[A novel single nucleotide polymorphism-based method for quantitative assessment of chimerism after allogeneic stem...

To develop a novel single nucleotide polymorphism (SNP)-PCR based method for quantitative detection of chimerism after allogeneic haemopoietic stem cell transplantation (allo-HSCT), and to explore its feasibility, accuracy and superiority.

18 SNP loci were sereened to identify informative markers for detecting chimerism in each donor/recipient pair before transplantation. Then the chimerism rate of each informative marker was analyzed by real-time quantitative PCR (RQ-PCR). The accuracy and sensitivity were verified by multiple proportion dilution and analogy chimerism compared with quantitative detection of short tandem repeat (STR)-PCR, fluorescence in situ hybridization (FISH) and fusion gene.

(1) The average slope of the 17 time amplications of the internal control plasmid was -3.39, the average intercept was 39.97, correlation coefficients were more than 0.995, which was close to the theoretical level. The intra- and interassay variability was 0.50% and 1.1%, respectively, which were both in the allowed ranges. A linear correlation with artificial mixed chimerism is above 0.99 and a sensitivity of 0.01% proved reproducible. (2) At least one informative marker could be found in over 95% of 40 donor/recipient pairs. The results of the chimerisms derived from SNP-PCR were consistent with that from STR-PCR (96.7%), FISH and fusion gene analasis (P > 0.05); the quantitative results of special fusion gene transcripts were negtive in complete chimerism samples, and positive in mixed chimerism samples.

This new assay which overcome the PCR competition and plateau biases of STR-PCR provides an accurate, reliable and rapid quantitative assessment of mixed chimerism after allo-transplantation. It is highly promising for of clinical application and may take the place of STR-PCR in the conventional chimerisim assessment.