UK biobank HLA imputation data

Question

[aleph9999]

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.

[O.rka]

The link doesn't work to the data file.

Answer 1

[matemanc]

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?

Answer 2

[mbrauer]

Not sure where he got this, but a colleague sent it along:

A_101    A_102    A_103    A_201    A_202    A_203    A_205    A_206    A_207    A_210    A_211    A_214    A_216    A_220    A_264    A_301    A_302    A_1101    A_1102    A_1103    A_2301    A_2402    A_2403    A_2404    A_2407    A_2410    A_2501    A_2601    A_2603    A_2608    A_2901A_2902    A_3001    A_3002    A_3004    A_3101    A_3103    A_3104    A_3201    A_3301    A_3303    A_3401    A_3402    A_3601    A_4027    A_4386    A_6601    A_6602    A_6801    A_6802    A_6817    A_6901    A_7401    A_7403    A_8001    B_702    B_705    B_801    B_1301    B_1302    B_1401    B_1402B_1501    B_1502    B_1503    B_1504    B_1505    B_1506    B_1507    B_1508    B_1509    B_1510    B_1511    B_1512    B_1513    B_1515    B_1516    B_1517    B_1518    B_1520    B_1521    B_1524    B_1525    B_1526    B_1527    B_1529    B_1530    B_1531    B_1537    B_1801    B_1802    B_1803    B_1804B_2702    B_2703    B_2704    B_2705    B_2706    B_2707    B_3501    B_3502    B_3503    B_3504    B_3505    B_3508    B_3509    B_3510    B_3512    B_3517    B_3519    B_3520    B_3521    B_3522    B_3541    B_3543    B_3701    B_3801    B_3802    B_3901    B_3902    B_3903    B_3905    B_3906    B_3908B_3909    B_3910    B_3911    B_3915    B_3924    B_4001    B_4002    B_4004    B_4006    B_4009    B_4010    B_4012    B_4101    B_4102    B_4104    B_4201    B_4402    B_4403    B_4404    B_4405    B_4407    B_4501    B_4601    B_4701    B_4801    B_4802    B_4803    B_4901    B_5001    B_5002    B_5101B_5102    B_5105    B_5106    B_5107    B_5108    B_5123    B_5201    B_5301    B_5401    B_5501    B_5502    B_5601    B_5603    B_5604    B_5701    B_5702    B_5703    B_5801    B_5802    B_5901    B_6701    B_7020    B_7301    B_7801    B_8101    B_8201    B_8202    C_102    C_202    C_210    C_302    C_303    C_304    C_305    C_306    C_401    C_403    C_407    C_501    C_602    C_701    C_702    C_704    C_726    C_801    C_802    C_804    C_1202    C_1203    C_1402    C_1403    C_1502    C_1504    C_1505    C_1601    C_1602    C_1604    C_1701    C_1801    DRB5_101    DRB5_102    DRB5_202    DRB5_9901    DRB4_101    DRB4_103    DRB4_9901    DRB3_101    DRB3_202    DRB3_210    DRB3_224    DRB3_301    DRB3_9901    DRB1_101    DRB1_102    DRB1_103    DRB1_301    DRB1_302    DRB1_401    DRB1_402    DRB1_403    DRB1_404    DRB1_405    DRB1_406    DRB1_407    DRB1_408    DRB1_410    DRB1_411    DRB1_701    DRB1_801    DRB1_802    DRB1_803    DRB1_804    DRB1_806    DRB1_807    DRB1_810    DRB1_811    DRB1_901    DRB1_1001    DRB1_1101    DRB1_1102    DRB1_1103    DRB1_1104    DRB1_1106    DRB1_1111    DRB1_1143    DRB1_1201    DRB1_1202    DRB1_1301    DRB1_1302    DRB1_1303    DRB1_1304    DRB1_1305    DRB1_1312    DRB1_1315    DRB1_1321    DRB1_1401    DRB1_1402    DRB1_1403    DRB1_1404    DRB1_1405    DRB1_1406    DRB1_1407    DRB1_1409    DRB1_1410    DRB1_1415    DRB1_1444    DRB1_1501    DRB1_1502    DRB1_1503    DRB1_1601    DRB1_1602    DQB1_201    DQB1_202    DQB1_301    DQB1_302    DQB1_303    DQB1_304    DQB1_401    DQB1_402    DQB1_501    DQB1_502    DQB1_503    DQB1_504    DQB1_601    DQB1_602    DQB1_603    DQB1_604    DQB1_605    DQB1_609    DQA1_101    DQA1_102    DQA1_103    DQA1_104    DQA1_201    DQA1_301    DQA1_302    DQA1_303    DQA1_401    DQA1_501    DQA1_503    DQA1_505    DQA1_509    DQA1_601    DPB1_101    DPB1_201    DPB1_202    DPB1_301    DPB1_401    DPB1_402    DPB1_501    DPB1_502    DPB1_601    DPB1_901    DPB1_902    DPB1_1001    DPB1_1101    DPB1_1301    DPB1_1401    DPB1_1501    DPB1_1601    DPB1_1701    DPB1_1801    DPB1_1901    DPB1_2001    DPB1_2101    DPB1_2201    DPB1_2301    DPB1_2601    DPB1_2801    DPB1_3001    DPB1_3101    DPB1_3301    DPB1_3401    DPB1_3501    DPB1_4001    DPB1_4501    DPB1_4801    DPB1_8101    DPB1_8501    DPA1_103    DPA1_104    DPA1_105    DPA1_107    DPA1_201    DPA1_202    DPA1_301    DPA1_401

[GenoMax]

Can you provide context about what this is and how it relates to the original question?

Answer 3

[ochaz]

Headers can now be found here: http://biobank.ctsu.ox.ac.uk/crystal/crystal/auxdata/ukb_hla_v2.txt or http://biobank.ctsu.ox.ac.uk/crystal/refer.cgi?id=2182