New Term Request: Sarcoma with BCOR genetic alterations

[LBCorson]

As a CIViC curator & editor for the ClinGen Pediatric Task Force, I would like to request the addition of a new, rare pediatric cancer type: Sarcoma with BCOR genetic alterations

Note that I will be submitting a dozen more. If you have suggestions/recommendations/preferences for the submission format, please let me know so I can incorporate into additional submissions.

---

WHO Classification of Tumours Online Entry Name: Sarcoma with BCOR genetic alterations Definition: Sarcomas with BCOR genetic alterations are clinically distinct sarcomas arising in soft tissues and bone, characterized by oncogenic BCOR fusion genes (BCOR fusion sarcomas) or internal tandem duplications (ITDs) in BCOR (BCOR ITD sarcomas). These sarcomas share a morphological spectrum and have similar immunoprofiles and gene expression.

ICD-O code: 9368/3 ICD-O name: Sarcoma with BCOR genetic alterations

---

NCIt NCIt Code: C178465 NCIt Name: Sarcoma with BCOR Genetic Alterations NCIt Definition: A group of rare primitive round cell sarcomas characterized by the presence of BCOR genetic alterations. This category includes sarcomas with BCOR-related gene fusions, most frequently BCOR-CCNB3, and sarcomas showing internal tandem duplication (BCOR-ITD).

---

Synonym: BCOR-Rearranged Sarcoma

The following would be included in the category of sarcoma with BCOR genetic alterations: Childhood Sarcoma with BCOR Genetic Alterations (NCIt: C189007); BCOR-CCNB3 Sarcoma (NCIt: C178466); BCOR ITD Sarcoma (NCIt: C178468); infantile undifferentiated round cell sarcoma; primitive myxoid mesenchymal tumour of infancy

Previously this tumor type was referred to as : Ewing-Like Sarcoma or Round Cell Sarcoma

---

PMID: 35730501

---

Thank you! Laura Corson

Contact Information: Laura.Beth.Corson@gmail.com 650-296-8520 Orcid: 0000-0003-2772-3375

[LBCorson]

Please include in cancer slim file so the cancer diagnosis will be imported into CIViC

[lschriml]

Thank you Laura !! We will get these added to the DO. I have added these new terms and their info into a google doc, which I have shared with you. If it works for you, it would be great to add in the additional terms to this shared doc.

Cheers, Lynn

On Thu, Nov 30, 2023 at 8:14 AM LBCorson @.***> wrote:

Please include in cancer slim file so the cancer diagnosis will be imported into CIViC

— Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1833765141, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DK2WCI7KMRGF7KVME3YHCBDPAVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZTG43DKMJUGE . You are receiving this because you are subscribed to this thread.Message ID: @.*** com>

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

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[LBCorson]

Thank you Lynn-

Attached is the list of additional cancer diagnoses that we would like to add. Should each row be a separate sheet in the google sheet you shared? Should I also enter a New Term Request for each?

I am a total "newbie" to GitHub & DO requests! ;)

Thanks for your help, Laura

On Thu, Nov 30, 2023 at 10:51 AM lschriml @.***> wrote:

Thank you Laura !! We will get these added to the DO. I have added these new terms and their info into a google doc, which I have shared with you. If it works for you, it would be great to add in the additional terms to this shared doc.

Cheers, Lynn

On Thu, Nov 30, 2023 at 8:14 AM LBCorson @.***> wrote:

Please include in cancer slim file so the cancer diagnosis will be imported into CIViC

— Reply to this email directly, view it on GitHub < https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1833765141>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABBB4DK2WCI7KMRGF7KVME3YHCBDPAVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZTG43DKMJUGE>

. You are receiving this because you are subscribed to this thread.Message ID: @.*** com>

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

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

— Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1834041572, or unsubscribe https://github.com/notifications/unsubscribe-auth/BEKWG2KAPP7KR4R7MHZY63TYHCTQLAVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZUGA2DCNJXGI . You are receiving this because you authored the thread.Message ID: @.***>

-- Laura Corson Email: @.*** Cell: 650-296-8520

[lschriml]

Hello Laura, You can add one row in that spreadsheet for each disease term, all in the same worksheet.

No need to enter a new term request for the additional terms.

Cheers, Lynn

On Thu, Nov 30, 2023 at 11:23 AM LBCorson @.***> wrote:

Thank you Lynn-

Attached is the list of additional cancer diagnoses that we would like to add. Should each row be a separate sheet in the google sheet you shared? Should I also enter a New Term Request for each?

I am a total "newbie" to GitHub & DO requests! ;)

Thanks for your help, Laura

On Thu, Nov 30, 2023 at 10:51 AM lschriml @.***> wrote:

Thank you Laura !! We will get these added to the DO. I have added these new terms and their info into a google doc, which I have shared with you. If it works for you, it would be great to add in the additional terms to this shared doc.

Cheers, Lynn

On Thu, Nov 30, 2023 at 8:14 AM LBCorson @.***> wrote:

Please include in cancer slim file so the cancer diagnosis will be imported into CIViC

— Reply to this email directly, view it on GitHub <

https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1833765141>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ABBB4DK2WCI7KMRGF7KVME3YHCBDPAVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZTG43DKMJUGE>

. You are receiving this because you are subscribed to this thread.Message ID: @.*** com>

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

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

— Reply to this email directly, view it on GitHub < https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1834041572>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/BEKWG2KAPP7KR4R7MHZY63TYHCTQLAVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZUGA2DCNJXGI>

. You are receiving this because you authored the thread.Message ID: @.***>

-- Laura Corson Email: @.*** Cell: 650-296-8520

— Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1834101841, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DNNWJLGN33E4HWHCWTYHCXIJAVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZUGEYDCOBUGE . You are receiving this because you commented.Message ID: @.***>

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

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[LBCorson]

Thanks Lynn- I added the additional cancer types with accompanying information. Please let me know if you need additional information? Cheers, Laura

[lschriml]

Working though the google doc, thank you Laura for the great information !!

[sumirp]

Hi @lschriml , as I am currently curating for CIVIC, could you please share the google doc , so I can check whether a new term I wish to request for CIVIC is not already present in the list shared by @LBCorson, so I do not duplicate it.

Regards, Sumir

[LBCorson]

Hi Sumir-

I just shared the google with your gmail @.*** Hopefully this works for you?

The google sheet is at https://docs.google.com/spreadsheets/d/1VYddDuDEQ_EpvuNE4O2QvdgcCq1WBcp-yI85DW5vnRI/edit#gid=0

Lynn - do you know what the timeframe is for getting these cancers added to Disease Ontology? I have been holding off the final acceptance of some of the CIViC entries until we have the DOIDs.

Please let me know if you need additional information for any of the diseases on the list?

Thank you! Laura

On Wed, Jan 3, 2024 at 12:52 AM SumirHPandit @.***> wrote:

Hi @lschriml https://github.com/lschriml , as I am currently curating for CIVIC, could you please share the google doc , so I can check whether a new term I wish to request for CIVIC is not already present in the list shared by @LBCorson https://github.com/LBCorson, so I do not duplicate it.

Regards, Sumir

— Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1874880149, or unsubscribe https://github.com/notifications/unsubscribe-auth/BEKWG2MMVJY7E4SJRUEQ72DYMTWY7AVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZUHA4DAMJUHE . You are receiving this because you were mentioned.Message ID: @.***>

-- Laura Corson Email: @.*** Cell: 650-296-8520

[lschriml]

Hello Laura,     We will focus on these terms to complete their review in January. I am currently out of the country, back next week.Please let us know if there are terms you want added first.Cheers,LynnSent from my iPhoneOn Jan 3, 2024, at 9:32 AM, LBCorson @.***> wrote: Hi Sumir-

I just shared the google with your gmail @.*** Hopefully

this works for you?

The google sheet is at

https://docs.google.com/spreadsheets/d/1VYddDuDEQ_EpvuNE4O2QvdgcCq1WBcp-yI85DW5vnRI/edit#gid=0

Lynn - do you know what the timeframe is for getting these cancers added to

Disease Ontology? I have been holding off the final acceptance of some of

the CIViC entries until we have the DOIDs.

Please let me know if you need additional information for any of the

diseases on the list?

Thank you!

Laura

On Wed, Jan 3, 2024 at 12:52 AM SumirHPandit @.***>

wrote:

Hi @lschriml https://github.com/lschriml , as I am currently curating

for CIVIC, could you please share the google doc , so I can check whether a

new term I wish to request for CIVIC is not already present in the list

shared by @LBCorson https://github.com/LBCorson, so I do not duplicate

it.

Regards,

Sumir

—

Reply to this email directly, view it on GitHub

https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1874880149,

or unsubscribe

https://github.com/notifications/unsubscribe-auth/BEKWG2MMVJY7E4SJRUEQ72DYMTWY7AVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZUHA4DAMJUHE

.

You are receiving this because you were mentioned.Message ID:

@.***>

--

Laura Corson

Email: @.***

Cell: 650-296-8520

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

[sumirp]

Hi yes @LBCorson thank you so much for the google sheet

[lschriml]

Working on these cancer terms, sarcoma with BCOR genetic alterations and it's subtypes have been added to the DO and the DO_cancer_slim.

Cheers, Lynn

[lschriml]

Hello Laura and Sumir, I just finished reviewing and adding in the new disease terms to the DO. They will be included in our release later this week.

Cheers, Lynn

On Wed, Jan 3, 2024 at 9:24 AM SumirHPandit @.***> wrote:

Hi yes @LBCorson https://github.com/LBCorson thank you so much for the google sheet

— Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1875453730, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DM6P3JZI4DRVXEB7ITYMVSZZAVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZVGQ2TGNZTGA . You are receiving this because you were mentioned.Message ID: @.***>

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

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[LBCorson]

Thank you Lynn!Laura @. Jan 29, 2024, at 11:52 AM, lschriml @.> wrote: Hello Laura and Sumir,

I just finished reviewing and adding in the new disease terms to the DO.

They will be included in our release later this week.

Cheers,

Lynn

On Wed, Jan 3, 2024 at 9:24 AM SumirHPandit @.***>

wrote:

Hi yes @LBCorson https://github.com/LBCorson thank you so much for the

google sheet

—

Reply to this email directly, view it on GitHub

https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1271#issuecomment-1875453730,

or unsubscribe

https://github.com/notifications/unsubscribe-auth/ABBB4DM6P3JZI4DRVXEB7ITYMVSZZAVCNFSM6AAAAABABFHJLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZVGQ2TGNZTGA

.

You are receiving this because you were mentioned.Message ID:

@.***>

--

Lynn M. Schriml, Ph.D.

Associate Professor

Institute for Genome Sciences

University of Maryland School of Medicine

Department of Epidemiology and Public Health

670 W. Baltimore St., HSFIII, Room 3061

Baltimore, MD 21201

P: 410-706-6776 | F: 410-706-6756

@.***

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

[sumirp]

Thank you @lschriml