Anxiety algorithm

Phenotype ID: 
1105
Status: 
Do Not List on the Collaboration Phenotypes List
Type of Phenotype: 
Data Modalities and Methods Used: 
Authors: 
John Connolly,
Contact Author: 
Institution: 
 

Suggested Citation

John Connolly,. CHOP. Anxiety algorithm. PheKB; 2018 Available from: https://phekb.org/phenotype/1105

Comments

The codes supplied in tables 2b, 4b and 5c are SNOMED codes for procedures.  Do you have a mapping to CPT or ICD procedure codes for these SNOMED codes?

Barbara

Hi Barbara - thanks fot your comment. We are not aware of any mapping to CPT or ICD for these procedures.  We also anticipate that some sites may not have access to these results.  The algorithm is robust without them, but of course it is a plus if the data is available

Best,

John 

Hello John,

We don't have a way of accessing the outlined SNOMED procedures if there aren't any ICD/CPT procedure mapping in place. However, Table 2/Table 4 are involved in ascertainment of a case. If I'm understanding correctly, you're saying we should be fine even without using these procedure codes when applying the logic to ascertain a case. Could you verify this? Thanks.

 

Ozan

Submitted by Wei-Qi Wei on

when we were uploading the file, the system kept showing "The value '-1' for 'AGE_AT_AD' (1st row) should be an integer, but appears to have non-numeric characters." So we replaced the '-1' with '0'.

Hi John, Thanks for answering.  It's not 100% clear to us in the pseudocode which Tables/codes are for inclusion/exclusion criteria for cases &/or controls, vs. just data to capture.  In the pseudocode, are only the tables that explicity say "case" or "control", and "incl/inclusion" or "exclusion" are the tables to use for inclusion & exclusion, & then do the data dictionary files list all the tables from which you want covariates for those dictionaries?

Hi Jen,

The relevant files (ICD, Meds etc.) have columns labeled case_incl/case_cov/case_excl/cont_cov/cont_excl. A "Y" (yes) on relevant columns gives you the classfification for each of the variables in the row.

Thanks,

John

Submitted by Dustin Key on

Hi John,

Should we apply a trailing wildcard to all ICD10 and ICD9 codes listed, regardless of the underscore?  I think that the summary indicates this, but would like to verify with you.  Thanks!  Dustin

 

Submitted by Dustin Key on

Hi John,

The algorithm specifies we would like to capture behavioral health / clinical physchology visits associated with controls when there is exactly one of them.    When we find such a visit for a control, is there information from the visit that needs to be recorded onto the data dictionaries?

Thanks!

Dustin

Thanks for the question and sorry for the delayed response - we somehow missed this in the shuffle.

For controls with exactly one visit to behavioral health, please add this to to hx of diseases works. We can change the name of the column to be ICD_Code_or_Dept (we can parse out which entries are ICDs and which are department names further down the line).

Hello John,

How would you like us to handle combination therapies? If we determine that patient is on a combination therapy that includes a medication in one of the tables but that combination therapy hasn't been directly provided in the table itself, what should we do?

 

Best,

Ozan

Thanks for the question, Ozan - if a combination therpay has its own unique code, it would be great to get that unique code (understanding we likely have not directly provided for it in the DD). Otherwise, it is acceptable to report the component that does match a medication in one of the tables. 

Best,

John 

Hello,

I wanted to confirm that for the cases, we want the inclusion codes to come from only inpatient visits? The code can't be from an outpatient visit?

Thanks,

Anika

Hi Anika, 

Inclusion codes should come from BOTH inpatient and outpatient visits. (Note, restrictions are/were for in-PERSON versus in-patient visits)

Best,
John 

Hi,

Can you explain which meds you want in Anxiety meds.csv. Do you want the additional medications in table 5 and 8 or all the medication used to find the cases and controls. In the Anxiety hx of other diseases.csv you have a variable to see if it's a case or control, but you don't have that in the meds.csv which is why I wanted to double check on what you wanted to include. 

In the document you also ask to 'capture the department visit for any control that has exactly 1 visit to a Behavioral Health/Clinical Psychology department at any age'. Where would you like us to note this in the data dictionary?

Thanks,

Anika

Hi Anika,

For the meds.csv, please report all the medications used to find cases and controls as well as the covariates.

For anxiety history, there is no need to report case/control status. 

For controls with exactly one visit to behavioral health, please add this to to hx of diseases works. Thank you for catching this, and please note, we can change the name of the column to be ICD_Code_or_Dept (we can parse out which entries are ICDs and which are department names (further down the line).

Best regards,

John 

Thank you John. I also wanted to confirm then that the data dictionary called anxiety hx of other diseases is just of the extra covariates you want us to find. Not of the inclusion codes?

Thanks,
Anika

Submitted by Dustin Key on

Hi John,

I'd like to double check which Rx should we use to  populate the meds.csv file for controls.  I've included the table 8 covariate Rx.  However, I can't think of any other meds related to controls that should populate meds.csv.  For instance, by definition I believe there shouldn't be any Rx from Table 7.  Would any other Rx from any of the tables go into meds.csv for controls?    Thanks!  Dustin

Submitted by Dustin Key on

Hi John,

I noticed an error upon posting our demographic implemenation.  It seems to occur for the race field when there are multiple races reported.  In the event of multpile races reported we had created a comma delimited string of each instance.  Let us know if we need to change the convention used.  I didn't see any other errors.  Thanks!  Dustin

Hi John,

In anxiety_meds_mr.csv, there are rows that contain drug classes. Are these rows meant to aid in readability by grouping the meds (i.e. just a section header row), are do you specifically mean to include an entire drug class?

Thanks, Ken