Updates to fix QC errors for multiple gene associations

[twhetzel]

Updates to fix or add qc exclusions for new qc check failures for #8316

FAIL Rule ../sparql/qc/mondo/qc-multiple-gene-associations.sparql: 4 violation(s)
entity,label,geneIdentifiers

• http://purl.obolibrary.org/obo/MONDO_0011974,retinitis pigmentosa 7,"http://identifiers.org/hgnc/10254, http://identifiers.org/hgnc/9942" --> exclude from QC check, see Multiple gene associations represented as EquivalentTo #8276
• http://purl.obolibrary.org/obo/MONDO_0100188,combined ApoA-I and ApoC-III deficiency,"http://identifiers.org/hgnc/600, http://identifiers.org/hgnc/610" --> see comment in post below
• http://purl.obolibrary.org/obo/MONDO_0100050,"Usher syndrome, type 1D/F","http://identifiers.org/hgnc/13733, http://identifiers.org/hgnc/14674" --> exclude from QC check, see Multiple gene associations represented as EquivalentTo #8276
• http://purl.obolibrary.org/obo/MONDO_0011908,juvenile myelomonocytic leukemia,"http://identifiers.org/hgnc/1541, http://identifiers.org/hgnc/9644, http://identifiers.org/hgnc/7765, http://identifiers.org/hgnc/17073" --> see comment in post below

[twhetzel]

• MONDO:0100188 'combined ApoA-I and ApoC-III deficiency' - based on the xref for the definition (PMID: 3118360) this term seems more related to OMIM:620058, which does have a single disease defining gene so I removed the two gene associations. In addition, if we agree that MONDO_0100188 is the same as OMIM:620058 then there is already another MONDO term for this, ie MONDO:0859290. @sabrinatoro or @katiermullen do you agree MONDO:0100188 is the same as MONDO:085929?
• MONDO:0011908 'juvenile myelomonocytic leukemia' - reading the OMIM record for OMIM:607785 it appears that mutations in a variety of genes have been found, however not all mutations are found in all patients therefore I suggest the gene association information for this Mondo term be removed.

[katiermullen]

@twhetzel Thanks for all of your work on this!

It seems based on this publication that these (MONDO:0100188 and MONDO:0859290) are different diseases:

"There are a number of forms of familial apolipoprotein A-I deficiency: those characterized by a lack of plasma apoA-I, apoC-III, and apoA-IV, those characterized by a lack of apoA-I and apoC-III, and those characterized by a lack of apoA-I only. These states are briefly reviewed below."

I hope this helps. Let me know if you need more info!

[sabrinatoro]

I agree with Katie, MONDO:0100188 and MONDO:0859290 are not the same.
A quick review show that MONDO:0100188 is caused by variation in both APOA1 amd APOC3 (at the same time). While MONDO:0859290 is caused by a deletion of the entire APOA1/C3/A4 gene complex.

[twhetzel]

Thanks for reviewing @katiermullen! Based on the reference you linked they do seem different if using labels of the terms for comparison. Do you think the PMID and OMIM references on MONDO:0100188 'combined ApoA-I and ApoC-III deficiency' are correct:

• PMID:3118360, "DNA inversion within the apolipoproteins AI/CIII/AIV-encoding gene cluster of certain patients with premature atherosclerosis"
• OMIM:618463 HYPOALPHALIPOPROTEINEMIA, PRIMARY, 2

[twhetzel]

To summarize the chat, the actions for MONDO:0100188 are to remove the synonym, change the PMID to PMID:20616715 that Katie kindly provided to use as a source for the definition and also use this PMID as the source for the gene association statements for APOA1 and APOC3.

[twhetzel]

To follow-up, the updates were done for MONDO:0100188 and the PR updated.