Beyond HLA: An adaptive nanopore sequencing assay for simultaneous HLA and blood group profiling in transplantation

Transplantation is a life-saving therapy but carries significant risks, including rejection, graft-versus-host disease, infection, and malignancy, which can lead to graft failure and death. These complications arise from the interaction between the recipient's immune system and the transplanted organ, requiring long-term toxic drugs to prevent immune injury. Traditional genetic pre-transplant assessment focuses on ABO and 11 human leukocyte antigen (HLA) genes, but advancing technologies now allow for the assessment of many more genes relevant to transplant success.

Using Oxford Nanopore Technology's (ONT) adaptive sampling approach, we have built a comprehensive proof-of-principle test to preemptively profile blood group and HLA phenotypes at the DNA sequence and methylation level. This test does not require preamplification, enrichment or enzymatic conversion, and can be easily adapted to enrich up to 10 % of the human genome, including the complete HLA locus (5.5 Mb) and all currently listed International Society of Blood Transfusion (ISBT) blood group genes.

This rapid all-in-one test currently achieves up to 370x (median 250x) region of interest coverage at a 4-day turnaround and a data quality that is suitable for blood group and HLA genotyping, which matched or outperformed gold standard assays.

As a field, we have dramatically reduced early post-transplant immune injury using molecular diagnostics and structural biology. Here, we demonstrate proof-of-concept of a personalized transplant risk assessment, which can be adapted to profile additional genes or genomic regions within minutes and yields multi-genic typing data at a 4-day turnaround. This approach represents the next step in refining precision medicine, improving patient outcomes, reducing healthcare costs, and enhancing life quality for transplant recipients.