Missing values in APOE

Diane Zheng

Hi, I’m new to working with genetic data and recently derived APOE status using instructions from a UK Biobank community post. In my PLINK output, I noticed a considerable amount of missing data: about 15% missing for rs429358_C and 10% missing for rs7412_T. I’d like to confirm whether this level of missingness is typical for the genotyped UKB data or if it suggests I may have made an error in the process.

I then used these SNPs to derive APOE genotype status, and below is the distribution.  Does this distribution look reasonable compared to what others have seen in UKB? Any feedback would be much appreciated!

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    Dr. Mc. Ninja

    When I was looking at missing calls vs. position, I saw a distinct trend, e.g. some regions were over-represented for missing values. However, this was actually the WES data, not the Chip data…

    I'd have guessed the rates would be available in the publication?

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