Highly Sensitive Patient-Specific Real-Time PCR SNP Assay for Chimerism Monitoring after Allogeneic Stem Cell Transplantation

Designing and experimental evaluation of gene-specific primers of pea (Pisum sativum) defense proteins

Real-time gene expression analysis by semi-quantitative and quantitative RT-PCR requires a set of gene-specific primers which should have the ability to amplify the gene of interest specifically. In the present study, we have standardized certain parameters for primer design using the freely available Primer3 software. We have designed the primers for defense genes such as ICS (isochorismate synthase), CCoAOMT (caffeoyl CoA O-methyltransferase), C4H (cinnamate 4-hydroxylase), and G-alpha in pea. We have also discussed, the way of sequence retrieval, when the sequence is not reported in the organism of interest. We have evaluated the designed primers using cDNA prepared from mRNA isolated from the pea leaves. By analyzing the results, we have found that primers are perfectly binding with the target and giving single sharp band on a DNA electrophoresis gel. It can be concluded that the parameters used for primer designing by Primer3 play a critical role in the experimental results and parameters defined in the present study resulting in a very good amplification during PCR.

Monitoring of hematopoietic chimerism by real-time quantitative PCR of micro insertions/deletions in samples with low DNA quantities

BACKGROUND

Sensitive and accurate methods to detect hematopoietic chimerism after hematopoietic stem cell transplantation (HSCT) are essential to evaluate engraftment and to monitor response to therapeutic procedures such as donor lymphocyte infusion. Continuous long-term follow up, however, requires large amounts of pre-HSCT samples limiting the application of many widely used techniques for sensitive chimerism monitoring.

METHODS

DNAs from 42 normal healthy donors and 16 HSCT donor/recipient pairs were employed to validate the use of allele-specific insertion/deletion (indel) quantitative real-time polymerase chain reaction (qPCR) to quantify chimerism in samples with low amounts of DNA. Consequently, indel-qPCR analyses of samples from 16 HSCT patients were compared to short-tandem repeat (STR) specific PCR analyses.

RESULTS

Typing with reduced amounts of input DNA (15 vs. 60 ng) allowed for the reliable distinction of positive (mean threshold cycle (ct) 28.05) and negative (ct >36) signals. The high informativity of primer/probe sets, with 12 out of 19 markers exceeding 20% informativity, was confirmed in our cohort (n = 74). Importantly, a fourfold reduction of input DNA compared to published protocols did not alter PCR efficiencies and allowed for a more sensitive detection of chimerism in 7 of 16 HSCT patients compared to results obtained by STR-PCR.

CONCLUSIONS

Our data suggest that indel-qPCR is a more sensitive technique for the detection of hematopoietic chimerism compared to STR-PCR and works efficiently for samples with low amounts of DNA.

Chimerism analysis following hematopoietic stem cell transplantation

Allogeneic hematopoietic stem cell transplantation (HSCT) is an effective therapeutic approach for several hematological diseases. Chimerism studies can be helpful to assess donor engraftment, detect early signs of graft rejection, and monitor minimal residual disease. Currently the most common method for monitoring chimerism following HSCT is by PCR amplification of STR loci followed by capillary electrophoresis. Prior to transplantation, multiple STR loci in both the donor and recipient are analyzed in order to identify loci that differentiate the two individuals. Informative loci are selected to calculate the percent donor and recipient present in post-transplant specimens. This is a rapid, sensitive, and cost-effective method for monitoring chimerism in patients following HSCT.

Recent advances in quantitative chimerism analysis

Quantitative chimerism analysis is a diagnostic tool used to monitor engraftment kinetics after allogeneic stem cell transplantation. It reflects the proportion of recipient and donor genotypes and is based on the identification of genetic markers characteristic to a given transplant pair. Currently, PCR amplification of short tandem repeats and single-nucleotide polymorphism-specific quantitative real-time PCR are the most widely used techniques for this purpose. In this review, we will address advances as well as technology-specific imperfections, of both techniques that have emerged over the recent years. We will discuss new principles that may simplify assay design, and improve its robustness and reliability. A better chimerism assay could then guide clinical interventions and may, eventually, improve the outcome of allogeneic stem cell transplantation.

Single nucleotide polymorphism-based system improves the applicability of quantitative PCR for chimerism monitoring

Recently, several studies demonstrated the feasibility of a real-time quantitative PCR (qPCR) approach for chimerism monitoring. qPCR offers a fast, sensitive, and elegant quantification of genotypes. However, before it becomes an established method for routine chimerism monitoring, a qPCR marker set for every transplant pair should be available. This requirement poses a major challenge since the genetic markers for qPCR--short insertions/deletions (Indels) and single nucleotide polymorphisms (SNPs)--published to-date do not guarantee applicability for every transplant pair. The aim of our study was to design and validate a new SNP allele-specific system to supplement an already existing Indel primer panel and improve applicability of the qPCR approach for chimerism status monitoring. Here, we present an approach for an economical in-house design of SNP allele-specific qPCR primers/probe sets with a locus-individualized reference system that allows for the accurate quantification of the respective informative locus using a simple DeltaDeltaCt method. We designed primers/probe sets specific for seven biallelic SNP loci and validated them in a population of 30 transplant pairs. Repeatability varied depending on the amount of quantifiable genotype. The combination of our SNP-qPCR system and Indel primers increased recipient genotype identification from 86.6% to 96.6% when tested in a population of our transplant pairs. These results demonstrate the feasibility of our SNP-based qPCR approach to improve the applicability of a qPCR for chimerism monitoring.

Assessing quantitative chimerism longitudinally: technical considerations, clinical applications and routine feasibility

In this review, we describe the current laboratory approach to quantitative chimerism testing based on short tandem repeats (STRs), focusing on a longitudinal analysis. The latter is based on relative changes appearing in the course of sequential samples, and as such exploits the ultimate potential of this intrinsically semiquantitative platform. Such an analysis is more informative than single static values, less likely to be confused with platform artifacts, and is individualized to the particular patient. It is particularly useful with non-myeloablative conditioning, where mixed chimerism is common. Importantly, longitudinal monitoring is a routinely feasible laboratory option because multiplex STR-polymerase chain reaction kits are available commercially, and modern software can be used to perform computation, reliability testing and longitudinal tracking in a rapid, easy to use format. The ChimerTrack application, a shareware, user friendly program developed for this purpose, produces a report that automatically summarizes and illustrates the quantitative temporal course of the patient's chimeric status. Such a longitudinal perspective enhances the value of quantitative chimerism monitoring for decisions regarding immunomodulatory post transplant therapy. This information also provides unique insights into the biological dynamics of engraftment underlying the fluctuations in the temporal course of a patient's chimeric status.