Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management.

Targeted next-generation sequencing panels are increasingly used to assess the value of gene mutations for clinical diagnostic purposes. For assay development, amplicon-based methods have been preferentially used on the basis of short preparation time and small DNA input amounts. However, capture sequencing has emerged as an alternative approach because of high testing accuracy. We compared capture hybridization and amplicon sequencing approaches using fresh-frozen and formalin-fixed, paraffin-embedded tumor samples from eight lymphoma patients. Next, we developed a targeted sequencing pipeline using a 32-gene panel for accurate detection of actionable mutations in formalin-fixed, paraffin-embedded tumor samples of the most common lymphocytic malignancies: chronic lymphocytic leukemia, diffuse large B-cell lymphoma, and follicular lymphoma. We show that hybrid capture is superior to amplicon sequencing by providing deep more uniform coverage and yielding higher sensitivity for variant calling. Sanger sequencing of 588 variants identified specificity limits of thresholds for mutation calling, and orthogonal validation on 66 cases indicated 93% concordance with whole-genome sequencing. The developed pipeline and assay identified at least one actionable mutation in 91% of tumors from 219 lymphoma patients and revealed subtype-specific mutation patterns and frequencies consistent with the literature. This pipeline is an accurate and sensitive method for identifying actionable gene mutations in routinely acquired biopsy materials, suggesting further assessment of capture-based assays in the context of personalized lymphoma management.

Epstein-Barr virus DNAemia in Iranian liver transplant recipients and assessment of its variation in posttransplant lymphproliferative disorder patients by quantitative polymerase chain reaction assay.

OBJECTIVES: Epstein-Barr virus primary infection and/or reactivation may play a major role in the incidence of posttransplant lymphoproliferative disorder in organ recipients. We assessed Epstein-Barr virus viral load in liver transplant patients suspected of having Epstein-Barr virus/ posttransplant lymphoproliferative disorder at specified times after transplant and evaluated the clinical findings and posttransplant complications. MATERIALS AND METHODS: In the 696 patients who underwent liver transplant in this retrospective study, Epstein-Barr virus viral load was examined intermittently in 127 liver transplant recipients who were suspected to have Epstein-Barr virus infection/disease. Sampling was performed during 4 years from July 2009 to May 2013 using real-time polymerase chain reaction assay. Clinical and pathologic data were gathered by reviewing medical records. RESULTS: There were 78 of the 127 suspected patients (61%) who exhibited Epstein-Barr virus DNAemia and 19 patients had posttransplant lymphoproliferative disorder. The median EBV viral load of posttransplant lymphoproliferative disorder patients was significantly higher than unaffected patients. Posttransplant lymphoproliferative disorder was diagnosed clinically in 34 subjects (4.9%). Estimated mortality rate of posttransplant lymphoproliferative disorder patients was 35% during 1.5-year follow-up after transplant. CONCLUSIONS: Monitoring Epstein-Barr virus load may enable detection of Epstein-Barr virus infection/disease in liver transplant patients suspected of having the virus, even several weeks before the onset of any clinical manifestations, especially in pediatric patients who have high incidence and mortality from posttransplant lymphoproliferative disorder.

Racial variation in the development of posttransplant lymphoproliferative disorders after renal transplantation.

BACKGROUND: We previously reported that posttransplant lymphoproliferative disorders (PTLD) occurred more frequently in non-African American (AF) kidney transplant recipients. An in-depth analysis of racial differences in the development of PTLD has not been reported. METHODS: We assessed Medicare claims for PTLD in a retrospective cohort of 53,719 patients who underwent transplantation from January 2000 to September 2006 and followed up through December 2007. RESULTS: There were 719 (1.3%) patients with claims for PTLD. Non-AF recipient race (including all races analyzed separately, adjusted hazard ratio [AHR] 1.38, 95% confidence interval [CI] 1.13-1.68), recipient Epstein-Barr virus (EBV) immunoglobulin G (IgG) seronegative status (AHR 1.88, 95% CI 1.53-2.34), and de novo sirolimus (AHR 1.22, 95% CI 1.03-1.45) were associated with an increased risk of PTLD. Furthermore, de novo sirolimus showed a significant interaction with EBV IgG; among EBV IgG-negative recipients, sirolimus use was significant (P = 0.003), but among EBV IgG-positive recipients, it was not significant (P = 0.18). EBV IgG-seronegative status was significant in all races except for AFs, and racial differences were a significant effect modifier for EBV IgG status and risk of PTLD. Mortality subsequent to PTLD did not differ by race. CONCLUSIONS.: AF kidney transplant recipients were at lower risk for PTLD, irrespective of the recipient EBV IgG serostatus. On the contrary, recipient EBV IgG-seronegative status was associated with a higher risk of PTLD in the non-AF population. De novo sirolimus therapy was associated with increased risk of PTLD in EBV IgG-negative recipients, regardless of race.

Serum-free light chain assessment in hepatitis C virus-related lymphoproliferative disorders.

OBJECTIVE: To evaluate the relevance of serum-free light chain (FLC) assessment in hepatitis C virus (HCV)-related lymphoproliferative disorders, including mixed cryoglobulinemia (MC) and B cell non-Hodgkin lymphoma (B-NHL). PATIENTS AND METHODS: A total of 59 patients infected with HCV were prospectively followed, including patients without MC (n = 17), with asymptomatic MC (n = 7) and with MC vasculitis (n = 35, 9 of whom had B-NHL). Clinical and biological data were recorded at the time of the initial evaluation and at the end of follow-up. Serum FLC quantitation was carried out using a serum FLC assay. RESULTS: The mean (SD) serum kappa FLC level was higher in patients with asymptomatic MC (27.9 (8.6) mg/litre), MC vasculitis (36.7 (46.2) mg/litre) and B-NHL (51.3 (78.3) mg/litre) than without MC (21.7 (17.6) mg/litre) (p = 0.047, 0.025 and 0.045, respectively). The mean serum FLC ratio was higher in patients with MC vasculitis (2.08 (2.33)) and B-NHL (3.14 (3.49)) than in patients without MC (1.03 (0.26)) (p = 0.008). The rate of abnormal serum FLC ratio (>1.65) correlated with the severity of HCV-related B cell disorder: 0/17 (0%) without MC, 0/7 (0%) asymptomatic MC, 6/26 (23%) MC vasculitis without B-NHL and 4/9 (44%) B-NHL (p = 0.002). Serum kappa FLC levels and the serum FLC ratio correlated with the cryoglobulin level (r = 0.32, p<0.001 and r = 0.25, p = 0.002, respectively) and the severity of the B cell disorder (r = 0.26, p = 0.045 and r = 0.41, p = 0.001, respectively). Among patients with an abnormal serum FLC ratio at baseline, the FLC ratio correlated with the virological response to HCV treatment. CONCLUSIONS: In patients infected with HCV, an abnormal serum FLC ratio appears to be a very interesting marker, as it is consistently associated with the presence of MC vasculitis and/or B-NHL. After antiviral therapy, the serum FLC ratio could be used as a surrogate marker of the control of the HCV-related lymphoproliferation.

The modification of high-dose therapy shortens the duration of neutropaenia by delay of leucocyte nadir.

Infections during neutropaenia contribute still significantly to mortality and morbidity after high-dose therapy and autologous stem cell transplantation. Further acceleration of haemopoietic recovery seems impossible for biological reasons. Another approach to shorten neutropaenia could be to remove drugs from high-dose therapy protocols with strong contribution to immunosuppression and neutropaenia and unproven antineoplastic activity. In this retrospective matched-pair analysis, conventional busulphan/cyclophosphamide (Bu/Cy) high-dose therapy was compared to single-agent busulphan conditioning before autologous stem cell transplantation. This modification led to a significant shorter neutropaenic interval by protraction of cell decrease and to a significant mitigation of neutropaenia. After single-agent busulphan conditioning, leucocytes dropped below 1/nl at median 1.5 days later when compared to the patients from the busulphanBu/Cy control group (P=0.001). In a significant percentage of patients (n=6, 60%) leucocytes did not fall below 0.5 cells/nl at any time. In contrast, all patients from the Bu/Cy control group experienced deep neutropaenia (P=0.004). Thrombocytopaenia and requirement for transfusions of platelets or red cells were not influenced. Antineoplastic activity seemed to be preserved as determined by survival analysis. In conclusion, modification of high-dose regimen with the intention to shorten neutropaenia with preserved antitumour activity could be an approach to reduce infection-related morbidity and mortality and to consider economic necessities.

Assessment of automated DNA extraction coupled with real-time PCR for measuring Epstein-Barr virus load in whole blood, peripheral mononuclear cells and plasma.

BACKGROUND: Epstein-Barr virus (EBV) DNA load monitoring in blood has been shown to be essential for the diagnosis of EBV-associated diseases. However, the methods currently used to assess EBV DNA load are often time-consuming and require prior blood separation. OBJECTIVES: The aim of this study was to evaluate the relative diagnostic value of EBV DNA load monitoring in whole blood, peripheral blood mononuclear cells (PBMCs) and plasma after automated DNA extraction using the MagNA Pure extractor followed by LightCycler real-time quantitative PCR (LC-PCR). STUDY DESIGN: First, EBV DNA load was assessed retrospectively after automated or manual extraction on 104 PBMC specimens. Second, EBV DNA load was determined prospectively with the automated extraction procedure in the whole blood, PBMCs and plasma of 100 samples from patients with EBV-related diseases (group 1, n = 20), HIV-seropositive individuals (group 2, n = 66), and healthy EBV carriers (group 3, n = 14). RESULTS: A good correlation was observed between automated and manual extraction on 104 PBMC specimens (r = 0.956; P < 0.0001). In the prospective study, 67 samples were positive in both whole blood and PBMCs, with a good correlation between EBV DNA loads in whole blood and PBMCs (r = 0.936; P < 0.0001). Only 18/100 samples were positive in plasma. Higher viral loads were regularly observed in the three blood compartments from group 1 than from groups 2 and 3. CONCLUSION: This study demonstrated that an automated extraction of EBV DNA is easier to perform in whole blood or plasma than in PBMCs and facilitates the standardisation of EBV DNA measurement by real-time quantitative PCR. The quantitative detection of EBV DNA load in whole blood appeared more sensitive than in plasma for infectious mononucleosis in immunocompetent patients, probably because of a rapid loss of plasmatic EBV DNA. In transplant patients, EBV DNA load monitoring in whole blood and in plasma turned out to be equivalent in terms of feasibility and accuracy for the early diagnosis of post-transplant lymphoproliferative diseases (PTLDs).

Flow cytometric assessment of TCR-Vbeta expression in the evaluation of peripheral blood involvement by T-cell lymphoproliferative disorders: a comparison with conventional T-cell immunophenotyping and molecular genetic techniques.

Molecular genetic T-cell receptor (TCR) and flow cytometric analysis using antibodies to conventional T-cell antigens and TCR beta-chain variable region families (TCR-Vbeta) were performed in 65 peripheral blood specimens evaluated for potential involvement by a T-cell lymphoproliferative disorder (TCLPD). A normal or reactive conventional T-cell immunophenotype was present in 36 cases; TCR-Vbeta flow cytometric and molecular TCR analyses were negative for clonality in 32 and 27 of these cases, respectively. In the remaining normal and reactive cases, one or both methods seemed to detect dominant cell populations in settings with limited T-cell diversity. We identified 29 TCLPDs; all studied cases had clonal molecular TCR results; 23 TCLPDs had clonal TCR-Vbeta flow cytometric results; the remaining were suggestive of (n = 3) or negative (n = 3) for clonality. TCR-Vbeta flow cytometric analysis is a powerful clinical laboratory tool that can be used to aid in the rapid diagnosis of peripheral blood involvement by T-cell malignant neoplasms.