[Revise subclass] Review classification of immune disorders

nicolevasilevsky commented 3 years ago

review this article: https://link.springer.com/article/10.1007/s10875-019-00737-x

See the 10 tables. Make sure our classification of these diseases are consistent with the tables.

Action item:

[ ] the tables have a list of gene deficiencies that are associated with various diseases. Each deficiency is linked to an OMIM gene (and on the OMIM page, the associated diseases are linked. I think that we have all (or most) of these diseases in Mondo - we need to make sure these diseases are grouped in the same subhierarchies as is in these tables.

Source: PMID:31953710

Update - this was discussed on the Mondo curation call on 11/11/21 with Sabrina and Peter and we should go ahead and redo the classifications and add new parents where needed.

If any questions arise, we should try to follow up with the author Kathleen E. Sullivan (Peter knows her).

nicolevasilevsky commented 3 years ago

Table 1.1: (note, these OMIM pages lead to the gene, and there are associated diseases with each gene)

[x] www.omim.org/308380
[x] www.omim.org/600173
[x] www.omim.org/146661
[x] www.omim.org/151460
[x] www.omim.org/186790
[x] www.omim.org/186830
[x] www.omim.org/186780
[x] www.omim.org/605000
[x] www.omim.org/602354

nicolevasilevsky commented 3 years ago

table 1.2 T-B- SCID

[x] www.omim.org/179615
[x] www.omim.org/179616
[x] www.omim.org/605988
[x] www.omim.org/615966
[x] www.omim.org/611290
[x] www.omim.org/601837
[x] www.omim.org/608958
[x] www.omim.org/103020
[x] www.omim.org/602049 Source: PMID:31953710

nicolevasilevsky commented 3 years ago

table 1.3 Combined immunodeficiency (CID), generally less profound than SCID (MONDO_0015131)

[ ] www.omim.org/308230
[ ] www.omim.org/606843
[ ] www.omim.org/604558
[ ] www.omim.org/605717
[ ] www.omim.org/186740
[ ] www.omim.org/186910
[ ] www.omim.org/269840
[ ] www.omim.org/617006
[ ] www.omim.org/170260
[ ] www.omim.org/170261
[ ] www.omim.org/601962
[ ] www.omim.org/109700
[ ] www.omim.org/600005
[ ] www.omim.org/603200
[ ] www.omim.org/601863
[ ] www.omim.org/601861
[ ] www.omim.org/603023
[ ] www.omim.org/243700
[ ] www.omim.org/603122
[ ] www.omim.org/174761
[ ] www.omim.org/600815
[ ] www.omim.org/602037
[ ] www.omim.org/614868
[ ] www.omim.org/615387
[ ] www.omim.org/615758
[ ] www.omim.org/186973
[ ] www.omim.org/615468
[ ] www.omim.org/615206
[ ] www.omim.org/616098
[ ] www.omim.org/615767
[ ] www.omim.org/615207
[ ] www.omim.org/615593
[ ] www.omim.org/615592
[ ] www.omim.org/604655
[ ] www.omim.org/604758
[ ] www.omim.org/618287
[ ] www.omim.org/300988
[ ] www.omim.org/616740
[ ] www.omim.org/164910
[ ] www.omim.org/613437

nicolevasilevsky commented 3 years ago

table 2.1 Immunodeficiency with congenital thrombocytopenia

[ ] www.omim.org/300392
[ ] www.omim.org/602357
[ ] www.omim.org/604223

nicolevasilevsky commented 3 years ago

table 2.2 DNA repair defects other than those listed in Table 1

[ ] www.omim.org/607585
[ ] www.omim.org/602667
[ ] www.omim.org/604610
[ ] www.omim.org/602900
[ ] www.omim.org/614064
[ ] www.omim.org/609937
[ ] www.omim.org/603946
[ ] www.omim.org/600259
[ ] www.omim.org/612688
[ ] www.omim.org/602638
[ ] www.omim.org/174762
[ ] www.omim.org/602670
[ ] www.omim.org/126391
[ ] www.omim.org/608243
[ ] www.omim.org/615667
[ ] www.omim.org/610608

nicolevasilevsky commented 3 years ago

table 2.3. Thymic defects with additional congenital anomalies

[ ] www.omim.org/602054
[ ] www.omim.org/608892
[ ] www.omim.org/608166
[ ] www.omim.org/601705
[ ] www.omim.org/600838
[ ] www.omim.org/601362
[ ] www.omim.org/147791

nicolevasilevsky commented 3 years ago

table 2.4. Immuno-osseous dysplasias

[ ] www.omim.org/157660
[ ] www.omim.org/606622
[ ] www.omim.org/612176
[ ] www.omim.org/601428
[ ] www.omim.org/617425

nicolevasilevsky commented 3 years ago

table 2.5. Hyper IgE syndromes (HIES)

[ ] www.omim.org/147060
[ ] www.omim.org/147880
[ ] www.omim.org/618523
[ ] www.omim.org/618282
[ ] www.omim.org/606944
[ ] www.omim.org/609192
[ ] www.omim.org/610168
[ ] www.omim.org/605010
[ ] www.omim.org/172100
[ ] www.omim.org/617638

nicolevasilevsky commented 3 years ago

table 2.6. Defects of vitamin B12 and folate metabolism

[ ] www.omim.org/613441
[ ] www.omim.org/229050
[ ] www.omim.org/172460

nicolevasilevsky commented 3 years ago

table 2.7. Anhidrotic ectodermodysplasia with immunodeficiency (EDA-ID)

[ ] www.omim.org/300248
[ ] www.omim.org/164008
[ ] www.omim.org/618204

table 2.8. Calcium channel defects

[ ] www.omim.org/610277
[ ] www.omim.org/605921

table 2.9. Other defects skipping this section because we wouldn't classify something as 'other' in Mondo.

table 3.1. Severe reduction in all serum immunoglobulin isotypes with profoundly decreased or absent B cells, agammaglobulinemia

[ ] www.omim.org/300300
[ ] www.omim.org/147020
[ ] www.omim.org/146770
[ ] www.omim.org/112205
[ ] www.omim.org/147245
[ ] www.omim.org/604515
[ ] www.omim.org/602839
[ ] www.omim.org/615214
[ ] www.omim.org/616941
[ ] www.omim.org/147141
[ ] www.omim.org/601416
[ ] www.omim.org/126431

table 3.2. Severe reduction in at least 2 serum immunoglobulin isotypes with normal or low number of B cells, CVID phenotype

[ ] www.omim.org/615513
[ ] www.omim.org/616005
[ ] www.omim.org/158350
[ ] www.omim.org/107265
[ ] www.omim.org/186845
[ ] www.omim.org/112210
[ ] www.omim.org/120650
[ ] www.omim.org/604907
[ ] www.omim.org/606269
[ ] www.omim.org/602695
[ ] www.omim.org/612907
[ ] www.omim.org/164011
[ ] www.omim.org/615577
[ ] www.omim.org/603023
[ ] www.omim.org/615332
[ ] www.omim.org/300972
[ ] www.omim.org/618459
[ ] www.omim.org/300310
[ ] www.omim.org/609213
[ ] www.omim.org/602049
[ ] www.omim.org/601336

table 3.3. Severe reduction in serum IgG and IgA with normal/elevated IgM and normal numbers of B cells, hyper IgM

[ ] www.omim.org/605257
[ ] www.omim.org/191525
[ ] www.omim.org/610169
[ ] www.omim.org/600678

table 3.4. Isotype, light chain, or functional deficiencies with generally normal numbers of B cells

[ ] www.omim.org/147200
[ ] www.omim.org/616452

table 4.1. Familial hemophagocytic lymphohistiocytosis (FHL syndromes)

[ ] www.omim.org/170280
[ ] www.omim.org/608897
[ ] www.omim.org/605014
[ ] www.omim.org/601717
[ ] www.omim.org/610884
[ ] www.omim.org/222700

table 4.2. FHL syndromes with hypopigmentation

[ ] www.omim.org/606897
[ ] www.omim.org/603868
[ ] www.omim.org/603401
[ ] www.omim.org/617050

table 4.3. Regulatory T cell defects

[ ] www.omim.org/300292
[ ] www.omim.org/147730
[ ] www.omim.org/618495
[ ] www.omim.org/123890
[ ] www.omim.org/606453
[ ] www.omim.org/610094
[ ] www.omim.org/102582
[ ] www.omim.org/605394
[ ] www.omim.org/173650

table 4.4. Autoimmunity with or without lymphoproliferation

[ ] www.omim.org/240300
[ ] www.omim.org/606409
[ ] www.omim.org/190470
[ ] www.omim.org/147795
[ ] www.omim.org/613230

table 4.5. Immune dysregulation with colitis

[ ] www.omim.org/124092
[ ] www.omim.org/146933
[ ] www.omim.org/123889
[ ] www.omim.org/604708
[ ] www.omim.org/618213
[ ] www.omim.org/618108

table 4.6. Autoimmune lymphoproliferative syndrome (ALPS, Canale-Smith syndrome)

[ ] www.omim.org/134637
[ ] www.omim.org/134638
[ ] www.omim.org/601762
[ ] www.omim.org/601763
[ ] www.omim.org/602457

table 4.7. Susceptibility to EBV and lymphoproliferative conditions

[ ] www.omim.org/300490
[ ] www.omim.org/300079
[ ] www.omim.org/615122
[ ] www.omim.org/602840
[ ] www.omim.org/615897
[ ] www.omim.org/602250
[ ] www.omim.org/603962
[ ] www.omim.org/610859
[ ] www.omim.org/300853
[ ] www.omim.org/615559

table 5.1. Congenital neutropenias

[ ] www.omim.org/130130
[ ] www.omim.org/600871
[ ] www.omim.org/605998
[ ] www.omim.org/611045
[ ] www.omim.org/610035
[ ] www.omim.org/602671
[ ] www.omim.org/300299
[ ] www.omim.org/610389
[ ] www.omim.org/300394
[ ] www.omim.org/607817
[ ] www.omim.org/613276
[ ] www.omim.org/616012
[ ] www.omim.org/616254
[ ] www.omim.org/138971
[ ] www.omim.org/601736
[ ] www.omim.org/189965
[ ] www.omim.org/607444
[ ] www.omim.org/617052
[ ] www.omim.org/617941
[ ] www.omim.org/601746
[ ] www.omim.org/604857

table 5.2. Defects of motility

[ ] www.omim.org/600065
[ ] www.omim.org/605881
[ ] www.omim.org/607901
[ ] www.omim.org/608203
[ ] www.omim.org/102630
[ ] www.omim.org/136537
[ ] www.omim.org/602365
[ ] www.omim.org/604734
[ ] www.omim.org/602421
[ ] www.omim.org/606078

table 5.3. Defects of respiratory burst

[ ] www.omim.org/306400
[ ] www.omim.org/608508
[ ] www.omim.org/618334
[ ] www.omim.org/608512
[ ] www.omim.org/608515
[ ] www.omim.org/613960
[ ] www.omim.org/305900

table 5.4. Other non-lymphoid defects. skipping this section because we wouldn't classify something as 'other' in Mondo.

table 6.1. Mendelian susceptibility to mycobacterial disease (MSMD)

[ ] www.omim.org/601604
[ ] www.omim.org/161561
[ ] www.omim.org/601642
[ ] www.omim.org/607562
[ ] www.omim.org/209950
[ ] www.omim.org/615978
[ ] www.omim.org/147569
[ ] www.omim.org/614892
[ ] www.omim.org/300645
[ ] www.omim.org/614893
[ ] www.omim.org/226990
[ ] www.omim.org/608238
[ ] www.omim.org/611521
[ ] www.omim.org/176941
[ ] www.omim.org/147571
[ ] www.omim.org/602943
[ ] www.omim.org/147795

table 6.2. Epidermodysplasia verruciformis (HPV)

[ ] www.omim.org/605828
[ ] www.omim.org/605829
[ ] www.omim.org/618267
[ ] www.omim.org/162643

table 6.3. Predisposition to severe viral infection

[ ] www.omim.org/600555
[ ] www.omim.org/600556
[ ] www.omim.org/147574
[ ] www.omim.org/605047
[ ] www.omim.org/107450
[ ] www.omim.org/602376
[ ] www.omim.org/146740
[ ] www.omim.org/606951
[ ] www.omim.org/614258
[ ] www.omim.org/617454
[ ] www.omim.org/617455

table 6.4. Herpes simplex encephalitis (HSE)

[ ] www.omim.org/613002
[ ] www.omim.org/608204
[ ] www.omim.org/601896
[ ] www.omim.org/607601
[ ] www.omim.org/604834
[ ] www.omim.org/616532
[ ] www.omim.org/607024

table 6.5. Predisposition to invasive fungal diseases

[ ] www.omim.org/607212

table 6.6. Predisposition to mucocutaneous candidiasis

[ ] www.omim.org/605461
[ ] www.omim.org/610925
[ ] www.omim.org/606496
[ ] www.omim.org/600555
[ ] www.omim.org/607043

table 6.7. TLR signaling pathway deficiency with bacterial susceptibility

[ ] www.omim.org/606883
[ ] www.omim.org/602170
[ ] www.omim.org/300283
[ ] www.omim.org/614382

table 6.8. Other inborn errors of immunity related to non-hematopoietic tissues

[ ] www.omim.org/271400
[ ] www.omim.org/141250
[ ] www.omim.org/603743
[ ] www.omim.org/608025
[ ] www.omim.org/601181
[ ] www.omim.org/602727
[ ] www.omim.org/614780
[ ] www.omim.org/607649
[ ] www.omim.org/611466
[ ] www.omim.org/604592
[ ] www.omim.org/603499
[ ] www.omim.org/602642
[ ] www.omim.org/605254
[ ] www.omim.org/613737
[ ] www.omim.org/613736

table 6.9. Other inborn errors of immunity related to leukocytes

[ ] www.omim.org/601900
[ ] www.omim.org/604113

table 7.1. Type 1 interferonopathies

[ ] www.omim.org/612374
[ ] www.omim.org/607575
[ ] www.omim.org/606609
[ ] www.omim.org/610326
[ ] www.omim.org/610330
[ ] www.omim.org/606034
[ ] www.omim.org/606754
[ ] www.omim.org/146920
[ ] www.omim.org/615846
[ ] www.omim.org/126350
[ ] www.omim.org/614420
[ ] www.omim.org/171640
[ ] www.omim.org/301220
[ ] www.omim.org/607057
[ ] www.omim.org/164350

table 7.2. Defects affecting the inflammasome

[ ] www.omim.org/249100
[ ] www.omim.org/134610
[ ] www.omim.org/260920
[ ] www.omim.org/191900
[ ] www.omim.org/120100
[ ] www.omim.org/607115
[ ] www.omim.org/611762
[ ] www.omim.org/616050
[ ] www.omim.org/616115
[ ] www.omim.org/614878
[ ] www.omim.org/614468
[ ] www.omim.org/617388
[ ] www.omim.org/615225

table 7.3. Non-inflammasome-related conditions (new term request?)

[ ] www.omim.org/142680
[ ] www.omim.org/604416
[ ] www.omim.org/186580
[ ] www.omim.org/614328
[ ] www.omim.org/609628
[ ] www.omim.org/612852
[ ] www.omim.org/614204
[ ] www.omim.org/602782
[ ] www.omim.org/602723
[ ] www.omim.org/118400
[ ] www.omim.org/256040
[ ] www.omim.org/609702
[ ] www.omim.org/616414
[ ] www.omim.org/615712
[ ] www.omim.org/616744
[ ] www.omim.org/615781
[ ] www.omim.org/171740
[ ] www.omim.org/606559
[ ] www.omim.org/618398

table 8. Complement deficiencies

[ ] www.omim.org/120550
[ ] www.omim.org/120570
[ ] www.omim.org/120575
[ ] www.omim.org/613785
[ ] www.omim.org/613785
[ ] www.omim.org/120810
[ ] www.omim.org/217000
[ ] www.omim.org/120700
[ ] www.omim.org/120900
[ ] www.omim.org/217050
[ ] www.omim.org/217070
[ ] www.omim.org/120950
[ ] www.omim.org/120930
[ ] www.omim.org/120960
[ ] www.omim.org/120940
[ ] www.omim.org/605102
[ ] www.omim.org/604973
[ ] www.omim.org/606860
[ ] www.omim.org/612924
[ ] www.omim.org/615561
[ ] www.omim.org/134350
[ ] www.omim.org/300383
[ ] www.omim.org/217030
[ ] www.omim.org/134370
[ ] www.omim.org/134371
[ ] www.omim.org/600889
[ ] www.omim.org/605336
[ ] www.omim.org/605337
[ ] www.omim.org/608593
[ ] www.omim.org/188040
[ ] www.omim.org/120920
[ ] www.omim.org/107271
[ ] www.omim.org/125240

table 9. Bone marrow failure

[ ] www.omim.org/617053
[ ] www.omim.org/611170
[ ] www.omim.org/127550
[ ] www.omim.org/187270
[ ] www.omim.org/604319
[ ] www.omim.org/616373
[ ] www.omim.org/268130
[ ] www.omim.org/616553
[ ] www.omim.org/224230
[ ] www.omim.org/613987
[ ] www.omim.org/613988
[ ] www.omim.org/613989
[ ] www.omim.org/615190
[ ] www.omim.org/616353
[ ] www.omim.org/616553
[ ] www.omim.org/602122
[ ] www.omim.org/618165
[ ] www.omim.org/613129
[ ] www.omim.org/617053

table 10.Phenocopies of inborn errors of immunity I'm not totally sure what this means, but there are not associated OMIM IDs, so I am skipping this.

nicolevasilevsky commented 2 years ago

I will convert this to a discussion because this is a big project.

monarch-initiative / mondo

[Revise subclass] Review classification of immune disorders #3958