Digital polymerase chain reaction quantification of hematopoietic chimerism by insertion/deletion: A personalized...

Clinical decision-making after allogeneic stem cell transplantation (HSCT) is partially based on hematopoietic chimerism analysis. Short tandem repeat (STR), the current gold standard for quantitative chimerism analysis, has limited sensitivity. Digital polymerase chain reaction (dPCR) offers precise quantification and high reproducibility with excellent sensitivity (usually ≤0.1%) across a wide measurement range. However, the reported dPCR-based chimerism detection methods were developed in non-Chinese cohorts and may not be directly applicable to the Chinese population.

To improve sensitivity and accuracy, we first screened out 14 insertions/deletions (indel) loci with high individual recognition rates in Asian populations based on literature and NCBI data. Then, we established a dPCR detection system for routine chimerism assessment ("dPCR-chimerism system") in Chinese transplant recipients. We compared the concordance between STR and dPCR in patient samples.

The newly developed dPCR-chimerism system covers all 12 pairs of autosomes, achieves a sensitivity of 0.01%, and demonstrates excellent linearity from 0.016% to 50%. For dual-donor samples, there was a strong correlation between STR and dPCR-chimerism detection values ( R2 = 0.9974). The R2 of the dPCR results was higher than STR when the theoretical chimerism rate of the single recipient was ≤5%. Clinical validation in 44 HSCT patients showed strong overall concordance between STR and dPCR (mean difference: 0.68%), although discrepancies were noted in some cases.

Our newly developed system demonstrates excellent repeatability and sensitivity, particularly in detecting. It is expected to show good applicability in Chinese transplant patients. Selecting between dPCR and STR testing based on individual chimerism status can facilitate sensitive and accurate analysis, enable timely therapeutic intervention, and support effective relapse monitoring in clinical practice.