Open Access Highly Accessed Methodology article

Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics

Martin Danzer1*, Norbert Niklas1, Stephanie Stabentheiner2, Katja Hofer1, Johannes Pröll1, Christina Stückler1, Edeltraud Raml1, Helene Polin1 and Christian Gabriel1

Author Affiliations

1 Department of Immunogenetics, Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, Linz 4017, Austria

2 Hamilton Robotics GmbH, Fraunhoferstraße 17, Martinsried 82152, Germany

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BMC Genomics 2013, 14:221  doi:10.1186/1471-2164-14-221

Published: 4 April 2013

Abstract

Background

Human leukocyte antigen matching at allelic resolution is proven clinically significant in hematopoietic stem cell transplantation, lowering the risk of graft-versus-host disease and mortality. However, due to the ever growing HLA allele database, tissue typing laboratories face substantial challenges. In light of the complexity and the high degree of allelic diversity, it has become increasingly difficult to define the classical transplantation antigens at high-resolution by using well-tried methods. Thus, next-generation sequencing is entering into diagnostic laboratories at the perfect time and serving as a promising tool to overcome intrinsic HLA typing problems. Therefore, we have developed and validated a scalable automated HLA class I and class II typing approach suitable for diagnostic use.

Results

A validation panel of 173 clinical and proficiency testing samples was analysed, demonstrating 100% concordance to the reference method. From a total of 1,273 loci we were able to generate 1,241 (97.3%) initial successful typings. The mean ambiguity reduction for the analysed loci was 93.5%. Allele assignment including intronic sequences showed an improved resolution (99.2%) of non-expressed HLA alleles.

Conclusion

We provide a powerful HLA typing protocol offering a short turnaround time of only two days, a fully integrated workflow and most importantly a high degree of typing reliability. The presented automated assay is flexible and can be scaled by specific primer compilations and the use of different 454 sequencing systems. The workflow was successfully validated according to the policies of the European Federation for Immunogenetics. Next-generation sequencing seems to become one of the new methods in the field of Histocompatibility.