Assessment of chimerism by next generation sequencing: A comparison to STR/qPCR methods

Darren Brow, Hiroko Shike, Jasmine Kendrick, Linnea Pettersson, Shin Mineishi, David F. Claxton, Baldeep Wirk, Joseph Cioccio, Robert J. Greiner, David Viswanatha, Mohamed A. Kharfan-Dabaja, Zhuo Li, Jennifer Tyler, Mohamed Elrefaei

Research output: Contribution to journalArticlepeer-review


Chimerism analysis is used to evaluate patients after allogeneic hematopoietic stem cell transplant (allo-HSCT) for engraftment and minimal measurable residual disease (MRD) monitoring. A combination of short-tandem repeat (STR) and quantitative polymerase chain reaction (qPCR) was required to achieve both sensitivity and accuracy in the patients with various chimerism statuses. In this study, an insertion/deletion-based multiplex chimerism assay by next generation sequencing (NGS) was evaluated using 5 simulated unrelated donor-recipient combinations from 10 volunteers. Median number of informative markers detected was 8 (range = 5 – 11). The limit of quantitation (LoQ) was determined to be 0.1 % recipient. Assay sample number/batch was 10–20 and total assay time was 19–31 h (manual labor = 2.1 h). Additionally, 50 peripheral blood samples from 5 allo-HSCT recipients (related: N = 4; unrelated: N = 1) were tested by NGS and STR/qPCR. Median number of informative markers detected was 7 (range = 4 – 12). Results from both assays demonstrated a strong correlation (Y = 0.9875X + 0.333; R2 = 0.9852), no significant assay bias (difference mean − 0.08), and 100 % concordant detection of percent recipient increase ≥ 0.1 % (indicator of increased relapse risk). NGS-based chimerism assay can support all allo-HSCT for engraftment and MRD monitoring and simplify clinical laboratory workflow compared to STR/qPCR.

Original languageEnglish (US)
Article number110794
JournalHuman Immunology
StateAccepted/In press - 2024

All Science Journal Classification (ASJC) codes

  • Immunology and Allergy
  • Immunology

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