Availability of APOE genotypes

Michael Lutz

Are APOE genotypes available from cohort browser, or must these be determined from downloading the SNP data (imputed or genotype calls) from the bulk folder?

Comments

8 comments

  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Michael,

    the cohort browser is based on the Whole Exome Sequence (WES) data. It does include the APOE SNPs. Please note that the WES data uses GRCh38 reference genome, whereas the genotype calls use GRCh37.  If you use the rsIDs, they will be independent of reference genome.

    To use the genotype calls, see this forum post 

    If you choose to use the cohort browser, I think you will need to save several different cohorts (homozygous for variant in rs 7412 / heterozygous for variant in rs 7412 / homozygous for variant in rs 429358 / heterozygous for variant in rs 429358) and then manipulate the data in a JupyterLab instance to identify which participants have which APOE isoform.

    Thank you for using the forum.

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  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hello again,

    The WES data is only available for 469574 participants, whereas the genotype calls cover 487921 participants.

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  • Comment author
    Qidong Liu

    Rachael W Hi Racheal, I want to know if I use the cohort browser to save cohorts of participants who are homozygous for the variant in rs7412 and heterozygous for the variant in rs7412, how can I confirm whether the rest of the participants are homozygous-reference for rs7412 or if they lack WES information?

    Thanks!

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  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Qidong,

    For one way to do this, please see Showcase Category 100314 , sub-Category 170  , tab “8 data fields”, for Field 32050 Release tranche .   Participants with no value (NULL)  in this field have no WES information.

    Thank you for using the forum.

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  • Comment author
    Guang Ji

    Hi Rachael,

    I am unable to locate the rs641738 variant in genotype calls, which has been commonly used in many published studies about uk biobank.

    Where could I obtain data for this specific variant?

    Thank you for your time and help.

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  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Guang Ji,

    rs641738 is not included in the genotype calls.  There is a browser for genotype calls in UKB Showcase, see https://biobank.ndph.ox.ac.uk/showcase/gsearch.cgi , which says “no loci match search criteria” ,

    UKB holds genotype calls, three versions of imputed genotypes, whole exome sequencing (WES) and whole genome sequencing (WGS) data.  The published studies should specify which kind of genetic data they used.  For more information on the genomic data, see Category 100314 , and the sub-categories in the “8 sub-categories” tab.

     

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  • Comment author
    Guang Ji

    Hi Rachael,

    Thank you for your help. We would like to know if the imputed genotypes, WES, and WGS data are fully included in https://biobank.ndph.ox.ac.uk/showcase/gsearch.cgi. Specifically, if rs641738 is not available here, is it still possible to obtain it elsewhere, such as in WES or WGS data?

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  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Guang Ji,

    the Showcase genomic search does not include the WES or WGS data.   I think it does not include the imputed genotypes either (but I am not entirely sure about that).

    To find out whether a SNP is covered by the WES data, please see the UKB-RAP Cohort Browser genomic search.  rs641738 is there.

    To find out whether rs641738 is covered by the WGS data, please see the publicly-available allele frequency browser https://afb.ukbiobank.ac.uk/ .  The SNP rs641738 is at chr19:54173068, see https://www.ncbi.nlm.nih.gov/snp/rs641738 , which gives https://afb.ukbiobank.ac.uk/region/chr19-54173068-54173068  .  The allele frequency browser contains summary data only, and cannot be used to find participants with the variant.

     

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