Research Associate University of British Columbia Vancouver, BC, Canada
Aim: 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 pre-transplant assessment focuses on 11 human leukocyte antigen (HLA) genes, but advancing technologies now allow for the assessment of many more genes relevant to transplant success.
Methods: Using Oxford Nanopore Technology’s (ONT) adaptive sampling approach, we have built a comprehensive transplant assessment panel as a proof-of-principle-test to preemptively profile immune risk at the DNA sequence and -methylation level. This test does not require any form of preamplification, enrichment or enzymatic conversion, and currently includes 164 regions of interest (ROIs): the complete HLA locus (5.5Mb), the T-cell receptor gene locus (0.8Mb), 50 ISBT blood group genes, as well as 112 CPIC non-HLA pharmacogenomics loci for drug response prediction of which 22 are classified as actionable.
Results: Our rapid all-in-one test currently achieves up to 100x (median ~75x) ROI coverage at a 2-day turnaround (Figure 1) and a data quality that is suitable for high confidence small and structural variant calling, allele phasing, and DNA methylation profiling in all ROIs as well as simultaneous whole genome copy number variation analysis (Epi2me human variation workflow). From the collected data, we are currently able to infer haplotypes for HLA (HLAminer - 2 fields, SpecHLA - 4 fields), for 46 ISBT blood group genes (RBCeq2), and for 20 CPIC Level-A PGx star alleles (PharmCAT).
Conclusion: 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 an all-in-one personalized transplant risk assessment, which can be adapted within minutes. This approach represents the next step in refining precision medicine, improving patient outcomes, reducing healthcare costs, and enhancing life quality for transplant recipients. Incorporating comprehensive genomic information into clinical decision-making will be crucial for reducing and eventually eliminating toxic immunosuppressive drugs through operational tolerance.
