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Table 3 Application of the score to public datasets

From: The use of haplotype-specific transcripts improves sample annotation consistency

Individual Sample description CEL file ID 203290_at HLA-DQA1 *0401 213831_at HLA-DQA1 *0103 209728_at HLA-DRB4 HLA-Score REDKX gender QC Flag Reason for flag Decision
55 Time point 1 GSM155503.CEL 28 4182 48 010 F    
  Time point 2 GSM155504.CEL 23 4606 72 010 F    
  Time point 3 GSM155505.CEL 10 2412 24 010 F    
  Time point 4 GSM155506.CEL 28 4765 21 010 F    
54 Time point 1 GSM155499.CEL 33 516 985 011 F    
  Time point 2 GSM155500.CEL 49 681 1245 011 F    
  Time point 3 GSM155501.CEL 28 1073 3142 011 F    
  Time point 4 GSM155502.CEL 26 914 2573 011 F    
45 Time point 1 GSM155495.CEL 45 8041 187 011 F HLA-score Intensity of 209728_at HLA-DRB4 slightly above threshold Not critical
  Time point 2 GSM155496.CEL 59 7619 123 010 F  
  Time point 3 GSM155497.CEL 32 6385 105 010 F  
  Time point 4 GSM155498.CEL 59 7062 40 010 F  
35 Time point 1 GSM155475.CEL 1218 42 6444 101 F HLA-score and REDKX QC-score Gender different for patient samples Possible sample mix-up; follow up
  Time point 2 GSM155476.CEL 436 1491 231 111 M    
  Time point 3 GSM155477.CEL 508 1751 200 111 M    
  Time point 4 GSM155478.CEL 126 113 5 000 M HLA-score Intensity of 209728_at HLA-DRB4 and 213831_at HLA-DQA1 10× to 46× smaller than those from other patient samples Possible sample mix-up; follow up
32 Time point 1 GSM155471.CEL 1235 32 8231 101 F HLA-score and REDKX QC-score   
  Time point 2 GSM155472.CEL 420 1878 291 111 M Gender different for patient samples Possible sample mix-up; follow up
  Time point 3 GSM155473.CEL 1807 49 7332 101 F
  Time point 4 GSM155474.CEL 1128 42 7122 101 F   
  1. Each sample of the dataset is labelled with a three-digit score (one “1” or “0” flag per probe set). The presence of intra-score differences elicits further follow-up investigation as to the nature and source of the difference. Intensity thresholds mark an “on” or “off”-status of the transcript expression, flagged as “1” or “0”, respectively. The thresholds were empirically determined for each marker separately. In some instances, the score difference is due to mild threshold violation, in other instances it may be due to sample mix-ups. The score picks up those samples which are being flagged by the REDKX gender QC, and detects further samples with issues (labeled in bold). REDKX panel expression values are provided in Additional file 1: Table S1.