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Add term for Distal duplication 11q #1367

Closed sbello closed 1 month ago

sbello commented 2 months ago

Please consider adding a term for Distal duplication 11q syndrome

See ORPHA:96103 https://www.orpha.net/en/disease/detail/96103 Reference set from the Orphanet record https://pubmed.ncbi.nlm.nih.gov/?term=(Trisomy+OR+duplication%5Bti%5D)+(11q*%5Bti%5D+OR+(chromosome+11+(long+arm%5Bti%5D)))+(distal+OR+telomer*+OR+qter+OR+terminal) The mouse paper sites PMID:15098242 and PMID:17219392 that are on this list

Orphanet defintion "Distal trisomy 11q is a rare chromosomal anomaly syndrome, resulting from the partial duplication of the long arm of chromosome 11, with high phenotypic variability principally characterized by craniofacial dysmorphism (brachycephaly/plagiocephaly, low-set, posteriorly rotated ears, short philtrum, micrognathia) and intellectual disability. Short stature and seizures, as well as cardiac (e.g. atrial septal defect), skeletal (incl. brachy/syndactyly) and genital (e.g. micropenis, cryptorchidism) abnormalities may also be associated. Neurodevelopmental anomalies (pain insensitivity, sensorineural hearing loss, expressive language deficiency) and neuropsychiatric disorders (autistic features, auditory hallucination, self-talking) have also been reported. "

Mouse model in PMID:37341808

No OMIM record

UMLS definition (https://www.ncbi.nlm.nih.gov/medgen/419166) A rare chromosomal anomaly syndrome resulting from the partial duplication of the long arm of chromosome 11 with high phenotypic variability. Principle characteristics are craniofacial dysmorphism (brachycephaly/plagiocephaly, low-set, posteriorly rotated ears, short philtrum, micrognathia) and intellectual disability. Short stature and seizures, as well as cardiac (atrial septal defect), skeletal (brachy/syndactyly) and genital (micropenis, cryptorchidism) abnormalities may also be associated. Neurodevelopmental anomalies (pain insensitivity, sensorineural hearing loss, expressive language deficiency) and neuropsychiatric disorders (autistic features, auditory hallucination, self-talking) have also been reported. [from SNOMEDCT_US]

Child of chromosomal duplication syndrome (DOID:0060429)

Suggested definition A chromosomal duplication syndrome characterized by variable phenotypic presentation, principally craniofacial dysmorphism (brachycephaly/plagiocephaly, low-set, posteriorly rotated ears, short philtrum, micrognathia) and intellectual disability, that has_material_basis_in duplication of the distal region the long arm of chromosome 11.

Orphanet synonyms

allenbaron commented 2 months ago

I'll take a look at this. Thanks Sue.

allenbaron commented 2 months ago

Some of the papers describing these chromosomal anomalies are pretty old. I'm surprised there's not something in OMIM. I searched everything I could think of and found nothing about 11q duplication.

There's a high amount of variability in what portion of 11q is duplicated and that's probably related to the phenotypic variability. The rarity of the various duplications would make it tough to create more descriptive and accurate diseases, so I think it makes sense to create this disease as you've suggested as a sort of catch all.

What are your thoughts on using a different name that doesn't include the word "distal"?

Orphanet's definition is inclusive of duplications that are not distal and it seems like the duplications and related disease phenotypes we'd want to capture are not always distal. Maybe we could name it similar to DO's existing duplication diseases, e.g. "chromosome 11q duplication syndrome". The only cons I see are that there are no current diseases that reference an entire arm with regard to duplication and .

Walker, et al (2022)[^3] stated:

We compared the phenotypes of all known “pure” trisomy 11q cases in the literature and find that trisomy 11q23-qter is both recurrent and the most common cytogenetic abnormality found in the reported cases. It is associated with the core features of trisomy 11q syndrome.

As an alternate approach we could create two diseases, one to match Orphanet's "distal" disease and another, maybe called "intersitial 11q duplication syndrome"... or something like that, to capture the diseases in the same region as FGF3/4 as described in the mouse paper. But given the phenotypic variability, I think one catch all disease is probably better.

[^1]: Zarate YA, Kogan JM, Schorry EK, Smolarek TA, Hopkin RJ. A new case of de novo 11q duplication in a patient with normal development and intelligence and review of the literature. Am J Med Genet A. 2007 Feb 1;143A(3):265-70. doi: 10.1002/ajmg.a.31519. PMID: 17219392. [^2]: Yelavarthi KK, Zunich J. Familial interstitial duplication of 11q; partial trisomy (11)(q13.5q21). Am J Med Genet A. 2004 May 1;126A(4):423-6. doi: 10.1002/ajmg.a.20610. PMID: 15098242. [^3]: Walker A, Wang X, Kim YM, Lu X, Taylor A, Demarzo D, Li S, Pang H. Molecular cytogenetic characterization of partial trisomy of the long arm of chromosome 11 in a patient with multiple congenital anomalies. Mol Cytogenet. 2022 Apr 19;15(1):17. doi: 10.1186/s13039-022-00595-0. PMID: 35440058; PMCID: PMC9019979.

sbello commented 2 months ago

The Orphanet hierarchy has partial duplication of chromosome 11 (ORPHA:262653) partial duplication of the long arm of chromosome 11 partial duplication of the short arm of chromosome 11

For MGI purposes (and Alliance) having a terms for 'partial duplication of chromosome 11' would work. It helps to move the annotations down from 'chromosomal duplication syndrome' at the least.

I agree that the Orpha and UMLS definition are basically defining 'partial duplication of the long arm of chromosome 11' not specifically the distal part of the long arm.

lschriml commented 2 months ago

How about: chromosome 11 partial duplication syndrome

allenbaron commented 2 months ago

I think adding full chromosome grouping terms is undesirable. It makes sense that we add a grouping term here, where the different duplications are overlapping and phenotypes are hard to define, but I doubt that would happen across the whole chromosome and favor keeping long and short arm events separate.

So, in this case, I'd recommend we use Lynn's name with a slight modification to limit it to the long arm of the chromosome, making the name 'chromosome 11q partial duplication syndrome'.

I also think it makes more sense for the the exact match/xref of this term to be Orphanet's 'partial duplication of the long arm of chromosome 11' (ORDO:262923), instead of 'Distal duplication 11q' (ORDO:96103) and to make the definition more like the 'chromosomal duplication syndrome' parent definition, something like:

A chromosomal duplication syndrome that has_material_basis_in extra copies of a region of the long arm of chromosome 11.

Is this disease too general?

Orphanet has two children for 'partial duplication of the long arm of chromosome 11' (ORDO:262923): the 'Distal duplication 11q' (ORDO:96103) we've been discussing and Microtriplication 11q24.1 (ORDO:289522), which appears to be defined by a single publication, PMID:21617255, which I can't access because of the paywall.

Do you think we should add both or either of these diseases as children?

sbello commented 2 months ago

I think the broad definition is helpful, since it has 'a region' it is flexible enough to act as a grouping term for various duplications of the long arm.

From the MO perspective I think that is enough and DO could skip the more specific children since those are still fairly broad groupings of subsections of the long arms.

The broadness of the proposed term would allow for the addition of specific children that are related by more than just the general region duplicated in the future if we need them.

The benefit I see to adding chromosome # duplication syndrome terms is that it allows easy grouping of sets of patients or models that duplicate some region of the specified chromosome. This means that when a novel duplication syndrome patient/model comes along you can at least use a chromosome specific term for the annotation rather than having to go up to chromosome duplication syndrome. It would also make it easier to see which named syndromes actually involve duplication of the same chromosome. For example right now if a a user wanted all CHr. 17 duplication syndromes they would need to poke around to find out that Potocki-Lupski syndrome to realize that it is a Chr. 17 duplication.

Partially this is just my aversion to flat hierarchies :)

allenbaron commented 1 month ago

Okay, apologies that I kicked this down the road a bit. I've decided to create the general disease covering chromosome 11, following Lynn's original suggestion, and I currently have this definition:

A chromosomal duplication syndrome that has_material_basis_in one or more extra copies of a region of chromosome 11.

I'm wondering if I should limit this exclusively to duplications that occur from and on chromosome 11 by adding something like 'without the involvement of regions of other chromosomes'. I know from prior reading that there can be translocations of some of these regions of chromosome 11 and, I think, they may sometimes occur with duplication events.

Example: Emanuel syndrome (extra chromosome derived from part of chromosome 11 and part of chromosome 22); see https://medlineplus.gov/genetics/chromosome/11/#conditions and https://medlineplus.gov/genetics/condition/emanuel-syndrome/

Thoughts?

sbello commented 1 month ago

Maybe ask the clinicians. At the mutation level duplication is distinct from translocation but is that true at the syndrome level. If the patient inherits the translocated chromosome and normal copies of the chromosome from which this translocated piece originated and thus has 3 copies of that segment would that end up in the 'duplication' syndrome bucket? I can't find any good reference for this question.

lschriml commented 1 month ago

Hello Carol, Can you please advise us on this issue ? (see notes below).

Thank you, Lynn

On Thu, Sep 19, 2024 at 1:58 PM Sue Bello @.***> wrote:

Maybe ask the clinicians. At the mutation level duplication is distinct from translocation but is that true at the syndrome level. If the patient inherits the translocated chromosome and normal copies of the chromosome from which this translocated piece originated and thus has 3 copies of that segment would that end up in the 'duplication' syndrome bucket? I can't find any good reference for this question.

— Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1367#issuecomment-2361840075, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DLQ4YGVZ6WU7ZNN5OTZXMGGFAVCNFSM6AAAAABL3JMGQSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRRHA2DAMBXGU . You are receiving this because you commented.Message ID: @.***>

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

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lschriml commented 1 month ago

If I understand the question correctly, then this will belong in at least two categories, chromosomal abnormality on the basis of mechanism, and “syndrome” on the basis of a set of features that are identifiable. Like a number of other conditions…..

I think the question is how to categorize if the duplication is a result of a balanced translocation. But if the duplication of 11q is the unbalanced result of a balanced translocation, then the patient should have not only a duplication of 11q but also a deletion of part of another chromosome. Unless there is something really strange, with the translocation involving an acrocentric chromosome, and that really would be weird…..

To be concrete. If the translocation involved 11 q and 6 p, and the patient had inherited the chromosome 6 with 11q material, and the normal 11 from the carrier parent, and a normal 6 and a normal 11 from the other parent, then the patient has duplication of the 11q material AND ALSO deletion of the 6 p material.

So that person fits in the category of 11q duplication syndrome, but that is not the only problem the patient has, unless the deleted region is so tiny that it has no known clinical consequences.

Not sure I’ve answered the question, possibly I need more information, and would be happy to go over the details with you and your colleague…..

CG

From: Lynn Schriml @.> Sent: Thursday, September 19, 2024 2:24 PM To: DiseaseOntology/HumanDiseaseOntology @.>; Greene, Carol @.> Cc: DiseaseOntology/HumanDiseaseOntology @.>; Comment @.***> Subject: Re: [DiseaseOntology/HumanDiseaseOntology] Add term for Distal duplication 11q (Issue #1367)

Hello Carol, Can you please advise us on this issue ? (see notes below).

Thank you, Lynn

On Thu, Sep 19, 2024 at 1:58 PM Sue Bello @.**@.>> wrote:

Maybe ask the clinicians. At the mutation level duplication is distinct from translocation but is that true at the syndrome level. If the patient inherits the translocated chromosome and normal copies of the chromosome from which this translocated piece originated and thus has 3 copies of that segment would that end up in the 'duplication' syndrome bucket? I can't find any good reference for this question.

— Reply to this email directly, view it on GitHubhttps://github.com/DiseaseOntology/HumanDiseaseOntology/issues/1367#issuecomment-2361840075, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABBB4DLQ4YGVZ6WU7ZNN5OTZXMGGFAVCNFSM6AAAAABL3JMGQSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRRHA2DAMBXGU. 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 @.**@.>

allenbaron commented 1 month ago

Okay great. I think Carol's comment clarifies this situation. If the duplication occurs with other duplicated or deleted genetic material, then the patient would have multiple diseases. So, I don't think it's necessary to add the extra 'without the involvement of regions of other chromosomes' text because that would discourage users from annotating to this disease in that scenario.

Presumably if the specific combined genetic changes happened frequently enough, clinicians would designate it a new disease. If that were to occur, we might need to clarify it somewhat (or deal with it hierarchically maybe) but these happen so rarely that it seems and with such variability that this seems unlikely.

allenbaron commented 1 month ago

Okay, this will be in the release out later today as DOID:0070614.