytic leukemia malignant epithelioid hemangioendothelioma PTEN hamartoma tumor syndrome

Are there any other terms you need ? Cheers, Lynn

[kkrysiak]

Complete list of diseases in CIViC that currently do not have a DOID. I'm not sure how many are currently in DO.

Can't find in DO Aggressive Fibromatosis / Desmoid Fibromatosis Anaplastic Thyroid Cancer Diffuse Intrinsic Pontine Glioma <- pediatric brainstem glioma Epithelioid Inflammatory Myofibroblastic Sarcoma <- rare subtype of Inflammatory Myofibroblastic Sarcoma Extranodal NK/T-cell lymphoma, nasal type <- subtype of mature T-cell and NK-cell lymphoma (0050743) (see 2016 WHO classification of lymphoid neoplasms http://www.bloodjournal.org/content/bloodjournal/early/2016/03/15/blood-2016-01-643569.full.pdf) Ovarian Sex Cord-stromal Tumours <- Is a type of granulosa cell tumor (2999) Pericytoma with t(7;12) or Pericytoma <- I'm not sure how to add this since this is becoming a molecularly defined disease but I don't know how prevalent this notation is (from our evidence item/source: https://civicdb.org/events/genes/2279/summary/variants/780/summary/evidence/1844) Endometrial Hyperplasia Solid Tumor <- not sure this fits into DO

Missing from cancer subset Chronic Eosinophilic Leukemia myeloid and lymphoid neoplasms associated with PDGFRA rearrangement myeloid and lymphoid neoplasms associated with FGFR1 abnormalities myeloid neoplasms associated with PDGFRB rearrangement Chronic Myelomonocytic Leukemia Chronic Neutrophilic Leukemia Hepatocellular Mixed Fibrolamellar Carcinoma Waldenstrom's Macroglobulinemia malignant epithelioid hemangioendothelioma PTEN Harmatoma Tumor Syndrome Polycythemia

We've added an advanced search to identify all evidence in CIViC that is missing a DOID. This may be for a few different reasons but that is how I generated the list above. https://civicdb.org/search/evidence/f081a82b-9b3a-438a-859e-427e16f5f487

[kkrysiak]

I'm working through these now and will edit above. Some are entries which should be added, some are entries which are missing from the cancer subset.

[susannasiebert]

@lschriml we're still missing "Chronic Neutrophilic Leukemia" (DOID:0080187) from the DO_cancer_slim.obo subset. Do you want me to make a new issue to have it added?

[lschriml]

Hello KK, No need, I've got it on my list of terms to add.

Much appreciated, Lynn

On Mon, Nov 12, 2018 at 9:58 AM Susanna Kiwala notifications@github.com wrote:

@lschriml https://github.com/lschriml we're still missing "Chronic Neutrophilic Leukemia" (DOID:0080187) from the DO_cancer_slim.obo subset. Do you want me to make a new issue to have it added?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/280#issuecomment-437911665, or mute the thread https://github.com/notifications/unsubscribe-auth/AEIeDZjOhCfpBJB5waq0T12hfGl1ssz5ks5uuYyXgaJpZM4M6pvW .

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 801 W. Baltimore St., Room 659 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 lschriml@som.umaryland.edu