[Revise subclass]patterned dystrophy of the retinal pigment epithelium

maglott commented 4 years ago

Mondo term (ID and Label) MONDO:0018973:patterned dystrophy of the retinal pigment epithelium

Suggested revision and reasons MONDO:0018973: has no definition. This is a child of genetic macular dystrophy which suggests this is macular (Orphanet:63454)

MONDO:0020381 patterned macular dystrophy: has a definition starting ... Butterfly-shaped pigment dystrophy is a patterned dystrophy of the retinal pigment epithelium... which makes it sound as if Butterfly-shaped pigment dystrophy is a subset of patterned macular dystrophy (Orphanet:99001) It also has an exact synonym of patterned dystrophy of retinal pigment epithelium which makes it hard to distinguish from MONDO:0018973

MONDO:0008210 has a comment: Synonym MACULAR dystrophy, BUTTERFLY-SHAPED PIGMENTARY. which is confusing because butterfly pattern seems to define MONDO:0020381

If these are indeed distinct entities, please clean up the exact and related synonyms and comments and define MONDO:0018973

I started looking at these records because I was trying to determine which label is specific to BUTTERFLY-SHAPED. Still not sure.

maglott commented 4 years ago

Just noticed that OMIM uses butterfly on https://www.omim.org/entry/608970, patterned macular dystrophy-2

nicolevasilevsky commented 4 years ago

MONDO:0008210 has a comment: Synonym MACULAR dystrophy, BUTTERFLY-SHAPED PIGMENTARY. which is confusing because butterfly pattern seems to define MONDO:0020381

I fixed this - it seems to be a typo, I made it an exact synonym, because it is so on OMIM: https://www.omim.org/entry/169150

nicolevasilevsky commented 4 years ago

Thanks for this feedback, @maglott I am going to have to ask the experts to weigh in. Orphanet has these two terms (patterned dystrophy of the retinal pigment epithelium (pattern dystrophy is the primary label in Orphanet) and 'patterned macular dystrophy' is a child Butterfly-shaped pigment dystrophy is the primary label).

Looks like @GARDInfoCenter also has a term for Patterned dystrophy of retinal pigment epithelium, but also without a definition.

@ana-rath-orphanet @annieolry @Orphanet

galyea-gard commented 4 years ago

Hi! There was a bit of confusion because we had a page listed as Patterned dystrophy of retinal pigment epithelium that was added several years ago and came from OMIM and OMIM had one of the subtypes (the butterfly one as a synonym). Pattern dystrophy is a disease that affects the macula, and the characteristic pattern of pigment deposition determines the clinical classification, but in some cases the specific type can change in a patient or they may be different patterns in each eye. Therefore, many question the clinical value of the classification. Current classification in Orphanet was in 1977 and includes 5 types : adult-onset foveomacular vitelliform dystrophy (AFVD), butterfly-shaped pigment dystrophy (BSPD), reticular dystrophy of the pigment epithelium, multifocal pattern dystrophy simulating fundus flavimaculatus, and fundus pulverulentus. However, in current clinical practice, the term “pattern dystrophy” applies to several and broad spectrum of acquired and hereditary pigmentary maculopathies (please see: https://www.researchgate.net/publication/330076143_Pattern_Dystrophy_An_Imprecise_Diagnosis_in_the_Age_of_Precision_Medicine

"Because of the large variation of the disease, there is currently no real consensus about what “pattern dystrophy” exactly represents and today, the phrase “pattern dystrophy” describes neither a unique phenotype nor a unique genotype."

Pattern dystrophy ORPHA:63454 Adult-onset foveomacular vitelliform dystrophy ORPHA:99000 Butterfly-shaped pigment dystrophy ORPHA:99001 Fundus pulverulentus ORPHA:99004 Multifocal pattern dystrophy simulating fundus flavimaculatus ORPHA:99003 Reticular dystrophy of the retinal pigment epithelium ORPHA:99002 ('fishnet-like')

I changed GARD name to Pattern dystrophy (which is the parent term) following Orphanet. Because we are still in our review process we will still be adding content and we will comment in the current issues.

nicolevasilevsky commented 3 years ago

Thank you @galyea-gard. I made the GARD term equivalent to MONDO:0018973 'patterned dystrophy of the retinal pigment epithelium'

@maglott From my investigations into this, I think Orphanet:99001 Butterfly-shaped pigment dystrophy is not equiv to OMIMPS:169150 Macular dystrophy, patterned, and I should split it out into its own class, which I will make a child of MONDO_0018973 'patterned dystrophy of the retinal pigment epithelium'.

@cmungall do you agree with this?

kanems commented 2 years ago

Looking at this entry and the Orphanet information, it looks like a few OMIM entries should be children of this concept? @ana-rath-orphanet Is Orphanet certain this isn't the same concept as OMIM PS169150 ? I know the OMIM children terms are not 100% overlapping but I wonder if maybe one of the Orphanet-> OMIM x-refs might just need an update? https://www.omim.org/phenotypicSeries/PS169150 Also UMLS has CUI and a SNOMED CT code that match the string for the Mondo preferred name that could be added as X-refs for this Mondo record. CUI: C4511237; SCTID 725590001

galyea-gard commented 2 years ago

Hi! As commented, this is really a bit confusing as there is no consensus in the medical literature about what this term really represents “Today, the phrase “pattern dystrophy” describes neither a unique phenotype nor a unique genotype”

Pattern dystrophy is the parent term which is equivalent to ORPHA:63454 and to GARD 9821. Recognized subtypes are: (as you can see we only list one of the subtypes in GARD)

Adult-onset foveomacular vitelliform dystrophyhttps://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=14017&disease=Adult-onset-foveomacular-vitelliform-dystrophy&search=Disease_Search_Simple ORPHA:99000 (GARD link: Adult-onset vitelliform macular dystrophy | Genetic and Rare Diseases Information Center (GARD) – an NCATS Program (nih.gov)https://rarediseases.info.nih.gov/diseases/10909/index and OMIM 608161
Butterfly-shaped pigment dystrophyhttps://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=14018&disease=Butterfly-shaped-pigment-dystrophy&search=Disease_Search_Simple ORPHA:99001 – linked to OMIM 602130, 608970 and 169150 (we do not have this one in GARD)
Fundus pulverulentushttps://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=14021&disease=Fundus-pulverulentus&search=Disease_Search_Simple ORPHA:99004 – not in OMIM or GARD
Multifocal pattern dystrophy simulating fundus flavimaculatushttps://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=14020&disease=Multifocal-pattern-dystrophy-simulating-fundus-flavimaculatus&search=Disease_Search_Simple ORPHA:99003 – not in OMIM or GARD
Reticular dystrophy of the retinal pigment epitheliumhttps://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=14019&disease=Reticular-dystrophy-of-the-retinal-pigment-epithelium&search=Disease_Search_Simple ORPHA:99002 –linked to OMIM: 179840 267800 617175 Note: OMIM entries 602130, 608970 and 169150 are linked to Orphanet 99001 as they share the same phenotype and different genotypes. OMIM 617111 is linked to Orphanet for 466718 for “Martinique crinkled retinal pigment epitheliopathy” – which is not included in the pattern dystrophy current classification. OMIM phenotypic class in based on the causative gene mutation. The first gene associated with pattern dystrophy was the PRPH2 which is the OMIM 169150 but we cannot say that is exactly equivalent to the Orphanet parent term.

As we are still in a review process we may add/retire many terms in GARD. Hope this helps. Gioconda

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Looking at this entry and the Orphanet information, it looks like a few OMIM entries should be children of this concept? [Image removed by sender. image]https://user-images.githubusercontent.com/71083858/149535509-7a6c943a-e7ab-4233-8fa2-e89fa1ffeaaf.png @ana-rath-orphanethttps://github.com/ana-rath-orphanet Is Orphanet certain this isn't the same concept as OMIM PS169150 ? I know the OMIM children terms are not 100% overlapping but I wonder if maybe one of the Orphanet-> OMIM x-refs might just need an update? https://www.omim.org/phenotypicSeries/PS169150 Also UMLS has CUI and a SNOMED CT code that match the string for the Mondo preferred name that could be added as X-refs for this Mondo record. CUI: C4511237; SCTID 725590001

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nicolevasilevsky commented 2 years ago

Also UMLS has CUI and a SNOMED CT code that match the string for the Mondo preferred name that could be added as X-refs for this Mondo record. CUI: C4511237; SCTID 725590001

I added these xrefs to 'butterfly-shaped pigment dystrophy'

nicolevasilevsky commented 2 years ago

@kanems from what I can tell, Orphanet_99001 is not equivalent to OMIMPS:PS169150. Different genes are implicated in the Orphanet record.

genes affected in OMIMPS are MAPKAP3, MDBS2, CTNNA1 and PRPH2.

The affected genes in Orphanet_99001 are CTNNA1, OTX2, PRPH2 (see: https://www.orpha.net/consor/cgi-bin/Disease_Genes_Simple.php?lng=EN&LnkId=14018&Typ=Pat&diseaseType=Gen&from=rightMenu)

If any other action is needed, please reopen this, thanks!

monarch-initiative / mondo

[Revise subclass]patterned dystrophy of the retinal pigment epithelium #1819