Table 2. Baseline validation on a homogeneous reference panel.

Threshold	Locus	# Validated	HLA*IMP:02			HLA:IMP:01
			Call Rate	Accuracy	T	Call Rate	Accuracy	T
T =  0.00	HLA-A	574	1.00	0.96		1.00	0.90
	HLA-B	2002	1.00	0.90		1.00	0.93
	HLA-C	596	1.00	0.96		1.00	0.96
	HLA-DQA1	446	1.00	0.87		1.00	0.87
	HLA-DQB1	758	1.00	0.98		1.00	0.97
	HLA-DRB1	1730	1.00	0.88		1.00	0.89
T = Matched	HLA-A	574	0.96	0.96	0.55	0.94	0.91	0.700
	HLA-B	2002	0.98	0.92	0.40	0.98	0.94	0.700
	HLA-C	596	0.99	0.96	0.60	0.99	0.97	0.700
	HLA-DQA1	446	0.99	0.88	0.40	0.99	0.88	0.700
	HLA-DQB1	758	0.99	0.98	0.60	0.99	0.97	0.700
	HLA-DRB1	1730	0.90	0.93	0.60	0.90	0.93	0.700

Non-thresholded and thresholded HLARES validation results for HLA*IMP:02 and HLA*IMP:01: the complete GS is used to impute HLARES_EU samples. Accuracy (PPV) is measured at 4-digit resolution. “# Validated” refers to the number of validated alleleles (pre-thresholding). Note that the call threshold for HLA*IMP:02 was matched to obtain equal or higher call rates than with HLA*IMP:01.