New Methods for HLA typing from RNA-Seq Data

The Human Leukocyte Antigen (HLA) is key to many aspects of human physiology and medicine. All current sequence-based HLA typing methodologies are targeted approaches requiring the amplification of specific HLA gene segments. Whole genome, exome and transcriptome shotgun sequencing can generate prodigious data but due to the complexity of HLA loci these data have not been immediately informative regarding HLA genotype.

Now, two groups have developed new methods for HLA typing from RNA-Seq sequence reads:

Scientists at TRON (Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Germany) have developed a new method, seq2HLA, for obtaining an individual’s HLA class I and II type and expression using standard NGS RNA-Seq data1. It comprises mapping RNA-Seq reads against a reference database of HLA alleles, determining and reporting HLA type, confidence score and locus-specific expression level.

They have applied seq2HLA to 50 CEU HapMap individuals previously HLA-typed, yielding 100% specificity and 94% sensitivity at a p-value of 0.1 for 2-digit HLA types. They determined HLA-type and expression for the previously un-typed Illumina Body Map tissues and a cohort of Korean lung cancer patients. Because the algorithm uses standard RNA-Seq reads and requires no change to lab protocols, it can be used for both existing datasets and future studies, thus adding a new dimension for HLA typing and biomarker studies.


Availability – Seq2HLA is / is written in python and R and available as stand-alone and Galaxy modules from:

Scientists at the BC Cancer Agency, Michael Smith Genome Sciences Centre, Canada have developed a new method, – a computational method for identifying HLA alleles directly from shotgun sequence datasets2. Their approach circumvents the additional time and cost of generating HLA-specific data and capitalizes on the increasing accessibility and affordability of massively-parallel sequencing.


Availability – HLAminer is available at:

  • Boegel S, Lower M, Schafer M, Bukur T, de Graaf J, Boisguerin V, Tureci O, Diken M, Castle JC, Sahin U. (2012) HLA typing from RNA-Seq sequence reads. Genome Med 4(12):102. [abstract]
  • Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA. (2012) Derivation of HLA types from shotgun sequence datasets. Genome Med 4(12):95. [abstract]