Table 2.
Predicted HLA types of the CEU trio samples with HLA-VBSeq.
| Sample | Predicted HLA types | |
|---|---|---|
| NA12878 (child) | A*01:01:01:01 | A*11:01:01 |
| B*08:01:01 | B*56:01:01 | |
| C*01:02:01 | C*07:01:01:01 | |
| DQA1*01:01:02 | DQA1*05:01:01:02 | |
| DQB1*02:01:01 | DQB1*05:01:01:02 | |
| DRB1*03:01:01:01 | DRB1*01:01:01 | |
| NA12891 (father) | A*01:01:01:01 | A*24:02:01:01 |
| B*07:02:01 | B*08:01:01 | |
| C*07:01:01:01 | C*07:02:01:03 | |
| DQA1*01:02:01:01 | DQA1*05:01:01:02 | |
| DQB1*02:01:01 | DQB1*06:02:01 | |
| DRB1*03:01:01:01 | DRB1*15:01:01:02 | |
| NA12892 (mother) | A*02:01:01:01 | A*11:01:01 |
| B*15:01:01:01 | B*56:01:01 | |
| C*01:02:01 | C*04:01:01:01 | |
| DQA1*01:01:02 | DQA1*01:01:02 | |
| DQB1*05:01:01:02 | DQB1*05:01:01:01 | |
| DRB1*01:01:01 | DRB1*01:01:01 | |
Predicted HLA types of HLA-A, -B, and -C loci with HLA-VBSeq were experimentally validated at 4-digit resolution in [10], which is shown in bold text. Predicted HLA types of HLA-DQA1, -DQB1 and -DRB1 loci with HLA-VBSeq were coincided with those with PHLAT at 6-digit resolution except DQA1*01:01:02 (one allele in NA12878 and two alleles in NA12892). PHLAT instead predicted them as DQA1*01:01:01, whose genomic sequence was missing in the IMGT database release 3.15.0., and hence HLA-VBSeq could not predict the HLA allele in our experimental condition.