Quantifying variant differences in DNA melting curves: Effects of length, melting rate, and curve overlay.

High resolution DNA melting of PCR products is a simple technique for sequence variant detection and analysis. However, sensitivity and specificity vary and depend on many factors that continue to be defined. We introduce the area between normalized melting curves as a metric to quantify genotype discrimination. The effects of amplicon size (51-547 bp), melting rate (0.01-0.64 °C/s) and analysis method (curve shape by overlay vs absolute temperature differences) were qualitatively and quantitatively analyzed. To limit experimental variance, we studied a single nucleotide variant with identical predicted wild type and homozygous variant stabilities by nearest neighbor thermodynamic theory. Heterozygotes were easier to detect in smaller amplicons, at faster melting rates, and after curve overlay (superimposition), with some p-values <10-20. As heterozygote melting rates increase, the relative magnitude of heteroduplex contributions to melting curves increases, apparently the result of non-equilibrium processes. In contrast to heterozygotes, the interplay between curve overlay, PCR product size, and analysis method is complicated for homozygote genotype discrimination and is difficult to predict. Similar to temperature cycling in PCR, if the temperature control and temperature homogeneity of the solution are adequate, faster rates improve melting analysis, just like faster rates improve PCR.

Cytokeratin 19-fragments (CYFRA 21-1) as a novel serum biomarker for response and survival in patients with advanced pancreatic cancer.

BACKGROUND: CYFRA 21-1 serves as biomarker in several epithelial malignancies. However, its role in pancreatic cancer (PC) has not yet been investigated. METHODS: Within a prospective single-centre study serial blood samples were collected from patients with confirmed advanced PC. Pre-treatment values and weekly measurements of CYFRA 21-1, carbohydrate antigen 19-9 (CA 19-9) and carcinoembryonic antigen (assessed by Elecsys 2010, Roche Diagnostics) during palliative first-line chemotherapy were obtained. Biomarker data were correlated with objective response (determined by RECIST) as well as time to progression (TTP) and overall survival (OS) using uni- and multivariate analyses. RESULTS: Seventy-eight patients were included, 45% of these received treatment in prospective clinical trials. Median TTP was 3.9 months, median OS 7.7 months. Pre-treatment CYFRA 21-1 levels were significantly associated with performance status (P=0.0399) and stage of disease (P=0.0001). Marker values before chemotherapy and at the 2-month staging of all three markers were considered significant predictors for objective treatment response. Pre-treatment CYFRA 21-1 levels, as well as CA 19-9 values, could be applied to define subgroups (categorised by tertiles) with a different OS outcome (CYFRA: 14.8 vs 7.1 vs 4.8 months, CA 19-9: 14.2 vs 7.1 vs 5.2 months; P<0.0001). CYFRA 21-1 and CA 19-9 (both as categorised and as continuous variables) showed a highly significant correlation with TTP and OS at nearly all-time points assessed in univariate analysis. In multivariate analysis, only CYFRA 21-1 and performance status were independent predictors for OS. CONCLUSIONS: CYFRA 21-1 may serve as a valuable tool for monitoring treatment response and assessing prognosis in advanced PC.

Photolysis of cell-permeant caged inositol pyrophosphates controls oscillations of cytosolic calcium in a ß-cell line.

Among many cellular functions, inositol pyrophosphates (PP-InsPs) are metabolic messengers involved in the regulation of glucose uptake, insulin sensitivity, and weight gain. However, their mechanisms of action are still poorly understood. So far, the influence of PP-InsPs on cellular metabolism has been studied by overexpression or knockout/inhibition of relevant metabolizing kinases (IP6Ks, PPIP5Ks). These approaches are, inter alia, limited by time-resolution and potential compensation mechanisms. Here, we describe the synthesis of cell-permeant caged PP-InsPs as tools to rapidly modulate intracellular levels of defined isomers of PP-InsPs in a genetically non-perturbed cellular environment. We show that caged prometabolites readily enter live cells where they are enzymatically converted into still inactive, metabolically stable, photocaged PP-InsPs. Upon light-triggered release of 5-PP-InsP5, the major cellular inositol pyrophosphate, oscillations of intracellular Ca2+ levels in MIN6 cells were transiently reduced to spontaneously recover again. In contrast, uncaging of 1-PP-InsP5, a minor cellular isomer, was without effect. These results provide evidence that PP-InsPs play an active role in regulating [Ca2+]i oscillations, a key element in triggering exocytosis and secretion in ß-cells.

Metabolism of pantethine in cystinosis.

D-Pantethine is a conjugate of the vitamin pantothenic acid and the low-molecular-weight aminothiol cysteamine. Pantethine is an experimental hypolipemic agent and has been suggested as a source of cysteamine in the treatment of nephropathic cystinosis. We treated four cystinotic children with 70-1,000 mg/kg per d oral D-pantethine and studied its metabolism. Pantethine was rapidly hydrolyzed to pantothenic acid and cysteamine; we could not detect pantethine in plasma after oral administration. The responsible enzyme, "pantetheinase," was highly active in homogenates of small intestinal mucosa and plasma. The Michaelis constant of the rat intestinal enzyme was 4.6 microM and its pH profile showed a broad plateau between 4 and 9. Pantothenate pharmacokinetics after orally administered pantethine followed an open two-compartment model with slow vitamin elimination (t1/2 = 28 h). Peak plasma pantothenate occurred at 2.5 h and levels over 250 microM were seen at 300 times normal. Apparent total body storage of pantothenate was significant (25 mg/kg), and plasma levels were elevated threefold for months after pantethine therapy. Plasma cysteamine concentrations after pantethine were similar to those reported after equivalent doses of cysteamine. However, at best only 80% white blood cell cystine depletion occurred. We conclude that pantethine is probably less effective than cysteamine in the treatment of nephropathic cystinosis and should only be considered in cases of cysteamine intolerance. Serum cholesterol was decreased an average of 14%, which supports the potential clinical significance of pantethine as a hypolipemic agent. Rapid in vivo hydrolysis of pantethine suggests that pantothenate or cysteamine may be the effectors of its hypolipemic action.

Uracil-DNA glycosylase in HeLa S3 cells: interconvertibility of 50 and 20 kDa forms and similarity of the nuclear and mitochondrial form of the enzyme.

Uracil-DNA glycosylase activity in HeLa S3 cells was found in nuclei (70%), mitochondria (15%) and cytosol (15%) after fractionation in hypotonic buffers. After fractionation in isotonic buffers the activity in cytosol was increased, apparently as a consequence of leakage from the nuclei. Both in the nuclear and the mitochondrial fraction, a major 50 and a minor 18 kDa form were found after gel filtration in the presence of 0.5 M NaCl. However, after glycerol, gradient sedimentation or gel filtration in the presence of 2 M NaCl or 20% glycerol most of the 50 kDa form dissociated into a 22 kDa form, which was also the smallest catalytically active form found after partial trypsin digestion. The dissociation of the 50 kDa form was reversible. Biochemical properties of the nuclear and mitochondrial forms were very similar. Thus, they had similar apparent Km values, pH optima, heat sensitivities and activation energies, and were stimulated 2-5-fold by 40-60 mM monovalent salt.

Detection of chromosomal translocations in formalin-fixed paraffin-embedded (FFPE) leukemic specimens by digital expression profiling.

INTRODUCTION: Detection of chromosomal translocations in formalin-fixed paraffin-embedded (FFPE) leukemic samples is important for confirmation of histopathological findings, classification, prognostication, and therapeutic decisions. Herein, we aim to determine whether digital expression profiling could detect chromosomal translocations in FFPE leukemic samples identified by RT-PCR, FISH, and/or karyotyping. METHODS: RNA was extracted from 28 FFPE bone marrow specimens from 19 patients diagnosed with leukemia. Eight patients were translocation t(9;22) positive, three inv(16)/t(16/16) positive, five translocation t(15;17) positive, and one translocation t(8;21) positive. Two patients (four specimens) were normal. The extracted RNA was hybridized to DNA reporter probes overnight at 65 °C, followed by purification of the labeled translocations. Six hundred fields of view were counted to enumerate the number of translocations. RESULTS: Digital expression profiling had 100% concordance with RT-PCR, FISH, or karyotyping analysis in the two normal individuals, eight translocation t(9;22) samples, five translocation t(15;17) samples, and one translocation t(8;21) sample. None of the inv(16) positive samples were detected. Digital expression profiling detected translocations with 0.014 p190 allelic burden. CONCLUSION: Digital expression profiling can be used to measure translocation t(9;22), t(15;17), and t(8;21) in FFPE samples and is useful when a confirmatory test from a FFPE sample is necessary.

Enzymes for liberation of pantothenic acid in blood: use of plasma pantetheinase.

Reported normal concentrations for human whole-blood total pantothenic acid vary from 1.1 to 12 mumol/L. This wide range may partly arise from the various enzymes used for liberation of pantothenic acid from coenzyme A, particularly the source of pantetheinase. A purified pantetheinase from pig kidney had greater than 100 times the specific activity and less than 0.01 times the pantothenate content of other commonly used extracts. Endogenous pantetheinase activity in human plasma was identified (11.2 +/- 2.0 mumol pantothenate .min-1.L-1, n = 29) and found comparable to the activity usually added from exogenous sources for liberation of pantothenate from whole blood (1-13 mumol.min-1.L-1). Alkaline phosphatase alone liberated as much pantothenate from hemolyzed whole blood as did alkaline phosphatase with pantetheinase. Previous reports of total blood pantothenate may be elevated by pantothenate in the pantetheinase extracts, an unnecessary source of error. Whole-blood total pantothenate concentrations less than 4.6 mumol/L are normal and do not indicate deficiency, as is often currently quoted.

Pantethine lipomodulation: evidence for cysteamine mediation in vitro and in vivo.

Recent human studies suggest rapid in vivo hydrolysis of the lipid-lowering drug, pantethine, to the vitamin pantothenic acid and the small aminothiol compound, cysteamine. To test whether the active agent is a hydrolysis product, we repeated three experimental models of pantethine's effect with pantothenate and cysteamine. In vitro experiments with human fetal fibroblasts showed equivalent modulation of cholesterol and methyl sterol synthesis by pantethine, cysteamine, or cystamine (the disulfide of cysteamine), but pantothenate had no effect. Similarly, in vivo experiments with 0.5% cholesterol-fed rabbits showed oral pantethine or equimolar cystamine significantly lowered plasma cholesterol, while pantothenate, cystine, and 2-hydroxyethyl disulfide did not. Lastly, diabetic male rats (40 mg/kg streptozotocin) fed 0.1% pantethine and lower plasma free fatty acids after 2 weeks than controls, an effect not seen with pantothenate and largely duplicated by cystamine. The efficacy of pantethine has previously been attributed to altered vitamin metabolism and increased coenzyme A concentration. Pantethine did increase CoA levels 45% in rat liver homogenates while equivalent amounts of cystamine or pantothenate did not. However, a causal relationship between CoA levels and pantethine's action as a hypolipemic agent has never been shown. At least in 3 independent experimental models, the lipomodulating effect of pantethine appears instead to be mediated by the hydrolysis product cysteamine.

Prevention of adverse clinical outcome by monitoring of cardiac transplant patients for murine monoclonal CD3 antibody (OKT3) sensitization.

We have previously reported that patients sensitized to murine monoclonal CD3 antibody (OKT3) and maintained on such therapy for induction of immunosuppression have a high mortality and/or allograft loss. In this follow-up study, we retrospectively reviewed all patients routinely and serially monitored by flow cytometry for plasma levels of OKT3 during a 21-month period beginning 1/90. A total of 112 patients were monitored during this period. We retrospectively tabulated the incidence of OKT3 sensitization, rejection pattern and impact on survival of withdrawal of OKT3 at the time of sensitization as compared with the previous study in which withdrawal was not done. Nine patients were excluded from analysis because of withdrawal for reasons other than sensitization: cytokine encephalopathy, infection, postoperative complications, or severe rejection. Twelve patients had OKT3 therapy aborted because of failure to achieve steady-state OKT3 levels or because of decline in levels while on therapy. These patients were thus defined as being sensitized to OKT3. No patient was aborted because of return of CD3 cells in the blood. Only one of the 12 patients sensitized to OKT3 died. Of 91 patients with steady-state OKT3 levels, 6 had high plasma levels (> 1000 ng/ml) and 6 had low plasma levels (< 500 ng/ml). None of these patients had OKT3 therapy aborted and all are alive. Twelve of these 91 patients had successful retreatment with OKT3 for refractory rejection, indicating that absence of sensitization on induction predicts safety of retreatment with OKT3. We also examined the frequency of associated human antimouse antibody (HAMA) production using the blocking assay modified from Jaffers and Mayes. Only the sensitized patients exhibited a significant association with HAMA production (6/7 tested, P = 0.05) Classification of the rejection pattern of the sensitized patients confirmed our previous results: eight of 12 had vascular rejection and 4/12 had mixed rejection. These patterns were prospectively determined. We conclude that serial monitoring of patients for plasma levels of OKT3 is an effective strategy to prevent adverse outcomes of induction with this agent.

Relationship of OKT3 sensitization and vascular rejection in cardiac transplant patients receiving OKT3 rejection prophylaxis.

We prospectively and serially monitored plasma levels of OKT3 in 20 patients who were receiving 14- or 21-day rejection prophylaxis with OKT3. We retrospectively compared plasma OKT3 levels with biopsy scores assessed by light microscopy and immunofluorescence, clinical findings, human antimouse antibody (HAMA) production assessed by a blocking assay and by ELISA, and circulating immune complex levels assessed by a flow cytometric Raji cell assay. Using these methods, we evaluated the relationship of OKT3 sensitization, a humorally mediated immune response, to the development of vascular rejection in these patients. We found that 6 of 20 patients had declines in plasma OKT3 levels to less than 50% of their steady-state value before the conclusion of therapy (OKT3 consumption). This fall in plasma OKT3 preceded a significant rise in the CD 3 lymphocyte level by up to 3 days. All 6 patients showed HAMA production by either blocking or ELISA assay (P = less than 0.02) and developed vascular rather than cellular rejection (P = less than 0.01). OKT3 sensitization was significantly more common in patients treated with 21-day rejection prophylaxis (4 of 6 patients, P = less than 0.01). Only 4 of 14 other patients showed vascular rejection; 2 of these 4 also developed HAMA without OKT3 consumption and both had been treated with 21-day rejection prophylaxis with OKT3. None of the 20 patients showed significant levels of circulating immune complexes. This study demonstrates that OKT3 sensitization is strongly associated with vascular rejection. Vascular rejection was usually demonstrated 7 days after OKT3 consumption was seen and was coincident with HAMA production. By contrast, 4 patients without OKT3 sensitization had vascular rejection demonstrable in the early posttransplant period; in such patients, prospective immunofluorescence of biopsies was the only reliable indicator of this rejection type. The higher incidence of vascular rejection in these 20 patients was definitely related to the use of 21-day OKT3 rejection prophylaxis. Overall, 7 of the 12 patients treated with this regimen developed vascular rejection. Allograft and patient survival among patients with vascular rejection was significantly worse than in patients with cellular rejection (P = less than 0.01). Prospective monitoring of patients treated with OKT3 by serial plasma levels and by biopsy immunofluorescence will identify patients at risk for these types of humoral rejection.

Rapid cycle DNA amplification: time and temperature optimization.

Rapid temperature cycling with hot air allows rigorous optimization of the times and temperatures required for each stage of the polymerase chain reaction. A thermal cycler based on recirculating hot air was used for rapid temperature control of 10-microliters samples in thin glass capillary tubes with the sample temperature monitored by a miniature thermocouple probe. The temperatures and times of denaturation, annealing and elongation were individually optimized for the amplification of a 536-base pair beta-globin fragment from human genomic DNA. Optimal denaturation at 92 degrees-94 degrees C occurred in less than one second; yield decreased with denaturation times greater than 30 seconds. Annealing for one second or less at 54 degrees-56 degrees C gave the best product specificity and yield. Non-specific amplification was minimized with a rapid denaturation to annealing temperature transition (9 seconds) as compared to a longer transition (25 seconds). An elongation temperature of 75 degrees-79 degrees C gave the greatest yield and increased yields were obtained with longer elongation times. Product specificity was improved with rapid air cycling when compared to slower conventional heat block cycling. Rapid thermal control of the temperature-dependent reactions in DNA amplification can improve product specificity significantly while decreasing the required amplification time by an order of magnitude.

PCR amplification using electrolytic resistance for heating and temperature monitoring.

An alternative method of rapid-cycle PCR for DNA amplification is demonstrated using electrolyte resistance for heating and temperature monitoring. The PCR amplification solution is electrically conductive and can be heated by passing an alternating current through the sample. The temperature of the solution is evaluated by monitoring its electrical resistance. Cooling is accomplished by forced air convection at ambient temperature. Heating and cooling rates of up to 20 degrees C/s were achieved. The 35 cycles of PCR were completed in less than 12 min with product yields equivalent to conventional temperature cycling. Electrolyte resistance provides a method for both direct heating and monitoring the temperature of PCR samples.

Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification.

Continuous fluorescence observation of amplifying DNA allows rapid and accurate quantification of initial transcript copy number. A simple and generic method for monitoring product synthesis with the double-stranded DNA dye, SYBR Green I provides initial template copy number estimation limited only by stochastic effects. To reach this degree of sensitivity, two methods were used. First, specific products generally have a higher melting temperature than nonspecific products, and therefore, specific product formation was monitored by fluorescence acquisition at temperatures at which only specific products are double-stranded. Second, anti-Taq antibodies were used to reduce nonspecific product generation. The log-linear portion of the fluorescence vs. cycle plot was extended to determine a fractional cycle number at which a threshold fluorescence was obtained. These fractional cycle numbers were plotted against the log of starting template copies to give linear standard curves from purified PCR products, allowing easy estimation of cDNA unknowns over a 10(6)-fold range. A single template molecule per reaction could be distinguished from the absence of template, although stochastic effects increased the variance of concentration estimates below 10 copies. Above 10 copies per reaction, typical replicate coefficients of variation were 6%-37%, with better precision at higher copy numbers.

Continuous fluorescence monitoring of rapid cycle DNA amplification.

Rapid cycle DNA amplification was continuously monitored by three different fluorescence techniques. Fluorescence was monitored by (i) the double-strand-specific dye SYBR Green I, (ii) a decrease in fluorescein quenching by rhodamine after exonuclease cleavage of a dual-labeled hydrolysis probe and (iii) resonance energy transfer of fluorescein to Cy5 by adjacent hybridization probes. Fluorescence data acquired once per cycle provides rapid absolute quantification of initial template copy number. The sensitivity of SYBR Green I detection is limited by nonspecific product formation. Use of a single exonuclease hydrolysis probe or two adjacent hybridization probes offers increasing levels of specificity. In contrast to fluorescence measurement once per cycle, continuous monitoring throughout each cycle monitors the temperature dependence of fluorescence. The cumulative, irreversible signal of hydrolysis probes can be distinguished easily from the temperature-dependent, reversible signal of hybridization probes. By using SYBR Green I, product denaturation, annealing and extension can be followed within each cycle. Substantial product-to-product annealing occurs during later amplification cycles, suggesting that product annealing is a major cause of the plateau effect. Continuous within-cycle monitoring allows rapid optimization of amplification conditions and should be particularly useful in developing new, standardized clinical assays.

The LightCycler: a microvolume multisample fluorimeter with rapid temperature control.

Experimental and commercial microvolume fluorimeters with rapid temperature control are described. Fluorescence optics adopted from flow cytometry were used to interrogate 1-10-microL samples in glass capillaries. Homogeneous temperature control and rapid change of sample temperatures (10 degrees C/s) were obtained by a circulating air vortex. A prototype 2-color, 32-sample version was constructed with a xenon arc for excitation, separate excitation and emission paths, and photomultiplier tubes for detection. The commercial LightCycler, a 3-color, 24-sample instrument, uses a blue light-emitting diode for excitation, paraxial epi-illumination through the capillary tip and photodiodes for detection. Applications include analyte quantification and nucleic acid melting curves with fluorescent dyes, enzyme assays with fluorescent substrates and techniques that use fluorescence resonance energy transfer. Microvolume capability allows analysis of very small or expensive samples. As an example of one application, rapid cycle DNA amplification was continuously monitored by three different fluorescence techniques, Which included using the double-stranded DNA dye SYBR Green I, a dual-labeled 5'-exonuclease hydrolysis probe, and adjacent fluorescein and Cy5z-labeled hybridization probes. Complete amplification and analysis requires only 10-15 min.

Aprosencephaly and cerebellar dysgenesis in sibs.

Aprosencephaly is a rare, lethal malformation sequence of the central nervous system that has been attributed to a postneuralation encephaloclastic process. We describe autopsy findings consistent with aprosencephaly in 2 fetuses conceived from a consanguineous mating (first cousins). Both showed anencephalic manifestations; however, the crania were intact, with fused sutures. The neuropathologic findings were essentially identical. Each fetus had complete absence of the telecephalon and pyramidal tracts, rudimentary diencephalic and mesencephalic structures, primitive cerebellar hemispheres, posterolateral clusters of primitive neural cells in the medullas suggesting an abnormality of neural migration, a normally-formed spinal cord, and retinal dysplasia within normally-formed globes. In addition, both fetuses manifested a peculiar perivascular mesenchymal proliferation seen only within the central nervous system. The similarity of these cases, coupled with parental consanguinity, suggests a primary malformation in brain development due to the homozygous representation of a mutant allele. We hypothesize that these patients may represent a defect in a gene important in brain development, the nature of which has yet to be elucidated.

Cytomegalovirus infection, fetal liver disease, and neonatal hemochromatosis.

Neonatal hemochromatosis is an uncommon disorder, clinicopathologically defined by severe and generally fatal liver disease of intrauterine onset associated with extrahepatic siderosis that spares reticuloendothelial elements (hemochromatotic siderosis). The agent or agents of liver disease in neonatal hemochromatosis are not known. It also is not known if intrauterine liver disease of defined infective etiology can lead to hemochromatotic siderosis. We present two patients with fetal liver disease and hemochromatotic siderosis whose cases help address these points. In the first patient rare hepatobiliary and numerous renal tubular cytomegalovirus (CMV) inclusions were found; CMV infection was confirmed by the polymerase chain reaction. Studies of the mother of the second patient 1, 5, and 9 weeks post-partum showed recent seroconversion against CMV; seroconversion against other infectious agents (toxoplasma, rubella, herpes, parvovirus B19, hepatitis A/B/C) was not present. Histologic, immunohistochemical, in situ hybridization, or polymerase chain reaction evidence of CMV infection was not present in infant tissues, even though peripartum maternal seroconversion against CMV was observed. We conclude that hemochromatotic siderosis may accompany chronic fetal liver disease of defined infective etiology (patient no. 1) and that recent maternal seroconversion against CMV in the presence of severe fetal liver disease does not necessarily mean that transplacentally acquired CMV infection caused the fetal liver disease (patient no. 2). Polymerase chain reaction documentation of infective-agent genomic sequences in fetal or infant tissues permits more accurate interpretation of maternal serologic data.

Sensitization to OKT3 monoclonal antibody in heart transplantation: correlation with early allograft loss.

Because administration of murine monoclonal anti-CD3 antibody (OKT3) may result in the formation of human antimouse antibody, which complexes with OKT3, we conducted this study to assess the incidence and effect of human antimouse antibody formation during prophylactic administration of OKT3 in heart transplantation. Human antimouse antibody developed in eight of 55 (14%) cardiac allograft recipients receiving OKT3 prophylaxis as measured by enzyme-linked immunosorbent assay. Additionally, two recipients had an inexplicable rise in CD3+ lymphocytes during therapy without detectable antibody. The outcome of these 10 sensitized recipients was compared with that of 45 nonsensitized recipients. Age, preoperative diagnosis, hemodynamics, and the need for intravenous inotropes or mechanical assistance before transplantation were similar in both groups. No female patients were in the sensitized group, whereas 33% of the nonsensitized group were female patients. A trend toward greater sensitization when prophylaxis was extended to 21 days (28%) compared with the more conventional 14-day administration (10%) was not statistically significant. Retransplantation because of rejection was required in a single patient in each group. Allograft survival was significantly lower by 3 months in the sensitized group, and allograft loss caused by rejection selectively accounted for that difference. In survivors, rejection frequency and infectious complications were similar. These findings suggest that sensitization to OKT3 occurs at low frequency after prophylactic administration in heart transplantation but is associated with an increased frequency of graft loss because of rejection.

Detection of bcl-1 gene rearrangement and B-cell clonality in mantle cell lymphoma using formalin-fixed, paraffin-embedded tissues.

Mantle cell lymphoma (MCL) has recently emerged as a distinct clinicopathologic entity with characteristic molecular genetic features. Specifically, MCL are clonal B-cell neoplasms and often harbor bcl-1 gene rearrangements. Although this genetic profile is well documented, scant or no data are available on the molecular assessment of MCL using formalin-fixed, paraffin-embedded tissue as a sample source. The polymerase chain reaction (PCR) was employed to study bcl-1 and immunoglobulin heavy chain (IgH) gene rearrangements (B-cell clonality) using formalin-fixed tissue from 12 cases of MCL. In addition, 12 cases of low grade B-cell lymphoma and 5 cases of reactive lymphocytic hyperplasia were studied as comparison controls. A hemi-nested PCR assay was developed to identify major translocation cluster (MTC) bcl-1 gene rearrangements, whereas IgH gene rearrangements were evaluated by both a single-step and hemi-nested approach. Bcl-1 gene rearrangements were amplified in 4 of 12 (33%) MCL, but in none of the controls. With the hemi-nested approach, B-cell monoclonality was demonstrated in 11 of 12 (92%) MCL; 6 of 6 (100%) small lymphocytic lymphomas; 1 of 2 marginal zone lymphomas; 1 of 4 follicular lymphomas; and 0 of 5 reactive lymphocytic hyperplasias. When one-step PCR was used for B-cell clonality assessment, the overall detection rate was lower, specifically: 8 of 12 (67%) MCL; 4 of 6 (67%) small lymphocytic lymphomas; 1 of 2 marginal zone lymphomas; 0 of 4 follicular lymphomas; and 0 of 5 reactive lymphocytic hyperplasias were identified as monoclonal. We have demonstrated that MTC bcl-1 gene rearrangements can be amplified from formalin-fixed tissue. In addition, monoclonal B-cell populations from MCL are better amplified with a hemi-nested approach rather than a single-step PCR assay. With specialized nucleic acid isolation techniques and appropriate PCR protocol design, formalin-fixed, paraffin-embedded tissue is an adequate source of DNA for assessing MTC bcl-1 and IgH gene rearrangements.