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Table 6 The effect of adding imputed SNPs to the HIBAG HLA allele imputation accuracy in ACCESS African Americans for HLA class II genes

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

 

Gene

Allele field

Testing set

   

All

PP > 0.5

   

N

Accuracy

N

Call rate

Accuracy

ACCESS Subset* - GWAS + 1000GP Imputed dataa

DRB1

One

164

95.4

149

90.9

97.0

 

Two

164

90.2

123

75.0

95.9

DQB1

One

188

99.2

185

98.4

99.5

 

Two

188

98.1

168

89.4

99.4

 

DPB1

One

250

87.3

160

64.2

97.5

  

Two

250

91.8

151

60.6

97.0

ACCESS Subset* - GWAS + 1000GP + TargetSeq Imputed datab

DRB1

One

164

94.8

147

89.6

97.0

 

Two

164

89.6

129

78.7

95.0

DQB1

One

188

99.2

186

98.9

99.2

 

Two

188

97.9

171

91.0

99.4

  1. Abbreviations: PP denotes, posterior prediction probability; N, count; Accuracy, imputation accuracy.
  2. *The models trained on the subset of ACCESS African Americans genotype data from a)GWAS + 1000 Genome project imputed data, b)GWAS + 1000 Genome project + targeted sequencing imputed data (DRB1 and DQB1 only) with training samples selected at random (from a total of 325) using 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).
  3. †One- and two-field estimates will be very similar for HLA-DPB1 as the first field uniquely identifies the two-field alleles, with the exceptions of *02:01 and *0202, and *04:01 and *04:02.