Accessing Disease Phenotype Data (e.g., CAD, CVD, T2D) on UKB RAP for GWAS
Hello,
I am working on a GWAS project and would like to use disease phenotypes such as Coronary Artery Disease (CAD), Cardiovascular Disease (CVD), and Type 2 Diabetes (T2D) from the UK Biobank dataset. I tried searching and visualizing using the cohort browser but failed.
How can I locate and access disease phenotype data on the UK Biobank Research Analysis Platform (RAP)?
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3 comments
Hello Saurabh. To do this, you can go into the cohort browser, then click on Data Preview, then click on Add Column. Then search the diagnoses you want in the Search Bar or just search for ICD 10 or ICD 9 depending.
The phenotypes you're looking for will likely be here: Health-related outcomes>Summary Diagnoses>Diagnoses - ICD 10 (you may be looking for more specific diagnoses, which are also available as you'll be able to see). Once, you find Diagnoses - ICD 10, you can click on it and then click Add to Data Preview. This will add a 2nd column to the data table (the first being the Participant ID) which will list all the ICD 10 diagnoses of each individual.
After this, you can click on Dashboard Actions in the top right, then click on Save Dashboard View and save this to your project. From there, you can use the Table Exporter app to create a TSV or CSV from your saved Dashboard view. And then you can use R or some other code/software to filter for individuals with your phenotypes of interest.
Hope this helps.
Thanks for your support!
Hi Saurabh,
To provide some extra information, the path already mentioned to “Diagnoses - ICD 10” on the UK Biobank Researcher Analysis Platform (UKB-RAP) will provide diagnosis data from hospital inpatient records. Depending on the conditions of interest, you may also wish to consider data from other sources, such as primary care and self-report, which may include further cases not resulting in hospitalisation. The fields in Category 1712 contain data showing the 'first occurrence' of any code mapped to 3-character ICD-10, drawn from primary care (for 45% of the cohort), hospital inpatient records, death registry records, and self-reported medical conditions. On the UKB-RAP this would be found at "Health-related outcomes > First occurrences," with more specific subcategories from there.
If you are interested in particular data fields or categories, it's worth having a look at the related resources, which are attached to the field or category on Showcase on a “Resources” tab. For more information about the first occurrence data, you can review Showcase Resource 593. For an overview of health outcomes data more generally, including available data sources and caveats, you may wish to review Resource 596.
I hope this helps,
Laura
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