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Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing


Date: 25th June 2020 | Source: Human Immunology

Authors: Timothy L.Mosbruger, Amalia Dinou, Jamie L. Duke, Deborah Ferriola, Hilary Mehler, Ioanna Pagkrati, Georgios Damianos, Eric Mbunwe, Mahdi Sarmady, Ioannis Lyratzakis, Sarah A. Tishkoff, Anh Dinh, Dimitri S. Monos.

The comprehensive characterization of human leukocyte antigen (HLA) genomic sequences remains a challenging problem. Despite the significant advantages of next-generation sequencing (NGS) in the field of Immunogenetics, there has yet to be a single solution for unambiguous, accurate, simple, cost-effective, and timely genotyping necessary for all clinical applications.

This report demonstrates the benefits of nanopore sequencing introduced by Oxford Nanopore Technologies (ONT) for HLA genotyping.

Samples (n = 120) previously characterized at high-resolution three-field (HR-3F) for 11 loci were assessed using ONT sequencing paired to a singleplex PCR protocol (Holotype) and to two multiplex protocols OmniType (Omixon) and NGSgo®-MX6-1 (GenDx).

The results demonstrate the potential of nanopore sequencing for delivering accurate HR-3F typing with a simple, rapid, and cost-effective protocol. The protocol is applicable to time-sensitive applications, such as deceased donor typings, enabling better assessments of compatibility and epitope analysis. The technology also allows significantly shorter turnaround time for multiple samples at a lower cost.

Overall, nanopore technology appears to offer a significant advancement over current next-generation sequencing platforms as a single solution for all HLA genotyping needs.

Read the full text Investigating SNVs and phasing with Nanopore Tom Nieto: HLA typing for renal transplants

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