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

Table 4 **HIBAG model* four-digit HLA allele prediction accuracy in ACCESS African Americans differs by local ancestry at HLA class II genes**

Gene	West African ancestral alleles†	N	Accuracy	P‡
DRB1	2	240	92.9	0.005
	1	78	80.8
	0	10	80.0
DQB1	2	292	98.6	0.040
	1	76	93.4
	0	8	100.0
DPB1	2	376	89.6	8.8*10^-4
	1	110	75.5
	0	14	85.7

Abbreviations: N=count; ACC=classification accuracy; P=p-value from a Fishers exact test.
*The models trained on the subset of ACCESS African Americans with training samples selected at random (from a total of 325) to match the number of subjects used to construct the published HIBAG African ancestry models: HLA-DRB1 (n=161), HLA-DQB1 (n=137), and HLA-DPB1 (n=75).
†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 locus in question.

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