Highly sensitive patient-specific real-time PCR SNP assay for chimerism monitoring after allogeneic stem cell transplantation.

Chimerism analysis after allogeneic stem cell transplantation (allo-SCT) is an important diagnostic tool for the documentation of engraftment, early detection of graft failure, and recurrence of the disease. Current assays rely on the genetic polymorphism between the donor and the recipient, and allow semiquantitative or quantitative analysis of chimerism. The most common method in use is based on the amplification of the short tandem repeats (STR). This method, with 1% to 5 sensitivity, is useful for the documentation of engraftment, but is insufficient for the detection of minimal residual disease or early relapse, when medical intervention is urgently needed. Recently, single-nucleotide polymorphism (SNP) has been suggested as an alternative, more accurate system to monitor chimerism. The purpose of our study was to develop an easy, economical, and sensitive method for the detection of chimerism following allo-SCT using the SNP technology. Our approach is based on SNP patient-specific quantitative real-time polymerase chain reaction (PCR) using nonlabeled primers. Our results show that this allele-specific SNP real-time PCR approach is sensitive, relatively cheap, and offers a fast and reliable assay for the monitoring of hematopoietic engraftment and for the detection of minimal residual disease in patients after allo-SCT.