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Table 1 Two-field accuracy and exact sequence matching for novel and partial alleles

From: HLAProfiler utilizes k-mer profiles to improve HLA calling accuracy for rare and common alleles in RNA-seq data

  HLAProfiler OptiType seq2hla HLAForest HLAminer PHLAT
Novel alleles*
 Sequence identified 63% - - - - -
 Sequence identified or two-field accuracy 68% - - - - -
 One-field accuracy 97% 15% 17% 19% 37% 96%
 Two-field accuracy 25% 4% 4% 3% 10% 26%
Partial alleles
 Sequence identified 67% - - - - -
 Sequence identified or two-field accuracy 85% - - - - -
 One-field accuracy 97% 95% 94% 19% 72% 97%
 Two-field accuracy 85% 41% 21% 3% 23% 46%
  1. Results are based on two sets of simulated data for 100 samples, each having exactly one partial allele or one novel allele. Accuracy for novel alleles is defined as identification of the exact sequence, one-field accuracy, or two-field accuracy
  2. *In the case of novel alleles, the correct protein sequence can be identified without correctly identifying one- or two-field precision, or one- or two-field precision can be identified while missing the exact protein sequence