Type 2 Diabetes - PRS Evaluation

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NOTE: 

The following files were updated on 4/9/2021 so that the output of the #feature table in the eMERGE_IV_OMOP_T2DM_PRS_algorithm script matches the data dictionary.

Files:

  • T2DM_DD_Feature_Count_OMOP_2021049.csv
  • eMERGE_IV_OMOP_T2DM_PRS_algorithm_20210409.txt
  • eMERGE_IV_OMOP_T2DM_PRS_algorithm_20210409.zip

 

 

Structured data: 
ICD10
ICD9
Data Source/clinical domain: 
medications
Files: 
T2DM Algorithm Implementation Document
T2DM Feature OMOP mapping
DMmeds BMJ Paper document
T2DM_DD_Feature_Count_OMOP_20210409.csv
eMERGE_IV_OMOP_T2DM_PRS_algorithm_20210409.zip
eMERGE_IV_OMOP_T2DM_PRS_algorithm_20210409.txt
Information
Phenotype ID: 
1546
Date Created: 
Wednesday, February 24, 2021
Status: 
Final
Do Not List on the Collaboration Phenotypes List
Contact information
Contact Author: 
Barbara Benoit
Authors: 
Elizabeth Karlson
Institution: 
Partners Healthcare
Network Associations: 
eMERGE
View Phenotyping Groups: 
eMERGE Phenotype WG
Owner Phenotyping Groups: 
eMERGE Harvard Group
Demographics
Age: 
Adult
 

Suggested Citation

Elizabeth Karlson. Partners Healthcare. Type 2 Diabetes - PRS Evaluation. PheKB; 2021 Available from: https://phekb.org/phenotype/1546

Comments

Submitted by Cong Liu on

Hi there,

If we can povide additional features (COD_MED_diabetes) + Common data variables asked by CC (in a certain format), do you have a script to generate the case/control you want? If yes, can you suggest what is the best way to collaborate and run the code. I will suggest you share the script which accept a standard input files (e.g. standard common data variable files collected by CC + COD_MED_diabetes) and output a PheKB compatible files.

Cong

1. What are the diagnosis codes that needs to be looked for? Also I want to confirm it’s 3 codes and not 3 visits. And 30 days or more between first and last date of any code and not same code
2. May I know what needs to be looked in clinical note (assume it’s progress note) ? Any particular term or something else. ?

The Data Floor flag is used to establish a minimal patient utilization.

It's 3 diagnosis codes from the entire ICD diagnosis catalog.  It is not specific to any disease or condition. Of patient's ICD diagnosis codes there needs to be at least 30 days between the first and last diagnosis code (there is no specific ICD diagnosis codes for this time constraint).

I do not know how notes are categorized at your site, the patient should have at least one note that is identified as a clinical note. The content of the note is not relevant.

Barbara

Is this what you're looking for in data floor? where note_ct is the count of patient clinical notes

case when (Meets_ICD9_10_Filter>0 AND note_ct >0) then 1
else 0
end Meets_DF