Table 7

Prediction accuracies of HLA alleles with frequency exceeding a threshold

Training set

Intermediate Resolution

High Resolution

HLA-

0.05*

0.03

0

0.05

0.03

0


Caucasians in the FHCRC cohort (N = 1280)

A

99

99

98

99

99

97

B

98

97

96

97

97

94

C

97

96

96

97

97

96

DRB1

97

97

97

91

91

88

DQB1

99

99

99

98

98

98


Caucasians in the STEP cohort (N = 832)

A

99

99

95

99

98

95

B

97

97

95

97

97

93

C

96

94

94

95

95

94

DRB1

98

98

98

98

95

91


* Threshold for HLA allele frequency

The accuracies of HLA predictive models, built with a training set of Caucasian samples from the FHCRC cohort

(genotyped on Affy 5.0) or the STEP cohort (genotyped on Illumina 1.2M), were evaluated using the WTCCC samples

(genotyped on Affy 500K) as the validation set (N = 1480). Only HLA alleles with frequency more than threshold

0.05, 0.03 or 0 in the validation set were evaluated for their prediction accuracies. The confidence threshold was set at CT = 0.

Zhang et al. BMC Genetics 2011 12:39   doi:10.1186/1471-2156-12-39

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