Clonal Characterization and Somatic Hypermutation Assessment by Next-Generation Sequencing in Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma: A Detailed Description of the Technical Performance, Clinical Utility, and Platform Comparison.

Somatic hypermutation status of the IGHV gene is essential for treating patients with chronic lymphocytic leukemia/small lymphocytic lymphoma. Unlike the conventional low-throughput method, assessment of somatic hypermutation by next-generation sequencing (NGS) has potential for uniformity and scalability. However, it lacks standardization or guidelines for routine clinical use. We critically assessed the performance of an amplicon-based NGS assay across 458 samples. Using a validation cohort (35 samples), the comparison of two platforms (Ion Torrent versus Illumina) and two primer sets [leader versus framework region 1 (FR1)] in their ability to identify clonotypic IGHV rearrangement(s) revealed 97% concordance. The mutation rates were identical by both platforms when using the same primer set (FR1), whereas a slight overestimation bias (+0.326%) was found when comparing FR1 with leader primers. However, for nearly all patients this did not affect the stratification into mutated or unmutated categories, suggesting that use of FR1 may provide comparable results if leader sequencing is not available and allowing for a simpler NGS laboratory workflow. In routine clinical practice (423 samples), the productive rearrangement was successfully detected by either primer set (leader, 97.7%; FR1, 94.7%), and a combination of both in problematic cases reduced the failure rate to 1.2%. Higher sensitivity of the NGS-based analysis also detected a higher frequency of double IGHV rearrangements (19.1%) compared with traditional approaches.

Quantitative Off-Target Detection of Epstein-Barr Virus-Derived DNA in Routine Molecular Profiling of Hematopoietic Neoplasms by Panel-Based Hybrid-Capture Next-Generation Sequencing.

Epstein-Barr virus (EBV) is associated with hematologic and solid tumors. We utilized a hybridization capture-based next-generation sequencing (NGS) platform targeting 400 genes associated with hematological malignancies to detect and quantify nontargeted viral-derived EBV reads that aligned to the EBV reference contig (NC_007605). We evaluated 5234 samples from 3636 unique patients with hematological neoplasms and found that 100 samples (1.9%) in 93 unique patients had ≥6 EBV reads (range, 6 to 32,325; mean, 827.5; median, 54). Most (n = 73, 73%) represented known EBV-associated conditions, and the most common was post-transplant lymphoproliferative disorders (n = 21, 29%). Documented EBV viremia was found in 4 of 27 samples with a moderate quantity of EBV reads and conditions not known to be EBV associated, whereas suspected viremia or low-level activation was likely in the remaining 23 samples. A good correlation (Spearman r = 0.8; 95% CI, 0.74-0.85) was found between EBV reads by NGS and systematic semiquantitative EBV-encoded RNA in situ hybridization in 162 available samples, particularly at greater EBV involvement. An optimal threshold for significant morphologic EBV involvement was found to be ≥10 reads by the receiver operating characteristic analysis (area under the curve, 0.990; 95% CI, 0.9974%-1.000%). Thus, in addition to mutational analysis, hybrid-capture-based NGS panels can detect and quantitate off-target EBV-derived viral DNA, which correlates well with morphology.

Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS.

Circulating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients.

Rapid EGFR Mutation Detection Using the Idylla Platform: Single-Institution Experience of 1200 Cases Analyzed by an In-House Developed Pipeline and Comparison with Concurrent Next-Generation Sequencing Results.

Mutations in the epidermal growth factor receptor (EGFR) are the most common targetable alterations in lung adenocarcinoma. To facilitate rapid testing, the Idylla EGFR assay was incorporated as a screening method before next-generation sequencing (NGS). Validation and experience using an in-house developed analysis pipeline, enhanced with a manual review algorithm is described. Results are compared with corresponding NGS results. In all, 1249 samples were studied. Validation demonstrated 98.57% (69/70) concordance with the reference methods. The limit of detection varied from 2% to 5% variant allele frequency for total EGFR quantitation cycle between 20 and 23. Of the 1179 clinical cases, 23.41% were EGFR-positive by Idylla. Concurrent NGS was successfully performed on 94.9% (799/842) requests. Concordance of Idylla with NGS was 98.62% (788/799) and 98.50% (787/799) using our in-house and Idylla analysis pipelines, respectively. Discordances involved missed mutations by both assays associated with low tumor/low input. Incorporating a manual review algorithm to supplement automated calls improved accuracy from 98.62% to 99.37% and sensitivity from 94.68% to 97.58%. Overall reporting time, from receipt of material to official clinical report, ranged from 1 to 3 days. Therefore, Idylla EGFR testing enables rapid and sensitive screening without compromising subsequent comprehensive NGS, when required. Automated calling, enhanced with a manual review algorithm, reduces false-negative calls associated with low tumor/low input samples.

Routine Evaluation of Minimal Residual Disease in Myeloma Using Next-Generation Sequencing Clonality Testing: Feasibility, Challenges, and Direct Comparison with High-Sensitivity Flow Cytometry.

The 2016 International Myeloma Working Group consensus recommendations emphasize high-sensitivity methods for minimal residual disease (MRD) detection, treatment response assessment, and prognostication. Next-generation sequencing (NGS) of IGH gene rearrangements is highly specific and sensitive, but its description in routine clinical practice and performance comparison with high-sensitivity flow cytometry (hsFC) remain limited. In this large, single-institution study including 438 samples from 251 patients, the use of NGS targeting the IGH and IGK genes for clonal characterization and monitoring, with comparison to hsFC, is described. The index clone characterization success rate was 93.6% (235/251), which depended on plasma cell (PC) cellularity, reaching 98% when PC ≥10% and below 80% when PC <5%. A total of 85% of cases were successfully characterized using leader and FR1 primer sets, and most clones showed high somatic hypermutation rates (median, 8.1%). Among monitoring samples from 124 patients, 78.6% (147/187) had detectable disease by NGS. Concordance with hsFC was 92.9% (170/183). Discordant cases encompassed 8 of 124 hsFC MRD+/NGS MRD- patients (6.5%) and 4 of 124 hsFC MRD-/NGS MRD+ patients (3.2%), all with low-level disease near detection limits for both assays. Among concordant hsFC MRD-/NGS MRD- cases, only 5 of 24 patients (20.8%) showed subsequent overt relapse at 3-year follow-up. HsFC and NGS showed similar operational sensitivity, and the choice of test may depend on practical, rather than test performance, considerations.

Off-the-shelf EBV-specific T cell immunotherapy for rituximab-refractory EBV-associated lymphoma following transplantation.

BACKGROUNDAdoptive transfer of donor-derived EBV-specific cytotoxic T-lymphocytes (EBV-CTLs) can eradicate EBV-associated lymphomas (EBV-PTLD) after transplantation of hematopoietic cell (HCT) or solid organ (SOT) but is unavailable for most patients.METHODSWe developed a third-party, allogeneic, off-the-shelf bank of 330 GMP-grade EBV-CTL lines from specifically consented healthy HCT donors. We treated 46 recipients of HCT (n = 33) or SOT (n = 13) with established EBV-PTLD, who had failed rituximab therapy, with third-party EBV-CTLs. Treatment cycles consisted of 3 weekly infusions of EBV-CTLs and 3 weeks of observation.RESULTSEBV-CTLs did not induce significant toxicities. One patient developed grade I skin graft-versus-host disease. Complete remission (CR) or sustained partial remission (PR) was achieved in 68% of HCT recipients and 54% of SOT recipients. For patients who achieved CR/PR or stable disease after cycle 1, one year overall survival was 88.9% and 81.8%, respectively. In addition, 3 of 5 recipients with POD after a first cycle who received EBV-CTLs from a different donor achieved CR or durable PR (60%) and survived longer than 1 year. Maximal responses were achieved after a median of 2 cycles.CONCLUSIONThird-party EBV-CTLs of defined HLA restriction provide safe, immediately accessible treatment for EBV-PTLD. Secondary treatment with EBV-CTLs restricted by a different HLA allele (switch therapy) can also induce remissions if initial EBV-CTLs are ineffective. These results suggest a promising potential therapy for patients with rituximab-refractory EBV-associated lymphoma after transplantation.TRIAL REGISTRATIONPhase II protocols (NCT01498484 and NCT00002663) were approved by the Institutional Review Board at Memorial Sloan Kettering Cancer Center, the FDA, and the National Marrow Donor Program.FUNDINGThis work was supported by NIH grants CA23766 and R21CA162002, the Aubrey Fund, the Claire Tow Foundation, the Major Family Foundation, the Max Cure Foundation, the Richard "Rick" J. Eisemann Pediatric Research Fund, the Banbury Foundation, the Edith Robertson Foundation, and the Larry Smead Foundation. Atara Biotherapeutics licensed the bank of third-party EBV-CTLs from Memorial Sloan Kettering Cancer Center in June 2015.

Establishment of Immunoglobulin Heavy (IGH) Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms.

Immunoglobulin heavy chain (IGH) clonality testing by next-generation sequencing (NGS) offers unique advantages over current low-throughput methods in the assessment of B-cell lineage neoplasms. Clinical use remains limited because assays are not standardized and validation/implementation guidelines are not yet developed. Herein, we describe our clinical validation and implementation of NGS IGH clonality testing and summarize our experience based on extensive routine use. NGS-based clonality testing targeting IGH FR1, FR2, FR3, and the conserved leader sequence upstream of FR1 was validated using commercially available kits. Data were analyzed by commercial and in-house-developed bioinformatics pipelines. Performance characteristics were evaluated directly comparing with capillary electrophoresis (CE) assays (BIOMED-2 primers). Assays were monitored after implementation (>1.5 years), concurrently testing by CE methods. A total of 1189 clinical samples were studied (94 validation, 1095 postimplementation). NGS showed superior performance compared with CE assays. For initial assessment, clonality detection rate was >97% for all malignancy types. Concordance with CE was 96%; discordances were related to higher sensitivity/resolution of NGS and improved detection in cases with high somatic hypermutation. Routine NGS clonality assessment is feasible and superior to existing assays, enabling accurate and specific index clone assessment and future tracking of all rearrangements in a patient sample. Successful implementation requires new standardization, validation, and implementation processes, which should be performed as a multicenter and multidisciplinary collaboration.

Comparison of manual hematocrit determinations versus automated methods for hematopoietic progenitor cell apheresis products.

BACKGROUND: Allogeneic hematopoietic stem cell donor selection is based primarily on human leukocyte antigen degree of match and it often occurs without regard to the red blood cell (RBC) compatibility between donor and recipient. When major ABO-mismatched grafts are infused, it is imperative that an accurate determination of the incompatible RBC content is made to ensure that the product is safe for infusion. RBC content determination requires the hematocrit (Hct) parameter which can be obtained via manual (directly measured) or automated (calculated) methods. STUDY DESIGN AND METHODS: Ninety-seven apheresis hematopoietic progenitor grafts were assessed for Hct by manual testing and by four commercially available automated hematology analyzer instruments. A clinical model was developed to assess the frequency of unnecessary RBC reductions or alteration in standard infusion practice. RESULTS: Significant (p < 0.001) differences were observed where the manual Hct value was markedly lower than automated Hct values. At stringent incompatible RBC threshold of 10 mL, the number of preventable RBC reduction procedures ranged from 18% to 69%. CONCLUSION: Accurate determination of RBC content of hematopoietic progenitor grafts is essential for patient safety. Despite the rapidity and convenience offered by automated Hct methods, they significantly overestimate the incompatible RBC content of grafts, which may trigger unnecessary RBC reduction procedures or split infusions. In products where automated Hct methods indicate excessive amounts of incompatible RBCs are present, we advise the performance of confirmatory testing with a manual Hct method to ensure that the automated Hct value is not a false positive.

Evaluation of new automated hematopoietic progenitor cell analysis in the clinical management of peripheral blood stem cell collections.

BACKGROUND: Successful peripheral blood stem cell transplantation (PBSCT) depends on the collection and infusion of adequate numbers of peripheral blood progenitor cells (PBPCs). Several predictors of PBPC yield are used currently, including white blood cell (WBC) count and CD34 analysis. This study evaluated the utility of the new automated hematopoietic progenitor cell count available on Sysmex XN hematology analyzers (XN-HPCs) in PBSCT. STUDY DESIGN AND METHODS: The performance characteristics of XN-HPC, CD34+, and WBC analysis were compared using 107 matched peripheral blood and apheresis samples. RESULTS: Good correlation was observed between XN-HPC and CD34+ cell counts in peripheral blood (r = 0.88; slope, 0.81) and apheresis collections (r = 0.91; slope, 0.89). Moreover, peripheral blood XN-HPC and CD34 analysis showed comparable ability to predict successful PBPC harvests (≥2 × 10(6) CD34+ cells/kg). At a cutoff of 20 × 10(6) progenitor cells/L, peripheral blood XN- HPC and CD34 analysis both showed negative predictive values (NPVs) of 100% and positive predictive values (PPVs) of 55.4 and 63%, respectively. Using an optimized cutoff of 38 × 10(6) progenitor cells/L, derived from receiver operating characteristic analysis, the PPV for XN-HPC and CD34 analysis increased to 71.4 and 78.9%, respectively, with relatively unchanged NPVs (XN-HPC 97.7%, CD34+ 98.0%). In contrast, the correlation between peripheral blood WBC and CD34 analysis was poor (r = 0.48; slope, 669.85), and the peripheral blood WBC count (cutoff, 10 × 10(9) /L) was a poor predictor of PBPC harvest (NPV 60%, PPV 43.1%). CONCLUSION: XN-HPC compares favorably with CD34 analysis and may be a surrogate for CD34 analysis to predict optimal timing of PBPC collections.

Atypical ductal hyperplasia at margin of breast biopsy--is re-excision indicated?

BACKGROUND: Atypical duct hyperplasia (ADH) observed during core needle biopsy is associated with a high rate of cancer upon excision. Controversy exists regarding the need to re-excise ADH involving a margin. The purpose of this study was to determine the rate of residual pathology in patients that underwent re-excision for ADH involving the margin. METHODS: In a retrospective review of the pathology database from 1 January 2000 to 1 June 2006, we identified 44 lumpectomy specimens with ADH involving the margin; 24 patients (55%) had a re-excision. Slides were reviewed to verify the diagnosis of ADH near the margin and the presence of residual disease on re-excision associated with the biopsy cavity. RESULTS: Patients had pure ADH (15, 63%), ADH and ductal carcinoma in situ (DCIS) (7, 29%) or ADH with invasive carcinoma (2, 8%). Residual ADH or cancer was found in 14 of 24 patients (58%). Of 15 patients with pure ADH, 6 (40%) had residual pathology: ADH (2), DCIS (2) and invasive carcinoma (2). In this group, 27% of patients were reassessed as having DCIS or invasive carcinoma. Of the 9 patients with cancer, 8 (89%) had residual disease in the form of ADH (4) or DCIS (4). CONCLUSIONS: ADH found at the margin of a lumpectomy specimen is associated with a high rate of residual ADH and cancer. Over one quarter of the patients with an initial diagnosis of ADH were reassessed as having DCIS or invasive carcinoma. Re-excision in all patients with ADH involving the margin is recommended.