missing and incorrect genes associated in fanconi disease group

[nicolevasilevsky]

From @dnahotline on January 13, 2017 19:18

Three newer fanconi complementation groups are missing from this page FANCU (XRCC2) FANCR (RAD51) FANCV (REV7)

Also three genes that were listed should not have been included FANCD2OS is not the right terminology MX1 and TNF are not fanconi genes

I'll follow up with pub med references for the new ones mucho help from @jmcmurry on this my first ticket!!!

Copied from original issue: monarch-initiative/monarch-disease-ontology-RETIRED#167

[nicolevasilevsky]

From @jmcmurry on January 15, 2017 2:23

There's also something odd about the gene to the number of gene-disease relations. Even after the associations above are fixed, there seems to be something wacky with the reasoning that the defacto parent disease doesn't have each of the child associations. Here are the results pivoted for clarity.

[nicolevasilevsky]

From @dnahotline on January 15, 2017 3:17

@jmcmurry i'm not used to looking at this. what do the 1's stand for in the columns and rows. BRCA2 has a 1 for BRCA2 but also for FANCA.

[nicolevasilevsky]

From @dnahotline on January 15, 2017 3:34

@jmcmurry also RAD51 FANCR is not on the list of FA genes and should be.

[nicolevasilevsky]

From @dnahotline on January 15, 2017 3:48

notes

• Mutation in RAD51C is associated with a Fanconi anemia-like syndrome (FANCO) (OMIM: 613390) **specific mutations in ERCC4 (XPF) are associated with xeroderma pigmentosum (OMIM: 278760) and XFE progeroid syndrome (OMIM: 610965) or FA (FANCQ) ***A dominant mutation in RAD51 (FANCR) is associated with a Fanconi anemia-like syndrome

[nicolevasilevsky]

From @mellybelly on January 15, 2017 16:15

Also had noticed we have one disease group "Fanconi's Anemia" https://monarchinitiative.org/disease/DOID:13636 that should have the label changed to Fanconi Anemia. Will make a ticket on the DO tracker for this one, but should make sure the capitalization/form is same for the whole collection.

[nicolevasilevsky]

From @cmungall on February 1, 2017 22:10

Was fixed https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/227

Unfortunately not yet in latest mondo

[nicolevasilevsky]

From @cmungall on February 1, 2017 22:17

Missing links to the grouping class: https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/250

[nicolevasilevsky]

From @mellybelly on September 16, 2017 17:42

what is the status of this? need to review all Fanconi subtypes and genes and phenotypes to ensure up to date. HIGH PRIORITY, Perhaps @nicolevasilevsky can work with @dnahotline.

[nicolevasilevsky]

@mellybelly let me know how I can help

[nicolevasilevsky]

From @mellybelly on October 31, 2017 19:32

we need a plan for how to address this asap. It involves fixes to Mondo and fixes to the annotations. Where should this be done? HPOA, as well as some boutique disease-gene/variant associations? Can we set up INCA for this or ???? @cmungall please advise. Also @pnrobinson

[nicolevasilevsky]

From @mellybelly on October 31, 2017 19:37

I think this will require some NER in combination with id mapping. Perhaps @TomConlin and @putmantime can assist?

[nicolevasilevsky]

From @pnrobinson on October 31, 2017 20:44

AS I recall, Fanconi was one of those diseases where people published the biochemistry in Nature Genetics but nobody published detailed phenotype analyses for the various subtypes.

Maureen, what is the best place to get annotation data for Fanconi?

-Peter

[nicolevasilevsky]

From @pnrobinson on October 31, 2017 21:17

Blanche alter and Arleen auerbach have the most phenotype data. There are paper in our shared doc paperpile. I can send later. Seems like someone who knows really knows data and ontology etc should go to the Fa patient meeting and catalog. I’ve gotten me and Melissa invited. Perhaps Peter You would like to attend?

[nicolevasilevsky]

@mellybelly @jmcmurry I moved this ticket over from the old MONDO repo - not sure if this is still an outstanding issue?

[nicolevasilevsky]

closing this, please reopen if needed