Analysis of hematopoietic stem cell transplant engraftment: use of loss or gain of microsatellite alleles to identify residual hematopoietic malignancy

Abstract

Polymorphic short tandem repeat (STR), or microsatellite, loci have been widely used to analyze chimerism status after allogeneic hematopoietic stem cell transplantation. The presence of a patient's DNA, as identified by STR analysis, may indicate residual or recurrent malignant disease or may represent normal hematopoiesis of patient origin. The ratio of patient-derived to donor-derived alleles is used to calculate the relative amount of patient cells (both benign and malignant) to donor cells. STRs on chromosomes known to be gained or lost in a patient's tumor are generally ignored because it is difficult to perform meaningful calculations of mixed chimerism. However, in this study, we present evidence that STR loci on gained or lost chromosomes are useful in distinguishing the benign or malignant nature of chimeric DNA. In the peripheral blood or bone marrow of 4 hematopoietic stem cell transplantation patients with leukemia or lymphoma, we identified tumor DNA on the basis of STR loci showing copy number alteration. We propose that a targeted evaluation of STR loci showing altered copy number in posttransplant chimerism analysis can provide evidence of residual cancer cells.

Fig. 1

Identifiler microsatellite analysis at loci D16S539 (A–D) and D7S820 (E–H) from case 1; pre-transplant samples of patient (A and E) and donor (B and F) and post-transplant samples at 1 month: unsorted bone marrow (C and G) and sorted CD3⁺ T cells (D and H). Arrows indicate the presence of a recipient-specific 268-base D16S539 allele in the post-transplant samples (C, D, H). The presence of the recipient-specific 268 base D16S539 allele and absence of a recipient-specific 263 base D7S820 allele (▼, G) in the bone marrow and the presence of the recipient-specific 263 base D7S820 allele in T cells (H) is consistent with residual leukemia with monosomy 7 among the bone marrow white cell population.

Fig. 2

Profiler microsatellite analysis at loci TPOX (A–D) and D7S820 (E–H) from case 2; pre-transplant samples of patient (A and E) and donor (B and F) and post-transplant peripheral blood samples at 5 months (C and G) and 6 months (D and H). Arrows indicate the presence of recipient-specific 223 base TPOX allele in the post-transplant samples (C and D). The presence of recipient-specific 223 base TPOX allele and absence of recipient-specific 280 base D7S820 allele (▼, G and H) at 5 and 6 months is consistent with residual leukemia cells with monosomy 7.

Fig. 3

Identifiler microsatellite analysis at loci D21S11 (A–D) and CSF1PO on chromosome 5q (E–H) from pre-transplant samples of case 3 (A and E) and donor (B and F) and post-transplant peripheral blood samples at 2 months (C and G) and 5 months (D and H). Arrows indicate the presence of a recipient-specific 196 base D21S11 allele in the post-transplant samples (C and D). The presence of the recipient-specific 196 base D21S11 allele and absence of a recipient-specific 325 base CSF1PO allele (▼ in G and H) indicate persistent residual leukemia cells with monosomy 5 or 5q deletion.

Fig. 4

Profiler microsatellite analysis at loci FGA (A–D) and D7S820 (E–H) from pre-transplant samples of case 4 (A and E) and donor (B and F) and post-transplant bone marrow sample at 6 months (C and G) and peripheral blood sample at 12 months (D and H). Arrows indicate the presence of recipient-specific 236 and 240 base alleles in the post-transplant samples (C and D). 276/268 = the peak height ratio of allele 276 to allele 268 (E, F, G and H). The increasing peak height ratio at 6 and 12 months (G and H) is consistent with gain of chromosome 7q and suggests recurrence of gamma/delta T cell lymphoma, a disease with a unique isochromosome 7q abnormality.