[GET-dev] RE: GET-Evidence: adding "age of onset" to clinical importance

Chung, Wendy wkc15 at mail.cumc.columbia.edu
Thu Dec 8 20:46:05 EST 2011

>From the practical point of view, a breakpoint should be at age 18 since guidelines for testing/reporting results if different for minors.  At the high end I would change

5 stars to age <1
4 stars ages 1-18

Rest is fine.


From: Madeleine Ball [mailto:mpball at gmail.com]
Sent: Thursday, December 08, 2011 7:39 PM
To: Joseph Thakuria; Tom Clegg
Cc: Chung, Wendy; get-editors at lists.freelogy.org; get-dev
Subject: GET-Evidence: adding "age of onset" to clinical importance

At this point I'm not sure who to include in an email regarding potential GET-Evidence improvements. I'm emailing this to Joe & Tom who have been core people in designing the system (medical & software respectively). I'm also cc'ing Wendy, who made the suggestion prompting this email, and I'm sending this to the get-editors and get-dev mailing lists.

In her comments on the draft of a paper we're hoping to submit soon, Wendy noted "I would add age of onset to the clinical importance" on a GET-Evidence diagram. I've been thinking about adding this too, hearing it come from another source convinces me we should think about doing it now (rather than after the paper's published!).

So... it requires some sort of definition. I'm going to throw one out there, anyone interested is invited to respond if they have some comments & ideas.

Age of onset: score according to the median age of onset for the disease as it manifests for individuals affected by this variant.
-- 0 stars: > 70 years of age
-- 1 star: 50-70 years of age
-- 2 stars: 30-50 years of age
-- 3 stars: 15-30 years of age
-- 4 stars: 5-15 years of age
-- 5 stars: Congenital or < 5 years of age

This is just a suggested set of ranges, comments are welcome. I have no idea what the distributions there are for age of onsets, or if median (rather than average) is a readily available number. (I just like medians better.) Also, I guess the fact it scores higher for less age could be confusing, but I think it's consistent with how other categories score more highly when "worse/more severe/strong effect".

Someday, in the mythic future, we would like to split of the annotation efforts into disease level pages (a variant implicated in the disease would default to the values of the disease page for the clinical importance section, but could be modified if that variant had a notably different ranking in some category e.g. unusually early onset, more resistant to standard treatment, etc). But for now, I think having this scoring on the variant page is better than nothing?


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