Evaluation of Chimerism Testing by Next-Generation Sequencing Using Insertion/Deletion Markers

Post-transplant engraftment monitoring is essential to assess the risk of complications after allogeneic hematopoietic transplantation, such as graft failure and disease relapse. It is based on the analysis of the percentage of chimerism detected in the recipient. Chimerism analysis has been routinely performed using short tandem repeats (STRs). Next-generation sequencing (NGS) has made possible the use of other genetic markers, such as single-nucleotide polymorphisms and insertions/deletions (indels). This study evaluated the performance characteristics of the NGStrack assay from GenDx to verify its accuracy, sensitivity, and reproducibility. It was determined that the assay can detect DNA contributed by donor and recipient within the range of 0.5% to 99.5%. The results of this assay were compared with an STR-based method, and examples of clinical utilization of the assay were provided using patient cases, including chimerism analysis on different cell subsets. It was confirmed that chimerism analysis using indel markers provides an increased sensitivity with respect to the reported sensitivity of assays using STR. The sensitivity for STR-based methods is in the range of 1% to 5%, whereas the sensitivity for the indel NGS-based method assessed here is 0.5%. The increased sensitivity and precise correlation between chimerism results with clinical events validates the usefulness of this assay for early diagnosis of disease relapse and graft failure and allows for more precise clinical management.