Rapid, highly accurate and cost-effective open-source simultaneous complete HLA typing and phasing of class I and II alleles using nanopore sequencing

Research output: Contribution to journalArticlepeer-review


  • Thomas Nieto
  • Elizabeth Wroe
  • Anthony Poles
  • Nicholas Inston
  • David Briggs

Colleges, School and Institutes

External organisations

  • MRC Health Data Research UK


Accurate rapid genotyping of the genes within the HLA region presents many difficulties because of the complexity of this region. Here we present the results of our proof of concept nanopore-based long read polymerase chain reaction (PCR) solution for HLA genotyping. For 15 HLA anthropology-based samples and 13 NHS Blood and Transplant derived samples 40 ng of genomic DNA underwent long-range PCR for class I and II HLA alleles. Pooled PCR products were sequenced on the Oxford Nanopore MinIoON R9.4.1 flow cell. Sequenced reads had HLA genotype assigned with HLA-LA. Called genotypes were compared with reference derived from a combination of short-read next-generation sequencing, Sanger sequence and/or single-site polymorphism (SSP) typing. For concordance, accuracy was 100%, 98.4%, 97.5% and 95.1% for the first, second, third and fourth fields, respectively, to four field accuracy where it was available, otherwise three field in 28 samples for class I calls and 17 samples for class II calls. Phasing of maternal and paternal alleles, as well as phasing based identification of runs of homozygosity, was shown successfully. Time for assay run was 8 hours and the reconstruction of HLA typing data was 15 minutes. Assay cost was £55 ($80USD)/sample. We have developed a rapid and cost-effective long-range PCR and nanopore sequencing-based assay that can genotype the genes within HLA region to up to four field accuracy, identify runs of homozygosity in HLA, reconstruct maternal and paternal haplotypes and can be scaled from multi-sample runs to a single sample.

Bibliographic note

© 2020 The Authors. HLA published by John Wiley & Sons Ltd.


Original languageEnglish
Pages (from-to)163-178
Number of pages16
Issue number2
Early online date18 May 2020
Publication statusPublished - Aug 2020


  • HLA, long read, nanopore