Table 5.
Local ancestry differences in two-field HLA allele imputation accuracy resolved by HIBAG models containing equal numbers* of ancestral West African and European chromosomes
| Gene | West African ancestral alleles† | N | Accuracy | P‡ |
|---|---|---|---|---|
|
DRB1 |
2 |
91 |
88.5 |
0.12 |
| |
1 |
75 |
81.3 |
|
| |
0 |
9 |
94.4 |
|
| |
Overall |
175 |
85.7 |
|
|
DQB1 |
2 |
91 |
95.1 |
1.00 |
| |
1 |
75 |
95.3 |
|
| |
0 |
9 |
100.0 |
|
| |
Overall |
175 |
95.4 |
|
|
DPB1 |
2 |
91 |
89.0 |
0.92 |
| |
1 |
75 |
89.6 |
|
| |
0 |
9 |
94.4 |
|
| Overall | 175 | 90.6 |
Abbreviations: N denotes, count; Accuracy, imputation accuracy; P, p-value from a Fishers exact test.
*150 individuals (300 chromosomes) from African American with two ancestral West African alleles at each gene as estimated by LAMP and 150 individuals from the ACCESS European American sample (i.e. 300 European chromosomes). The test set for these models included the remaining 175 African Americans who were not a part of the 150 used to build the model.
†Number of West African ancestral alleles at each gene estimated by the Local Ancestry in Admixed Populations (LAMP) method.
‡Test for difference in imputation accuracy proportions across individuals with 0, 1, or 2 West African alleles at each gene.