Quantitation of follicular non-Hodgkin's lymphoma cells carrying t(14;18) in a patient before and after allogeneic bone marrow transplantation

Statistical algorithm for assuring similar efficiency in standards and samples for absolute quantification by real-time reverse transcription polymerase chain reaction

Reverse transcription (RT) followed by the polymerase chain reaction (PCR) is the method of choice for quantifying rare transcripts in biological samples. A key assumption underlying the absolute quantification of transcripts is similar amplification efficiencies of all external standards and samples. However, efficiencies can vary between individual reactions, a problem that can be magnified when quantifying transcripts of low abundance. Here, an algorithm to assure that calibration standards and samples meet the assumption of similar amplification efficiencies underlying absolute quantification is presented. Individual reaction efficiency is estimated by fitting an exponential growth model to the fluorescence data in the exponential phase of the reaction. Next, reactions of standards with outlying estimates of amplification rates are eliminated using the boxplot outlier detection rule. Then, estimates of amplification rates of outlier-free standards are employed to define exact tolerance intervals, which are used to eliminate kinetic outliers from test samples. This algorithm was employed to eliminate kinetic outliers prior to defining the baseline expression of guanylyl cyclase C mRNA, a marker for colorectal cancer, in blood of healthy volunteers. These studies demonstrate that elimination of kinetic outliers from calibration standards and test samples improves the accuracy of absolute transcript quantification by RT-PCR.

Tumor load in patients with follicular lymphoma post stem cell transplantation may correlate with clinical course

The purpose of this study was to evaluate if the tumor load, as determined by a real-time quantitative PCR (RQ-PCR) assay, correlated with the clinical course of follicular lymphoma patients after stem cell transplantation (SCT). Cryopreserved bone marrow and/or peripheral blood samples obtained at different time intervals after SCT from 11 patients (seven allogeneic, T-cell depleted/four autologous) were tested for tumor load, as defined by t(14;18) positive cells/total cells, using RQ-PCR. None of the six patients who remained in remission had samples with a tumor load >0.01% after SCT, although fluctuating tumor loads of </=0.01% were observed in three of these patients. In contrast, four of the five patients (three allogeneic/two autologous) with relapsed/progressive disease had increasing tumor loads of >0.01% after SCT (0/6 vs 4/5, P<0.02, Fisher's exact). Our results suggest that RQ-PCR measurable tumor load >0.01% after SCT may correlate with relapsed/progressive disease. Prospective studies with greater numbers of cases are indicated to better determine the critical tumor load that predicts poor outcome after SCT with RQ-PCR.

Allogeneic haemopoietic stem cell transplantation for non-Hodgkin's lymphoma

This chapter outlines the rationale for allogeneic haemopoietic stem cell transplantation in non-Hodgkin's lymphoma and pertinent results from published studies. Trials comparing allogeneic with autologous transplantation are discussed, as are disease-specific results for low-grade (including transformed), mantle cell and high-grade (Burkitt's and lymphoblastic) subtypes of the disease. Allogeneic transplantation for non-Hodgkin's lymphoma in the paediatric population, the use of unrelated donors, allografting after failed autologous or allogeneic transplantation, the graft-versus-lymphoma effect, the use of donor leukocyte infusions and non-myeloablative allografts are considered.

Lack of correlation between numbers of circulating t(14;18)-positive cells and response to first-line treatment in follicular lymphoma

In follicular lymphoma, the t(14;18) status of the peripheral blood and bone marrow analyzed by polymerase chain reaction (PCR) is assumed to correlate with disease activity in patients with relapsed disease. The clinical significance of quantitating circulating lymphoma cells by real-time PCR is reported in patients on first-line treatment. Thirty-four consecutive patients with previously untreated follicular lymphoma and detectable t(14;18)-positive cells in pretreatment peripheral blood samples were monitored. All patients were treated with standard chemotherapy in combination with interferon alfa-2b. Before and after induction therapy, blood samples were taken for quantitative analysis of t(14;18). At presentation, a median of 262 t(14;18)-positive cells per 75,000 normal cells was found (range, 1-75 000). Patients with lower numbers of circulating tumor cells more frequently had bulky disease (P =.02). Seventy-nine percent of the patients responded clinically to treatment. In 22 of 28 patients, including 4 patients in whom treatment had failed clinically, the number of circulating t(14;18)-positive cells decreased to undetectable or low levels after therapy. In the remaining responding patients, circulating tumor cells persisted after therapy. These quantitative data on circulating t(14;18)-positive cells call into question the usefulness of molecular monitoring of the blood in a group of patients with follicular lymphoma uniformly treated with a noncurative first-line regimen. T(14;18)-positive cells decreased in peripheral blood after treatment, irrespective of the clinical response. Therefore, the significance of so-called molecular remission should be reconsidered in follicular lymphoma. (Blood. 2001;98:940-944)

A novel method to compensate for different amplification efficiencies between patient DNA samples in quantitative real-time PCR

Quantification of residual disease by real-time polymerase chain reaction (PCR) will become a pivotal tool in the development of patient-directed therapy. In recent years, various protocols to quantify minimal residual disease in leukemia or lymphoma patients have been developed. These assays assume that PCR efficiencies are equal for all samples. Determining t(14;18) and albumin reaction efficiencies for sixteen follicular lymphoma patient samples revealed higher efficiencies for blood samples than for lymph node samples in general. However, within one sample both reactions had equivalent efficiencies. Differences in amplification efficiencies between patient samples (low efficiencies) and the calibrator in quantitative analyses result in the underestimation of residual disease in patient samples whereby the weakest positive patient samples are at highest error. Based on these findings for patient samples, the efficiency compensation control was developed. This control includes two reference reactions in a multiplex setting, specific for the beta-actin and albumin housekeeping genes that are present in a constant ratio within DNA templates. The difference in threshold cycle values for both reference reactions, ie, the Ct(2) value, is dependent on the amplification efficiency, and is used to compensate for efficiency differences between patient samples and the calibrator. The beta-actin reference reaction is also used to normalize for DNA input. Furthermore, the efficiency compensation control facilitates identification of patient samples that are so contaminated with PCR inhibitory compounds that different amplification reactions are affected to a different extent. Accurate quantitation of residual disease in these samples is therefore impossible with the current quantitative real-time PCR protocols. Identification and exclusion of these inadequate samples will be of utmost importance in quantitative retrospective studies, but even more so, in future molecular diagnostic analyses.

Development and validation of a quantitative polymerase chain reaction assay to evaluate minimal residual disease for T-cell acute lymphoblastic leukemia and follicular lymphoma

The presence of occult disease in cancer patients after therapy is one of the major problems faced by oncologists. For example, although 95% of pediatric T-cell acute lymphoblastic leukemia (T-ALL) patients have a complete therapeutic response to multiagent chemotherapy, half will relapse, indicating that they must have harbored low levels of residual cancer cells at the end of therapy. Sensitive detection assays promise to help identify those patients that carry this minimal residual disease (MRD) and are at risk of relapse. We have developed and validated a quantitative polymerase chain reaction (PCR) assay targeting tumor-specific chromosomal rearrangements, including del(1) involving the tal-1 locus in pediatric T-ALL and t(14;18) involving the bcl-2 locus in follicular lymphoma. This quantitative PCR assay utilizes a synthetic internal calibration standard (ICS) that contains priming sequences identical to those found flanking the chromosomal rearrangement breakpoints. Using this ICS-PCR method, the limits of detection were 5 tumor cells at ratios of 1 tumor cell in 10(5) normal cells and a linear range up to 100% tumor cells. This ICS-PCR method has also performed well in terms of precision and accuracy as indicated by low coefficients of variation, minimal random, proportional, and constant errors, and good clinical sensitivity and specificity characteristics. This technique will allow for the evaluation of parameters such as the rate of therapeutic response and the levels of MRD as predictors of patient outcome.

Allogeneic bone marrow transplantation with T-cell-depleted marrow grafts for patients with poor-risk relapsed low-grade non-Hodgkin's lymphoma

We present the clinical results of allogeneic bone marrow transplantation (BMT) with T-cell-depleted grafts from HLA-matched sibling donors in patients with poor-risk relapsed low-grade non-Hodgkin's lymphoma (NHL). Poor risk was defined as relapse within 12 months after or progression during prior treatment. The conditioning regimen consisted of cyclophosphamide and total-body irradiation with or without additional idarubicin. Donor marrow was depleted of T lymphocytes using counterflow centrifugation. Post-BMT prophylaxis of graft-versus-host disease (GvHD) consisted of cyclosporine A. 15 patients with a median age of 47 years (range 30-57) were transplanted. All patients engrafted. After a median follow-up of 36 months (range 9-78), 10 patients were alive and in complete remission (CR). Two of them had relapsed after BMT but re-entered CR following infusions of leucocytes from the original bone marrow donor. Five patients died; causes of death were cardiomyopathy (n = 1), chronic GvHD (n = 1) and infection during chronic GvHD (n = 3). We conclude that allogeneic T-cell-depleted bone marrow transplantation is an efficacious treatment for patients with poor-risk relapsed low-grade NHL. Infusions of donor leucocytes reinduced CR in the two patients with relapse after BMT.

Minimal residual disease post-bone marrow transplantation for hemato-oncological diseases

The detection of minimal residual disease (MRD), which is important in cancer treatment, gained special significance in bone marrow transplantation (BMT-) due to the possibility not just to detect but recently also to prevent, treat and reinduce remission in patients that relapsed post-BMT by immunotherapy. The various modern techniques of MRD detection are described including cytogenetics, analysis of restriction fragment length polymorphism, variable number of tandem repeats by Southern Blot or polymerase chain reaction (PCR), microsatellite sequences, PCR amplification products of the Y chromosome or the Amelogenin gene, quantitative PCR and fluorescence in situ hybridization. The role of MRD detection in refinement of indications for BMT, autografting, prediction of relapse, adoptive immunotherapy, mixed chimerism in nonmalignant diseases and in solid organ transplantation is discussed.

Quantitative analysis of DNA aberrations amplified by competitive polymerase chain reaction using capillary electrophoresis

We compared the use of capillary electrophoresis (CE) in a polymer network with the use of slab gel electrophoresis for the quantitative analysis of polymerase chain reaction (PCR)-amplified DNA samples. We quantified residual lymphoma cells carrying a translocation between chromosomes 14 and 18, in consecutive patient peripheral blood samples that were amplified by competitive PCR. For CE analysis we used a 4% linear polyacrylamide network. Results show that the calculated number of translocations in patient samples using both analyses were comparable. We conclude that CE is a sensitive, non-radioactive, fast and accurate method for quantitation of competitive PCR products.