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Omixon test HLA calls (http://www.omixon.com/hla-typing-example-data/) with hg38 and bwakit
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| sample | locus | mismatches | options | alleles | p-groups | expected | validates | |
|---|---|---|---|---|---|---|---|---|
| NA12878 | A | 1 | 5421 | HLA-A*01:01:01:01;HLA-A*11:01:01 | HLA-A*01:01P;HLA-A*11:01 | HLA-A*01:01;HLA-A*11:01 | yes | |
| NA12878 | B | 2 | 154 | HLA-B*08:01:01;HLA-B*56:01:01 | HLA-B*08:01P;HLA-B*56:01 | HLA-B*08:01;HLA-B*56:01 | yes | |
| NA12878 | C | 1 | 397 | HLA-C*01:02:01;HLA-C*07:01:01:01 | HLA-C*01:02P;HLA-C*07:01P | HLA-C*01:02;HLA-C*07:01 | yes | |
| NA12878 | DQA1 | 0 | 3 | HLA-DQA1*01:01:01;HLA-DQA1*05:01:01:01 | HLA-DQA1*01:01;HLA-DQA1*05:01P | |||
| NA12878 | DQB1 | 0 | 127 | HLA-DQB1*02:01:01;HLA-DQB1*05:01:01:01 | HLA-DQB1*02:01P;HLA-DQB1*05:01P | |||
| NA12878 | DRB1 | 0 | 3 | HLA-DRB1*01:01:01;HLA-DRB1*03:01:01:01 | HLA-DRB1*01:01P;HLA-DRB1*03:01P | |||
| NA12891 | A | 1 | 42 | HLA-A*01:01:01:01;HLA-A*24:243 | HLA-A*01:01P;HLA-A*24:243 | HLA-A*01:01;HLA-A*24:02 | no | |
| NA12891 | B | 0 | 12 | HLA-B*07:02:35;HLA-B*08:01:01 | HLA-B*07:02;HLA-B*08:01P | HLA-B*07:02;HLA-B*08:01 | yes | |
| NA12891 | C | 0 | 5936 | HLA-C*07:01:09;HLA-C*07:02:01:01 | HLA-C*07:01;HLA-C*07:02P | HLA-C*07:01;HLA-C*07:02 | yes | |
| NA12891 | DQA1 | 0 | 2 | HLA-DQA1*01:02:01:01;HLA-DQA1*05:01:01:01 | HLA-DQA1*01:02P;HLA-DQA1*05:01P | |||
| NA12891 | DQB1 | 0 | 146 | HLA-DQB1*02:01:01;HLA-DQB1*06:02:01 | HLA-DQB1*02:01P;HLA-DQB1*06:02P | |||
| NA12891 | DRB1 | 1 | 35 | HLA-DRB1*03:01:01:01;HLA-DRB1*15:01:02 | HLA-DRB1*03:01P;HLA-DRB1*15:01 | |||
| NA18526 | A | 9 | 1 | HLA-A*24:120;HLA-A*24:120 | HLA-A*24:120;HLA-A*24:120 | HLA-A*24:02;HLA-A*33:03 | no | |
| NA18526 | B | 0 | 107 | HLA-B*35:63;HLA-B*40:01:35 | HLA-B*35:63;HLA-B*40:01 | HLA-B*40:01;HLA-B*58:01;HLA-B*58:02 | no | |
| NA18526 | C | 4 | 70 | HLA-C*03:162;HLA-C*07:49 | HLA-C*03:162;HLA-C*07:49 | HLA-C*03:02 HLA-C*07:02 | no | |
| NA18526 | DQA1 | 0 | 4 | HLA-DQA1*05:01:01:01;HLA-DQA1*06:02 | HLA-DQA1*05:01P;HLA-DQA1*06:02 | |||
| NA18526 | DQB1 | 0 | 21 | HLA-DQB1*02:01:01;HLA-DQB1*02:01:01 | HLA-DQB1*02:01P;HLA-DQB1*02:01P | |||
| NA18526 | DRB1 | 0 | 11 | HLA-DRB1*03:01:01:01;HLA-DRB1*12:09 | HLA-DRB1*03:01P;HLA-DRB1*12:09 | |||
| NA18912 | A | 4 | 3 | HLA-A*34:02:01;HLA-A*74:01 | HLA-A*34:02P;HLA-A*74:01 | HLA-A*34:02;HLA-A*74:01 | yes | |
| NA18912 | B | 0 | 2 | HLA-B*53:01:01;HLA-B*53:01:01 | HLA-B*53:01P;HLA-B*53:01P | HLA-B*53:01;HLA-B*53:01 | yes | |
| NA18912 | C | 0 | 8 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*04:01;HLA-C*04:01 | yes | |
| NA18912 | DQA1 | 0 | 3 | HLA-DQA1*01:02:01:01;HLA-DQA1*02:01 | HLA-DQA1*01:02P;HLA-DQA1*02:01 | |||
| NA18912 | DQB1 | 0 | 153 | HLA-DQB1*02:01:02;HLA-DQB1*06:02:01 | HLA-DQB1*02:01;HLA-DQB1*06:02P | |||
| NA18912 | DRB1 | 0 | 5851 | HLA-DRB1*11:01:02;HLA-DRB1*11:01:02 | HLA-DRB1*11:01P;HLA-DRB1*11:01P | |||
| NA18964 | A | 0 | 39 | HLA-A*26:01:01;HLA-A*26:06 | HLA-A*26:01;HLA-A*26:06 | HLA-A*26:01;HLA-A*26:03 | no | |
| NA18964 | B | 1 | 6 | HLA-B*35:101:02;HLA-B*40:02:01 | HLA-B*35:101;HLA-B*40:02P | HLA-B*35:01;HLA-B*40:02 | no | |
| NA18964 | C | 0 | 1797 | HLA-C*01:02:01;HLA-C*03:03:01 | HLA-C*01:02P;HLA-C*03:03P | HLA-C*03:03;HLA-C*03:04 | no | |
| NA18964 | DQA1 | 0 | 3 | HLA-DQA1*01:02:01:01;HLA-DQA1*03:03:01 | HLA-DQA1*01:02P;HLA-DQA1*03:01P | |||
| NA18964 | DQB1 | 0 | 36 | HLA-DQB1*04:01:01;HLA-DQB1*06:02:01 | HLA-DQB1*04:01;HLA-DQB1*06:02P | |||
| NA18964 | DRB1 | 2 | 2 | HLA-DRB1*04:05:01;HLA-DRB1*15:01:01:01 | HLA-DRB1*04:05;HLA-DRB1*15:01P | |||
| NA19000 | A | 0 | 27 | HLA-A*24:02:01:01;HLA-A*24:02:01:01 | HLA-A*24:02P;HLA-A*24:02P | HLA-A*24:02;HLA-A*24:02 | yes | |
| NA19000 | B | 7 | 1 | HLA-B*14:08:02;HLA-B*55:02:07 | HLA-B*14:08;HLA-B*55:02 | HLA-B*54:01;HLA-B*67:01 | no | |
| NA19000 | C | 1 | 1 | HLA-C*01:05;HLA-C*01:23 | HLA-C*01:05;HLA-C*01:23 | HLA-C*01:02;HLA-C*07:02 | no | |
| NA19000 | DQA1 | 0 | 3 | HLA-DQA1*01:01:01;HLA-DQA1*03:03:01 | HLA-DQA1*01:01;HLA-DQA1*03:01P | |||
| NA19000 | DQB1 | 0 | 5 | HLA-DQB1*04:01:01;HLA-DQB1*05:01:01:01 | HLA-DQB1*04:01;HLA-DQB1*05:01P | |||
| NA19000 | DRB1 | 7 | 24 | HLA-DRB1*01:01:05;HLA-DRB1*04:05:01 | HLA-DRB1*01:01;HLA-DRB1*04:05 | |||
| NA19130 | A | 3 | 24 | HLA-A*33:31;HLA-A*36:01 | HLA-A*33:31;HLA-A*36:01 | HLA-A*33:03;HLA-A*36:01 | no | |
| NA19130 | B | 6 | 358 | HLA-B*13:01:01;HLA-B*35:01:01:01 | HLA-B*13:01P;HLA-B*35:01P | HLA-B*13:02;HLA-B*35:01 | no | |
| NA19130 | C | 0 | 8 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*04:01;HLA-C*04:01 | yes | |
| NA19130 | DQA1 | 0 | 6 | HLA-DQA1*04:01:01;HLA-DQA1*05:05:01:01 | HLA-DQA1*04:01;HLA-DQA1*05:01P | |||
| NA19130 | DQB1 | 0 | 53 | HLA-DQB1*03:01:14;HLA-DQB1*04:02:01 | HLA-DQB1*03:01;HLA-DQB1*04:02 | |||
| NA19130 | DRB1 | 0 | 15 | HLA-DRB1*08:04:01;HLA-DRB1*13:03:01 | HLA-DRB1*08:04;HLA-DRB1*13:03 | |||
| NA19172 | A | 1 | 2 | HLA-A*30:12;HLA-A*68:01:14 | HLA-A*30:12;HLA-A*68:01 | HLA-A*30:02;HLA-A*68:01 | no | |
| NA19172 | B | 1 | 74 | HLA-B*35:01:01:01;HLA-B*44:76 | HLA-B*35:01P;HLA-B*44:76 | HLA-B*35:01;HLA-B*44:03 | no | |
| NA19172 | C | 0 | 8 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*04:01;HLA-C*04:01 | yes | |
| NA19172 | DQA1 | 0 | 2 | HLA-DQA1*02:01;HLA-DQA1*03:02 | HLA-DQA1*02:01;HLA-DQA1*03:01P | |||
| NA19172 | DQB1 | 0 | 4 | HLA-DQB1*02:02:01;HLA-DQB1*02:02:01 | HLA-DQB1*02:02;HLA-DQB1*02:02 | |||
| NA19172 | DRB1 | 3 | 1 | HLA-DRB1*07:01:07;HLA-DRB1*15:03:01:01 | HLA-DRB1*07:01;HLA-DRB1*15:03P | |||
| sample_1 | A | 255 | 2493220 | HLA-A*01:01:01:01;HLA-A*01:01:01:01 | HLA-A*01:01P;HLA-A*01:01P | HLA-A*02:01;HLA-A*26:01 | no | |
| sample_1 | B | 255 | 4262194 | HLA-B*08:01:01;HLA-B*08:01:01 | HLA-B*08:01P;HLA-B*08:01P | HLA-B*38:01:01;HLA-B*41:01 | no | |
| sample_1 | C | 255 | 1667218 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*12:03;HLA-C*17:01 | no | |
| sample_1 | DRB1 | 255 | 742387 | HLA-DRB1*01:01:01;HLA-DRB1*01:01:01 | HLA-DRB1*01:01P;HLA-DRB1*01:01P | HLA-DRB1*03:01;HLA-DRB1*14:54 | no | |
| sample_2 | A | 255 | 2493220 | HLA-A*01:01:01:01;HLA-A*01:01:01:01 | HLA-A*01:01P;HLA-A*01:01P | HLA-A*03:01:01;HLA-A*26:01:01 | no | |
| sample_2 | B | 255 | 4262194 | HLA-B*08:01:01;HLA-B*08:01:01 | HLA-B*08:01P;HLA-B*08:01P | HLA-B*07:02;HLA-B*38:01 | no | |
| sample_2 | C | 255 | 1667218 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*07:02;HLA-C*12:03 | no | |
| sample_2 | DRB1 | 255 | 742387 | HLA-DRB1*01:01:01;HLA-DRB1*01:01:01 | HLA-DRB1*01:01P;HLA-DRB1*01:01P | HLA-DRB1*11:04:01;HLA-DRB1*15:01 | no | |
| sample_3 | A | 255 | 2493220 | HLA-A*01:01:01:01;HLA-A*01:01:01:01 | HLA-A*01:01P;HLA-A*01:01P | HLA-A*01:01;HLA-A*68:01 | yes | |
| sample_3 | B | 255 | 4262194 | HLA-B*08:01:01;HLA-B*08:01:01 | HLA-B*08:01P;HLA-B*08:01P | HLA-B*08:01:01;HLA-B*44:03 | yes | |
| sample_3 | C | 255 | 1667218 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*04:01;HLA-C*07:01 | yes | |
| sample_3 | DRB1 | 255 | 742387 | HLA-DRB1*01:01:01;HLA-DRB1*01:01:01 | HLA-DRB1*01:01P;HLA-DRB1*01:01P | HLA-DRB1*03:01;HLA-DRB1*07:01 | no | |
| sample_4 | A | 255 | 2493220 | HLA-A*02:01:01:01;HLA-A*02:01:01:01 | HLA-A*02:01P;HLA-A*02:01P | HLA-A*02:01;HLA-A*32:01:01 | yes | |
| sample_4 | B | 255 | 4262194 | HLA-B*08:01:01;HLA-B*08:01:01 | HLA-B*08:01P;HLA-B*08:01P | HLA-B*40:01;HLA-B*51:01 | no | |
| sample_4 | C | 255 | 1667218 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*03:04:01;HLA-C*14:02:01 | no | |
| sample_4 | DRB1 | 255 | 742387 | HLA-DRB1*01:01:01;HLA-DRB1*01:01:01 | HLA-DRB1*01:01P;HLA-DRB1*01:01P | HLA-DRB1*07:01:01;HLA-DRB1*11:01 | no | |
| sample_5 | A | 255 | 2493220 | HLA-A*01:01:01:01;HLA-A*01:01:01:01 | HLA-A*01:01P;HLA-A*01:01P | HLA-A*01:01;HLA-A*02:01 | yes | |
| sample_5 | B | 255 | 4262194 | HLA-B*08:01:01;HLA-B*08:01:01 | HLA-B*08:01P;HLA-B*08:01P | HLA-B*38:01;HLA-B*40:01 | no | |
| sample_5 | C | 255 | 1667218 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*12:03;HLA-C*17:01 | no | |
| sample_5 | DRB1 | 255 | 742387 | HLA-DRB1*01:01:01;HLA-DRB1*01:01:01 | HLA-DRB1*01:01P;HLA-DRB1*01:01P | HLA-DRB1*01:02:01;HLA-DRB1*13:02:01 | no | |
| sample_6 | A | 255 | 2493220 | HLA-A*02:01:01:01;HLA-A*02:01:01:01 | HLA-A*02:01P;HLA-A*02:01P | HLA-A*02:05:01;HLA-A*26:01 | no | |
| sample_6 | B | 255 | 4262194 | HLA-B*08:01:01;HLA-B*08:01:01 | HLA-B*08:01P;HLA-B*08:01P | HLA-B*35:01;HLA-B*50:01:01 | no | |
| sample_6 | C | 255 | 1667218 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*04:01;HLA-C*06:02 | yes | |
| sample_6 | DRB1 | 255 | 742387 | HLA-DRB1*01:01:01;HLA-DRB1*01:01:01 | HLA-DRB1*01:01P;HLA-DRB1*01:01P | HLA-DRB1*12:01;HLA-DRB1*13:01 | no | |
| sample_7 | A | 255 | 2493220 | HLA-A*02:01:01:01;HLA-A*02:01:01:01 | HLA-A*02:01P;HLA-A*02:01P | HLA-A*29:02:01;HLA-A*68:01:01 | no | |
| sample_7 | B | 255 | 4262194 | HLA-B*08:01:01;HLA-B*08:01:01 | HLA-B*08:01P;HLA-B*08:01P | HLA-B*40:01;HLA-B*44:02:01:01 | no | |
| sample_7 | C | 255 | 1667218 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*03:04;01;HLA-C*16:01:01 | no | |
| sample_7 | DRB1 | 255 | 742387 | HLA-DRB1*01:01:01;HLA-DRB1*01:01:01 | HLA-DRB1*01:01P;HLA-DRB1*01:01P | HLA-DRB1*04:01:01;HLA-DRB1*13:02:01 | no | |
| sample_8 | A | 255 | 2493220 | HLA-A*01:01:01:01;HLA-A*01:01:01:01 | HLA-A*01:01P;HLA-A*01:01P | HLA-A*01:01;HLA-A*02:01 | yes | |
| sample_8 | B | 255 | 4262194 | HLA-B*08:01:01;HLA-B*08:01:01 | HLA-B*08:01P;HLA-B*08:01P | HLA-A*08:01:01;HLA-A*51:01:01 | no | |
| sample_8 | C | 255 | 1667218 | HLA-C*04:01:01:01;HLA-C*04:01:01:01 | HLA-C*04:01P;HLA-C*04:01P | HLA-C*07:01;HLA-C*15:02 | no | |
| sample_8 | DRB1 | 255 | 742387 | HLA-DRB1*01:01:01;HLA-DRB1*01:01:01 | HLA-DRB1*01:01P;HLA-DRB1*01:01P | HLA-DRB1*03:01;HLA-DRB1*11:01 | no |
bwakit may not be reporting to the correct level of nomenclature resolution.
Reporting HLA-A*01:01:01:01 yet having 1 mismatch is breaking the rules. Depending on whether the mismatch is in exon 2 or exon 3, in another exon, in an intron, or in flanking sequence, a different or even a "novel" allele should be reported.
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For 60x exome samples from 1000 genomes (NA*), bwakit provides good resolution of alleles. It gives an exact match in half of the cases and the same allele group in the majority of the other cases. We need to investigate better resolution and selection of alternative choices. It did not work at all for high depth targeted data (2000x).