Human Inborn Errors of Immunity: 2022 Update. - Table 1

[sabrinatoro]

Part of https://github.com/monarch-initiative/mondo/issues/7362 Focussing on Table 1.

Spreadsheet to use is here: https://docs.google.com/spreadsheets/d/1PY5b4urSuz3tPvEjWflzV3R-up5OJTapzxB_rD3NwD8/edit#gid=0

Step 1 : Confirm high-level classification in Mondo Step 2: Classify diseases based on Table 1 from PMID:35748970

[sabrinatoro]

Step 1: High-level classification in Mondo

Classification in [PMID:35748970]

Classification in Mondo

Sabrina's questions (I have a path forward depending on the answers): 1) Mondo classification: where should "inborn error of immunity" be classified? Should it be under 'immunodeficiency disease' (OMIMPS:300755) instead of 'immune deficiency disease' (OMIM:242850)?

2) Please confirm that "combined immunodeficiency" is a "inborn error of immunity"

3) The following terms are not in the publication. Are these terms used in the literature/medical world?

• non-SCID combined immunodeficiency
• T+ B+ severe combined immunodeficiency

[sabrinatoro]

@pnrobinson and @ahamosh, Could you please answer the 3 questions above? Thank you!

[ahamosh]

242850 is an edge case garbage entry in OMIM. I will try to get Joanna to throw it out. The OMIMPS:300755 is the big PS for immunodeficiencies, but doesn't include the SCIDs, which are PS601457. Both phenotypic series are inborn errors of immunity. Non-SCID combined immunodeficiencies is what they are calling combined immunodeficiencies. I haven't seen that term in the literature lately T+B+ immunodeficiency is general not so severe as to be a SCID.

[pnrobinson]

There should be a top level term called inborn errors of immunity, but this is not a child of immunodeficiency, it is vice versa

Why are the separate terms immunodeficiency and immune deficiency? Please merge

[sabrinatoro]

Thank you for the quick answer, @ahamosh and @pnrobinson

Why are the separate terms immunodeficiency and immune deficiency?

This is related to this issue where we found conflicting information about these terms being actually the same concept.

I think I have enough information to move forward. Thank you!

[sabrinatoro]

Step 1 TO DO

To do:

• [ ] obsolete 'immune deficiency disease' MONDO:0009453 (OMIM:242850) based on “historical disease”
• [ ] ‘inborn error of immunity' (MONDO:0003778) should have “exclude subclass” - immunodeficiency disease (MONDO:0021094)
• [ ] ‘inborn error of immunity' (MONDO:0003778) should be child of 'immune system disorder' (MONDO:0005046)
• [ ] merge terms representing SCID grouping terms: MONDO:0031520 (OMIMPS:601457) and MONDO:0015974
• [ ] 'severe combined immunodeficiency' (MONDO:0015974) should be child of 'combined immunodeficiency' (MONDO:0015131) - note it should already be
• [ ] Obsolete ‘non-SCID combined immunodeficiency' (MONDO:0018814) based on it being a grouping term that is not used in the literature. (note that all children would become children of 'combined immunodeficiency' (MONDO:0015131)
• [ ] Obsolete ‘T+ B+ severe combined immunodeficiency’ (MONDO:0044201) based on it being a grouping term that is not used in the literature. (note that all children would become children of 'combined immunodeficiency' (MONDO:0015131)

[sabrinatoro]

Step 2: Classify diseases based on Table 1 from PMID:35748970

• [ ] All diseases in sub-table 1 (T-B+ Severe Combined Immune Deficiency (SCID)) should be children of 'T-B+ severe combined immunodeficiency' (MONDO:0044200)
• [ ] All diseases in sub-table 2 (T-B- SCID) should be children of 'T-B- severe combined immunodeficiency' (MONDO:0017855)
• [ ] All diseases in sub-table 3 (Combined Immunodeficiency (CID), Generally Less Profound than SCID) should be children of 'combined immunodeficiency' (MONDO:0015131)

Note:

• some of the OMIM numbers in the table are a mixed bag of phenotypes and genes
• If some Mondo diseases are currently under the 'severe combined immunodeficiency' (MONDO:0015974), but are not in subtable 1 or 2: the MONDO:0015974 parent should be removed, and these terms should probably be under 'combined immunodeficiency' (MONDO:0015131)***
  • if these are not mentioned at all in table 1, the terms should be investigated to determine whether these are ‘inborn error of immunity' (MONDO:0003778)