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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

From: Performance of HLA allele prediction methods in African Americans for class II genes HLA-DRB1, −DQB1, and –DPB1

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

 
  1. Abbreviations: N denotes, count; Accuracy, imputation accuracy; P, p-value from a Fishers exact test.
  2. *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.
  3. †Number of West African ancestral alleles at each gene estimated by the Local Ancestry in Admixed Populations (LAMP) method.
  4. ‡Test for difference in imputation accuracy proportions across individuals with 0, 1, or 2 West African alleles at each gene.