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Type of Phenotype:
Thursday, October 31, 2013
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Lyam Vazquez. CHOP. Atopic Dermatitis Algorithm. PheKB; 2013 Available from: https://phekb.org/phenotype/184
Atopic dermatitis data dictionary
Wondering if you have a data dictionary developed for the atopic dermatitis phenotype yet? We would like to validate the algorithm and pull the covariate data. Thanks!
is secondary site validation complete, i.e. is this ready to go? thanks.
I think it is still in process - Marshfield only got it from us week 2 of December, so they'll likely need some more time. Will let you know as soon as we have any updates.
Last 5 years...
Do you want at least 2 visits in the last five years as in, within 5 years of pull date, or within the last five years of the last date in the record?
We would like at least 2 visits within the last 5 years of the last date in the record.
since Marshfield submitted an implemenation, does that mean this phenotype is ready to be implemented by other sites? thanks.
Yes, it's ready to go. Thanks
Yes, it's ready to go. Thanks!
Table 1 in Atopic Dermatitis Phenotype Algorithm.docx
For this list of Medications related to Atopic Dermatitis:
- for the subgroup of Antihistamines, are you looking for topical and oral preps (and no other route of administration), for all drugs listed here?
- for the subgroup of Phototherapy, looks like these should be procedures - do you have a list of CPT proc codes that you pulled for these?
- for the subgroup of Other, are you looking for topical and oral preps for all drugs listed here?
same question would apply to Medications for control exclusion:
- phototherapy cpt codes
- subgroup Other - topical and oral?
tab "Visit Type" in Atopic dermatitis data dictionary.xlsx
is this tab requesting data, or simply describing the types of visits to include in tab "Visits for Controls and Cases"
Table 1 and visit type
-Yes, for the subgroup of antihistamines would be oral and topical preps.
-The CPT codes for phototherapy are listed in the CPT codes tab in the data dictionary. (96912,96913,96910,96900)
-For the subgroup of other, it would be mainly oral except Doxepin that would be topical.
-The visit types tab is just describing the types of visits to include in the tab for visits for controls and cases.
tab "Hx of AD medications"
would you like the phototherapy CPT codes included in this table, perhaps inserting the CPT code into the Drugcode field (where otherwise the name of the prescribed drug is inserted)?
Hx of AD meds
Yes, that sounds good. Thanks!
the "labs" tab in the data dictionary
While pulling the CPT codes that identify allergy testing is straightforward, getting the results of these tests here at GHRI is not. This is an uncharted area of exploration, and may be possible, but not without considerable work. I see that the element Allergen is noted as required in the DD, whereas lgE and wheal_flare are not noted as required.
Will it be acceptable to give you just SUBJID, Age, and CPT for the labs tab?
Ok, if it's a considerable amount of work, you can send us whatever you can get. If later on in the analysis we find that it would be important to have more information we can go back and ask you...sounds good?
data dict demographics tab
data dictionary shows C46119=Male. other phenotypes have C46109=Male - assume you really want 46109?
data dict dem tab
Yes, I'm sorry, it's a typo. I'll change it now to C46109=Male. Thanks!!
an overall meds question
Related to the question Submitted by Jane Grafton on Fri, 2014-03-07 17:28:
For the topical vs. oral meds, is it safe to assume if we just use the names provided in the tables, that they will be the correct route, or, esp. for generic names, do we need to somehow tease out the route in our data to be sure they are topical (which we may not be able to do for all of our medication records, in which case if we can’t what should we do – assume oral if it does not specify route maybe)?
For generic names you will have to somehow make sure they are topical. For example, when we pulled the meds data, we had topical, optic solutions, inhaled etc and we eliminated all the routes we didn't want.
In the table of therapy tab in the data dictionary, there is a complete list of the meds we used after eliminating the unwanted routes. Maybe you'll find that helpful. If you need any help with a list of medications that you pull from your database, I'll be glad to help.
Low number of cases by ICD9 screen
At Mount Sinai we found only 16 cases by ICD9 screen. We question the utility of proceeding to run the full algorithm with such a small yield?
Low number of cases by ICD9 screen
Lyam and I just discussed. We'd obviously be happy to take your 16, but if you are pressed for time with the other algorithms etc., we understand if you'd prefer to sit this one out.
I think the other sites will each have at least >50, with several >400.
Thanks for following-up,
Atopic dermatitis case control set from Harvard site
We have implemented the algorithm to define atopic dermatitis at the Harvard Site. We have found 72 cases and 1037 controls. Vivian Gainer will be in touch regarding getting the dataset to you for the following variables: case control status, sex, race, ethinicity, year of birth (4 digit). Beth
Atopic dermatitis cases and controls
We have implemented the atopic dermatitis algorithm to define 72 cases and 1037 controls at the Harvard site. Can you tell us which covariates you would like included in the file? Thanks, Beth