Introduction: Chimerism analysis of recipient and donor cells enables the assessment of engraftment, minimal residual disease, and early detection of relapse post hematopoietic stem cell transplantation (HSCT). This is the first study to evaluate the use of two novel multiplex next generation sequencing (NGS) chimerism assays.

Methods: DNA extracted from peripheral blood samples with known mixed chimerism percentages were used in two multiplex NGS chimerism assays following manufacturer’s instructions to assess accuracy, reproducibility, lower limits of detection of chimerism. DNA sequencing was performed on the Illumina MiSeq system and analysis was completed using the associated manufacturer software.

Results: Chimerism assay 1 (Devyser) utilized 10/24 informative markers and the lower limit of detection was 0.1%. Chimerism assay 2 (GenDx) utilized 17/32 informative markers and the lower limit of detection was 0.5%. Both assays demonstrated excellent comparable accuracy and reproducibility throughout all tested chimerism ratios.

Conclusion: High sensitivity chimerism assays using NGS technology may allow better quantitative monitoring of engraftment post HSCT compared to the current gold standard short tandem repeat-based PCR with capillary electrophoresis (STR PCR CE) method.