ICD9 versus ID10 in UK BRAP

Question

[zizigolu]

Hi

I am going to explore a cancer type in UK biobank research platform

When I use ICD9 I find 9 participants but when I use ICD10 as filter I find 4000 participants

I am sure which ICD I should trust

Any of you has exprience with UK RAP system?

[LauferVA]

The only way to answer this question is to know what the research question of interest is. Without that knowledge it is impossible to choose one or the other. Once you know that, you need to study what are the differences between ICD9 and ICD10 codes for the individuals that are the same and different, then try to figure out why the results are so discrepant.

We cannot help you with any of that without more information.

Answer 1

[Kevin Blighe]

Hello again Friend, how are you?

I am familiar with UKB RAP and have worked on the UKB data via many of the largest pharmaceutical companies in the World.

You should use ICD10, not ICD9.

Kind regards,

Kevin

[zizigolu]

Thanks

I have access to population level WGS vcf files (pVCF)

In pVCF we may have several participants like the image below

If I have a list of participants IDs for colon cancer, can I calculate variant allele frequency and count (AF, AC) using pVCF files or for a certain cancer type I must use individual-level WGS vcf files (gVCF) ?

Thanks for any intuition