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Question: UK biobank HLA imputation data
1
gravatar for aleph9999
9 months ago by
aleph9999 • 10
aleph9999 • 10 wrote:

I'm interested in HLA imputation results from UK biobank (which was created by HLA*IMP 2 algorithm) and I have registered to have the access of HLA imputation values (field 22182 https://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=22182). However, these values are not annotated and I am unable to interpret results despite a bunch of values just like example data (https://biobank.ctsu.ox.ac.uk/crystal/examples/eg_hla_impute.dat).

Have anyone analyzed HLA imputation values from UK biobank before? How do you interpret the results (and if possible, how to compare HLA allele frequency in interested phenotype, is chi-square with FDR adjustment enough). Any suggestion is appreciated.
imputation uk biobank hla • 528 views
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modified 7 months ago by matemanc • 0 • written 9 months ago by aleph9999 • 10
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gravatar for matemanc
7 months ago by
matemanc • 0
matemanc • 0 wrote:

I have the same issue.

Field 22181 contains Q2 values of HLA:IMP*02 output. 362 values for each individual (separated by commas) is available and each value represents the probability of a given allele. However, there is no information in the downloaded data, which of the 362 values refer to which allele.

I have already written to UK Biobank, the programmer of HLA:IMP*02 and the authors, who contributed to HLA genotyping, but have received no answer yet. Have you had any handy solution in the previous two months?
ADD COMMENT • link written 7 months ago by matemanc • 0
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