Table 2:
Resolving genotypic ambiguity
| A: Family2A | |||
|---|---|---|---|
| Subject | Relationship | Original | Reduced |
| 767 | child | DPB1*03:01:01+DPB1*05:01:01| DPB1*135:01+DPB1*104:01 |
DPB1*03:01:01+ DPB1*05:01:01 |
| 768 | child | DPB1*03:01:01+DPB1*04:01:01| DPB1*124:01+DPB1*350:01 |
DPB1*03:01:01+ DPB1*04:01:01 |
| 769 | father | DPB1*03:01:01+DPB1*13:01:01| DPB1*03:01:01+DPB1*107:01 |
DPB1*03:01:01+ DPB1*13:01:01/DPB1*107:01 |
| 76A | mother | DPB1*04:01:01:01+DPB1*05:01:01 | DPB1*04:01:01:01+DPB1*05:01:01 |
| B: Family2B | |||
|---|---|---|---|
| Subject | Relationship | Original | Reduced |
| 2B1 | child | DPB1*05:01:01+ DPB1*05:01:01 |
DPB1*05:01:01+ DPB1*05:01:01 |
| 2B2 | child | DPB1*05:01:01+ DPB1*135:01 |
DPB1*05:01:01+ DPB1*135:01 |
| 2B3 | child | DPB1*05:01:01+ DPB1*13:01:01/DPB1*107:01| DPB1*135:01+DPB1*519:01 |
DPB1*05:01:01+ DPB1*13:01:01/DPB1*107:01 |
| 2B4 | father | DPB1*05:01:01+DPB1*135:01 | DPB1*05:01:01+DPB1*135:01 |
| 2B5 | mother | DPB1*05:01:01+ DPB1*13:01:01/DPB1*107:01| DPB1*135:01+DPB1*519:01 |
DPB1*05:01:01+ DPB1*13:01:01/DPB1*107:01 |
| C: | ||||
|---|---|---|---|---|
| Family | Subject | Relationship | Original | Reduced |
| 7457 | 158B | child | DPB1*02:01:02+DPB1*104:01| DPB1*124:01+DPB1*414:01 |
DPB1*02:01:02+DPB1*104:01 |
| 7457 | 158A | mother | DPB1*02:01:02+DPB1*104:01| DPB1*124:01+DPB1*414:01 |
DPB1*02:01:02+DPB1*104:01 |
| 7457 | 1589 | father | DPB1*02:01:02+DPB1*104:01| DPB1*124:01+DPB1*414:01 |
DPB1*02:01:02+DPB1*104:01 |
| 73 | 78B82 | mother | DPB1*04:01:01:01+DPB1*04:02:01:02| DPB1*105:01+DPB1*126:01 |
DPB1*04:01:01:01+DPB1*04:02:01:02 |
| 73 | 78B83 | child | DPB1*04:01:01:01+DPB1*04:02:01:02| DPB1*105:01+DPB1*126:01 |
DPB1*04:01:01:01+DPB1*04:02:01:02 |
| 73 | 78B84 | father | DPB1*04:01:01:01+DPB1*04:02:01:02| DPB1*105:01+DPB1*126:01 |
DPB1*04:01:01:01+DPB1*04:02:01:02 |
| 273 | 1934 | child | DPB1*03:01:01+DPB1*04:01:01:01| DPB1*124:01+DPB1*350:01 |
DPB1*03:01:01+DPB1*04:01:01:01 |
| 273 | 1935 | father | DPB1*03:01:01+DPB1*04:01:01:01| DPB1*124:01+DPB1*350:01 |
DPB1*03:01:01+DPB1*04:01:01:01 |
| 273 | 1936 | mother | DPB1*03:01:01+DPB1*04:01:01:01| DPB1*124:01+DPB1*350:01 |
DPB1*03:01:01+DPB1*04:01:01:01 |
The original HLA genotypes that are obtained from NGS HLA typing software applications are shown in the “Original” column. The prefix “HLA-” is omitted from gene names in this table. Table 2A shows a family (Family2A) in which two children had genotypic ambiguities in their HLA-DPB1 genotypes. These genotype ambiguities are not resolvable when these individual’s HLA genotypes are reviewed. When the father’s (HLA-DPB1*03:01:01+HLA-DPB1*13:01:01/HLA-DPB1*107:01) and mother’s (HLA-DPB1*04:01:01:01+HLA-DPB1*05:01:01) genotypes are reviewed, the only possible genotypes for child1 and child2 are HLA-DPB1*03:01:01+HLA-DPB1*05:01:01 and HLA-DPB1*03:01:01+HLA-DPB1*04:01:01, respectively. Table 2B shows another family (Family2B) in which a child (2B3) and mother (2B5) share genotypic ambiguity. In Family2B, if subject 2B3 were the only child, then it would not be possible to resolve the genotypic ambiguity; the genotypes of children 2B1 and 2B2 made it possible to establish haplotype phase. Table 2C: We identified four families in which all family members had the same ambiguous HLA-DPB1 genotype. Of these four families, Table 2C shows three such families. The fourth family had the same HLA-DPB1 genotype as family 273, and was omitted from the table. This is an uninformative genotype example, in which haplotypes cannot be built using segregation. HaplObserve selected the lowest-digit allele name combination as a default.