Using nanopore RNA-Seq to HLA genotype and correlate donor HLA expression with flow cytometric crossmatch results

Transplant centers are increasingly using virtual crossmatching (VXM) to evaluate recipient and donor compatibility. However, the current state of VXM fails to incorporate donor HLA expression in the assessment, despite numerous studies that demonstrated the impact of donor HLA expression on physical crossmatch outcomes. Whole-transcriptome sequencing (RNA-Seq) for HLA enables simultaneous determination of HLA genotyping and relative HLA expression. Ultimately the RNA-Seq needs to be faster to incorporate into the VXM process. However, to demonstrate feasibility, Oxford Nanopore Technologies’ MinION sequencer was evaluated in combination with RNA-Seq to generate HLA genotypes and determine HLA class I expression.

Although HLA class I expression varied among individuals, the pattern of HLA expression remained relatively consistent, HLA-B>-A=-C. HLA-A and HLA-C had similar expression profiles. The impact of donor HLA expression was evaluated using serum samples containing a single donor-specific antibody (DSA). By making DSA consistent, donor HLA expression variability could be assessed. With consistent DSA MFI, there was a direct relationship between the donor HLA expression to which the DSA is against and FCXM median channel shifts.