Comparison of variable number tandem repeat and short tandem repeat genetic markers for qualitative and quantitative chimerism analysis post allogeneic stem cell transplantation.

BACKGROUND Analysis of donor chimerism has become a routine procedure for the documentation of engraftment after allogeneic hematopoietic stem cell transplantation. Quantitative analysis of chimerism kinetics has been shown to predict graft failure or relapse. In this study, we compared the use of variable number tandem repeats (VNTR) and short tandem repeats (STR) as polymorphic genetic markers in chimerism analysis. This study included qualitative and quantitative assessment of both techniques to assess informative yield and sensitivity. PATIENTS AND METHODS We analyzed 206 samples representing 40 transplant recipients and their HLA-identical sibling donors. A panel of six VNTR loci, 15 STR loci and 1 sex chromosome locus was used. Amplified VNTR products were visualized in an ethidium bromide-stained gel. STR loci were amplified using fluorescent primers, and the products were analyzed by capillary electrophoresis. RESULTS VNTR and STR analysis gave comparable qualitative results in the majority of cases. The incidence of mixed chimerism (MC) by STR analysis was 45% compared to 32% in cases evaluated by VNTR analysis. STR markers were more informative; several informative loci could be identified in all patients. Unique alleles for both patient and donor could be identified in all patients by STR versus 32/40 by VNTR analysis. The STR markers were also more sensitive in the detection of chimerism. The size of VNTR alleles and differences between the size of donor and recipient VNTR alleles affected the sensitivity of detection. With both techniques, quantitative assessment of chimerism showed some discrepancies between the estimated and the calculated percentage of donor DNA. Discordance between the two estimates was observed in 8/19 patients with MC. However, sequential monitoring of the relative band intensity of VNTR alleles offered some insight into the direction of change in engraftment over time. CONCLUSION The higher yield of informative loci with STR and the automated measurement of amplified STR 103 products offered the advantages of more rapid and accurate quantitative assessment of chimerism. The choice between these two techniques depends on the need for quantitative or qualitative information, the availability of equipment, and the cost.