Short Tandem Repeats (STRs) as Biomarkers for the Quantitative Follow-Up of Chimerism after Stem Cell Transplantation: Methodological Considerations and Clinical Application

Abstract

Chimerism refers to the relative proportion of donor and recipient DNA after hematopoietic stem cell transplantation (HSCT) and its quantitative follow-up is of great clinical utility in this setting. PCR of short tandem repeats (STR-PCR) constitutes the gold standard method for chimerism quantification, although more sensitive PCR techniques (such as qPCR) have recently arisen. We compared the sensitivity and the quantification capacity of both techniques in patient samples and artificial mixtures and demonstrated adequate performance of both methods, with higher sensitivity of qPCR and better quantification skills of STR-PCR. By qPCR, we then prospectively followed up 57 patients that were in complete chimerism (CC) by STR-PCR. Twenty-seven patients (59%) showed 0.1–1% recipient DNA in the bone marrow. Only 4 patients presented 0.1–1% recipient DNA in peripheral blood (PB), and one of them relapsed. Finally, by qPCR, we retrospectively studied the last sample that showed CC by STR-PCR prior to relapse in 8 relapsed patients. At a median of 59 days prior to relapse, six patients presented mixed chimerism by qPCR in PB. Since both approaches have complementary characteristics, we conclude that different techniques should be applied in different clinical settings and therefore propose a methodological algorithm for chimerism follow-up after HSCT.

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“…This is also true for markers which are shared between the donor and the recipient, given the impossibility of identifying the origin of the STR alleles [ 18 , 35 , 36 , 37 , 41 ]. As claimed by Kristt et al [ 28 ] and Navarro-Bailón et al [ 34 ], this latter circumstance is more common in the case of transplantation occurring between related donor–recipient pairs than in the case of transplantation between unrelated pairs. In accordance with Lion et al [ 41 ], STR markers differing significantly in size between the donor and the recipient should also be excluded from the calculation, because their different length may result in preferential amplification of the smaller allele, which in turn may cause allelic imbalance and errors in the interpretation from a quantitative point of view.…”

“…However, even if pre-transplantation donor and recipient DNA are not available, several solutions for STR-PCR follow-up exist. Indeed, Navarro-Bailón et al [ 34 ] asserted that donor or recipient genotypes can be obtained through successive DNA extraction and analysis from buccal swab or from other biological sources. Moreover, they also stated that if only one between the donor or the recipient is available for DNA extraction, STR variability (which implies a low probability that donor and recipient share the same STR alleles) allows for the identification of the amount of recipient cells after allogeneic HSCT [ 34 ].…”

“…Indeed, Navarro-Bailón et al [ 34 ] asserted that donor or recipient genotypes can be obtained through successive DNA extraction and analysis from buccal swab or from other biological sources. Moreover, they also stated that if only one between the donor or the recipient is available for DNA extraction, STR variability (which implies a low probability that donor and recipient share the same STR alleles) allows for the identification of the amount of recipient cells after allogeneic HSCT [ 34 ]. Li et al [ 51 ] pointed out that, after the transplantation, the collection of recipient biological material through buccal swab may represent a problem given that a buccal swab after allogeneic HSCT can manifest MC.…”

“…Li et al [ 51 ] pointed out that, after the transplantation, the collection of recipient biological material through buccal swab may represent a problem given that a buccal swab after allogeneic HSCT can manifest MC. However, for Navarro-Bailón et al [ 34 ], when donor STR profile is available, it is possible to ignore those peaks of the recipient’s buccal swab electropherogram corresponding to donor alleles, permitting the ready identification of those of the recipient. Furthermore, Li et al [ 51 ] also demonstrated that the recipient’s profile could be easily obtained from other biological material, such as hair follicles or semen, for which the genome is 100% recipient type.…”

“…However, other DNA polymorphisms such as variable number of tandem repeats (VNTR), single nucleotide polymorphisms (SNPs), or insertion/deletion polymorphisms (Indel) can be used. The main reason STRs are more suitable for chimerism analysis compared with other polymorphisms is their higher informativity rate [ 31 , 32 , 33 , 34 ]. Nevertheless, a careful selection of STR alleles is required to select the most suitable STR for chimerism monitoring considering all the variables which can affect the analysis [ 18 , 35 , 36 ].…”