Minimal Residual Disease Diagnostics Research Articles

The Evolving Landscape of Flowcytometric Minimal Residual Disease Monitoring in B-Cell Precursor Acute Lymphoblastic Leukemia.

Detection of minimal residual disease (MRD) is a major independent prognostic marker in the clinical management of pediatric and adult B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL), and risk stratification nowadays heavily relies on MRD diagnostics. MRD can be detected using flow cytometry based on aberrant expression of markers (antigens) during malignant B-cell maturation. Recent advances highlight the significance of novel markers (e.g., CD58, CD81, CD304, CD73, CD66c, and CD123), improving MRD identification. Second and next-generation flow cytometry, such as the EuroFlow consortium's eight-color protocol, can achieve sensitivities down to 10-5 (comparable with the PCR-based method) if sufficient cells are acquired. The introduction of targeted therapies (especially those targeting CD19, such as blinatumomab or CAR-T19) introduces several challenges for flow cytometric MRD analysis, such as the occurrence of CD19-negative relapses. Therefore, innovative flow cytometry panels, including alternative B-cell markers (e.g., CD22 and CD24), have been designed. (Semi-)automated MRD assessment, employing machine learning algorithms and clustering tools, shows promise but does not yet allow robust and sensitive automated analysis of MRD. Future directions involve integrating artificial intelligence, further automation, and exploring multicolor spectral flow cytometry to standardize MRD assessment and enhance diagnostic and prognostic robustness of MRD diagnostics in BCP-ALL.

Rapid Capture NGS Identifies Genomic Rearrangements in BCP-ALL for MRD Diagnostics

BackgroundImmunoglobin heavy chain (IGH), T-cell receptor δ (TRδ) rearrangements and translocations have frequently been described in patients with B-cell precursor (BCP) ALL. In order to detect the various types of fusions we used a high-throughput sequencing (HTS) assay based on direct capturing and sequencing of enriched genomic DNA fragments. Our approach focused on enrichment and direct paired-end sequencing of IG/TR rearrangements to analyze clonality and to detect kinase- and/or cytokine-receptor fusion breakpoints. We selected the corresponding chromosomal regions spanning exonic as well as intronic genomic areas from IGH-JH, TRδ and from several “Ph-like”-associated genes (ABL1, ABL2, CSF1R, CRLF2, EPOR, JAK2, PDGFRß). For the identification of clonality and fusion breakpoints we used Vidjil (www.Vidjil.org) and “segemehl” bioinformatics algorithms, respectively. Clonal rearrangements and genomic breakpoints were subsequently compared for their use in detection of minimal residual disease (MRD).Patients and methodsFor combined clonality and breakpoint analysis, 162 BCP ALL patients (MLL-; TEL-AML1-, BCR-ABL1-) were selected due to the MRD status at the end of induction (EOI) therapy, which include a substantial proportion of ALL samples (n = 68) with a high MRD burden (≥ 1 x 10-2). To test the feasibility of the analytical approach, additional BCR-ABL1+ ALLsamples (n=19) were included for genomic breakpoint analysis. Captured genomic DNA from eighty ALL samples was sequenced on a HiSeq2500 Illumina device, the remaining samples were subjected to several MiSeq (Illumina) runs multiplexing up to 12 samples using MiSeq Reagent Kit v3 (600 cycle) chemistry.ResultsFor TRδ, a total of 267 clonal rearrangements were characterized in 142/162 samples (88%). Beside clonal Vδ2-Dδ3, Dδ2-Dδ3, Vδ2-Jα, we identified a novel group of recurrent Dδ-Jα rearrangements in 46 samples (28%), comprising Dδ2 or Dδ3 segments fused predominantly to Jα29. For IGH-JH, 304 clonal rearrangements were identified in 152/162 samples, including several novel VDJ joinings usually not detectable by standard PCR-based approaches. In BCR-ABL1+ ALL, genomic breakpoints were identified in 17/19 cases. In BCP-ALL lacking a classical rearrangement, 50 gene fusions were detected, between IGH-JH and either DUX4, EPOR or CRLF2 in 21 of 162 cases. In addition, EBF1-PDGFRß or PAR1 deletions were detected in 5 and 10 cases, respectively. Prolonged MRD was observed in ALL carrying CRLF2rearr, EPORrearr -, PDGFR-ßrearr and as an unanticipated finding in 8/10 DUX4rearr patients who mainly underwent hematopoietic stem cell transplantation in first remission (n=5) or had a relapse (n=2). MLPA revealed a non-deleted ERG status in these 8 DUX4rearr ALL samples. A distinct subgroup of MRD high-risk patients were characterized by a complete lack of IGH-VDJ rearrangements, but they exhibited frequent IKZF1del (7/10) and a variety of other genomic rearrangements (n=3 EPORrearr, n=3 DUX4rearr, n=1 CRLF2rearr, n=1 EBF1-PDGFRß or n=1 FOXP1-ABL1). Among gene-fusion positive ALLs, breakpoint- specific real-time quantitative MRD assays at EOI were established, which demonstrated equivalent or superior sensitivity and specificity compared to conventional TR/IG targeted MRD measurements.ConclusionsThe HTS approach presented here yields classical IGH/TRδ-related clonal MRD targets and genomic breakpoints from gene fusions at a time, the latter of which can subsequently serve as robust markers for follow-up monitoring. The MRD high-risk group (≥ 1 x 10-2 at EOI) revealed an enrichment of aberrant gene fusions/rearrangements in 31 of 68 (46%) patients compared to 19 of 94 (20%) in the moderate-risk MRD group (>1 x 10-4 < 1 x 10-2). Rapid capture sequencing in a clinical diagnostics setting allows for specific ABL or JAK-STAT pathway directed early intervention in the majority of gene-fusion positive patients. DisclosuresNo relevant conflicts of interest to declare.

Real-World Experience with Minimal Residual Disease Testing with Next Generation Flow Cytometry and Functional Imaging in Multiple Myeloma

Background: Minimal residual disease (MRD) diagnostics in multiple myeloma (MM) are gaining increasing importance to determine response depth beyond complete remission (CR) since novel agents have shown to induce high rates of deep clinical responses. Moreover, recent reports indicated combining functional imaging with next generation flow cytometry (NGF) could be beneficial in predicting clinical outcome. This applies in particular to the subset of patients suffering from relapsed/refractory multiple myeloma (RRMM) who tend to show a higher incidence of residual focal lesions despite serological response. Here, we report our institutions experience with implementing both functional imaging and NGF-guided MRD diagnostics in clinical practice. Methods: Our study included patients with newly diagnosed multiple myeloma (NDMM) and RRMM achieving VGPR, CR or sCR. Bone marrow aspirates were obtained for MRD-testing according to IMWG 2016 criteria. Samples were collected between July 2019 and July 2020 and analyzed with NGF (according to EuroFlowTM guidelines) at a sensitivity level of 10-5. Results were compared to functional imaging obtained with positron emission tomography (PET) and diffusion-weighted magnetic resonance imaging (DW-MRI). High-risk disease was defined as presence of deletion 17p, translocation (14;16) or (4;14). Results: We included 66 patients with NDMM (n=39) and RRMM (n=27) who achieved VGPR or better. In patients with RRMM the median number of treatment lines was 2 (range 2-11). Fifteen patients suffered from high-risk disease. Median age at NGF diagnostics was 64 years (range 31-83). Among patients achieving VGPR (n=27), CR (n=10) and sCR (n=29) seventeen (26%) were MRD-negative by NGF testing. CR or better was significantly associated NGF MRD-negativity (p=0.04). Notably, rates of NGF MRD-negativity were similar among patients with NDMM (28%) and RRMM (26%). Even some heavily pretreated patients who underwent ≥ 4 lines of therapy achieved MRD-negativity on NGF (2 of 9). Functional imaging was performed in 46 (70%) patients with DW-MRI (n=22) and PET (n=26). Median time between NGF and imaging assessment was 2 days (range 0-147). Combining results from imaging and NGF, 12 out of 46 (26%) patients were MRD-negative with both methods (neg/neg). Three patients displayed disease activity as measured with both, imaging and NGF (pos/pos). Twenty-nine of the remaining patients were MRD-positive only according to NGF (pos/neg), while two patients were positive on imaging only (neg/pos). More patients demonstrated combined MRD-negativity on NGF and imaging (neg/neg) in the NDMM setting than in RRMM (32% versus 19%). We also observed that 30% of the patients with high-risk genetics showed MRD-negativity on both imaging and NGF. Of note, none of the patients with very advanced disease (≥4 previous lines) was MRD-negative on both techniques. Conclusion In the clinical routine, MRD diagnostics could be used to tailor maintenance and consolidation approaches for patients achieving deep responses by traditional IMWG criteria. Our real-world experience highlights that MRD-negativity can be achieved in patients suffering from high-risk disease and also in late treatment lines, supporting its value as endpoint for clinical trials. However, our data also support MRD diagnostics to be combined with functional imaging at least in the RRMM setting to rule out residual focal lesions. Future studies using MRD for clinical decision-making are highly warranted. Disclosures Einsele: Takeda: Consultancy, Honoraria, Speakers Bureau; Janssen: Consultancy, Honoraria, Research Funding, Speakers Bureau; Novartis: Honoraria, Speakers Bureau; Amgen: Consultancy, Honoraria, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Research Funding, Speakers Bureau; GlaxoSmithKline: Honoraria, Research Funding, Speakers Bureau; Bristol-Myers Squibb: Consultancy, Honoraria, Research Funding, Speakers Bureau; Sanofi: Consultancy, Honoraria, Research Funding, Speakers Bureau. Rasche:Celgene/BMS: Honoraria; GlaxoSmithKline: Honoraria; Oncopeptides: Honoraria; Skyline Dx: Research Funding; Janssen: Honoraria; Sanofi: Honoraria.

Current concepts and future directions for hemato-oncologic diagnostics.

At present, hemato-oncologic diagnostics is facing dynamic changes. This applies to the exploration and introduction of novel technologies such as next-generation sequencing or digital droplet PCR for myeloid and lymphatic malignancies in laboratory routine, or liquid biopsy for patients with lymphoid malignancies. Targeted therapies such as FLT3 or IDH1/IDH2 inhibitors for acute myeloid leukemia are entering clinical practice. Thus, the demand for hematologic precision diagnostics both at initial diagnosis and during the course of the disease are equally increasing, and a short turn-around time becomes crucial. NGS expands the armamentarium for minimal residual disease diagnostics, but novel questions arise relating to sensitivity, the appropriate time points of this analysis, or the thresholds triggering therapeutic interventions. In this review article, we summarize some of the most relevant current changes and subsequent challenges for diagnostics in various myeloid and lymphatic malignancies. Future directions of hemato-oncologic diagnostics in the next 5-10 years are highlighted.

Minimal Residual Disease Detection in Acute Lymphoblastic Leukemia.

Minimal residual disease (MRD) refers to a chemotherapy/radiotherapy-surviving leukemia cell population that gives rise to relapse of the disease. The detection of MRD is critical for predicting the outcome and for selecting the intensity of further treatment strategies. The development of various new diagnostic platforms, including next-generation sequencing (NGS), has introduced significant advances in the sensitivity of MRD diagnostics. Here, we review current methods to diagnose MRD through phenotypic marker patterns or differential gene patterns through analysis by flow cytometry (FCM), polymerase chain reaction (PCR), real-time quantitative polymerase chain reaction (RQ-PCR), reverse transcription polymerase chain reaction (RT-PCR) or NGS. Future advances in clinical procedures will be molded by practical feasibility and patient needs regarding greater diagnostic sensitivity.

PF188 NGS COMBINED WITH ASO REAL‐TIME PCR BASED MRD DETECTION ASSAY FOR PEDIATRIC ALL PATIENTS

Background:Monitoring of minimal residual disease (MRD) has become routine clinical practice in frontline treatment of pediatric acute lymphoblastic leukemia (ALL) patients. MRD diagnostics has proven to be the strongest prognostic factor, allowing for risk group assignment into different treatment categories, ranging from significant treatment reduction to mild or strong intensification. MRD diagnostics is also guiding treatment decisions in relapsed ALL patients and patients undergoing stem cell transplantation.Aims:Our aim is to develop and apply a sensitive (≤ 10–4), universal, accurate, reliable and fast assay for MRD detection in ALL patients. To date, flow cytometry and polymerase chain reaction (PCR) analysis of rearranged immunoglobulin and T‐cell receptor genes (allele‐specific oligonucleotide [ASO]‐PCR) are claimed to meet these criteria, but classical flow cytometry does not reach a solid 10–4, whereas classical ASO‐PCR is time‐consuming and labor intensive.Methods:LymphoTrack® IGH + TRG Assay – MiSeq is applied on diagnosis sample using the Illumina MiSeq platform. This is used for the identification of clonal IGH VH‐JH and TRG V‐J rearrangements, DNA sequences and the distribution frequency of V and J segment utilization. The clone sequence is then compared against the germline sequences contained in the IMGT V‐QUEST databases for the identification of patient‐specific junctional regions following by the design of six different D‐N‐J specific ASOs primers for each clone according to UKALL protocol. Five point standard curve is used with triplicates at 5x10^‐5 and 1x10^‐5 for more reliable results at the critical lower level and six pooled negative controls for confirmation of the specificity of the assay.Results:Forty pediatric ALL patients have been tested at several time points. All informative patient sample dilutions reached 5x10^‐5, and most of the patients reached 1x10^‐5. The R2 of standard curves were within the expected range (≥0.98), and all slopes within range (3.1–3.9) with an average of 3.21 +/‐ 0.16. In most negative control samples no amplification was detected. In 8 assays amplification was detected in two negative control samples. In these cases the CT value was more than 3 CT from the Quantitative Range (QR).Our coupled NGS‐ASO‐PCR method sensitivity was compared to Flow cytometry and Fusion Transcript Real Time PCR methods. NGS‐ASO based MRD method has detected MRD populations in several samples were Flow cytometry or real time PCR failed. None of the patient tested were positive by other methods and was negative by ASO based MRD method.Summary/Conclusion:In the ALL field, MRD has become part of diagnostic patient care. Consequently, standardized MRD diagnostics should be available for assessment of treatment response in each individual ALL patient, to be used for personalized medicine such as accurate risk group assignment with risk‐adapted treatment. The coupled NGS‐ASO‐PCR method seams to fulfill a series of requirements for acceptance in the field, such as broad availability, easy implementation, applicability in the vast majority of patients, sufficient sensitivity (quantitative range of 5x10^‐5) and fast (short turn‐around time, particularly for follow‐up samples).

MRD Detection in B-Cell Non-Hodgkin Lymphomas Using Ig Gene Rearrangements and Chromosomal Translocations as Targets for Real-Time Quantitative PCR.

Minimal residual disease (MRD) diagnostics is of high clinical relevance in patients with indolent B-cell non-Hodgkin lymphomas (B-NHL) and serves as a surrogate parameter to evaluate treatment effectiveness and long-term prognosis. MRD diagnostics performed by real-time quantitative PCR (RQ-PCR) is still the gold standard and currently the most sensitive and the most broadly applied method in follicular lymphoma (FL) and mantle cell lymphoma (MCL). Alternatively, droplet digital PCR (ddPCR) can be used for MRD monitoring in multiple myeloma, mantle cell lymphoma, and follicular lymphoma with comparable sensitivity, accuracy, and reproducibility.The most broadly applicable MRD target in B-NHL is the junctional regions of the rearranged immunoglobulin heavy chain gene (IGHV). Chromosomal translocations like the t(14;18) translocation in FL and t(11;14) translocation in MCL can be used as MRD target in selected lymphoma subtypes. In patients with B-cell chronic lymphocytic leukemia, both flow-cytometry and RQ-PCR are equally suited for MRD assessment as long as a sensitivity of 10-4 shall be achieved.MRD diagnostics targeting the IGHV gene is complex and requires extensive knowledge and experience because the junctional regions of each lymphoma have to be identified before the patient-specific RQ-PCR assays can be designed for MRD monitoring. In addition, the presence and load of somatic hypermutation (SHM) within the rearranged IG heavy variable (IGHV) gene occurring as during B-cell development of germinal center and post-germinal center lymphomas may hamper appropriate primer binding leading to false-negative results. The translocations mentioned above have the advantage that consensus forward primers and probes, both placed in the breakpoint regions of chromosome 18 in FL and chromosome 11 in MCL, can be used in combination with a reverse primer placed in the IGH joining region of chromosome 14. RQ-PCR-based methods can reach a good sensitivity (≤10-4). This chapter provides all relevant background information and technical aspects for the complete laboratory process from detection of the clonal IGHV gene rearrangement and the chromosomal translocations at diagnosis to the actual MRD measurements in clinical follow-up samples of B-NHL. However, it should be noted that MRD diagnostics for clinical treatment protocols has to be accompanied by regular international quality control rounds to ensure the reproducibility and reliability of the MRD results.

Combination of Flow Cytometry and Functional Imaging for Monitoring of Residual Disease in Myeloma

IntroductionThe iliac crest is the usual sampling site for minimal residual disease (MRD) monitoring in Multiple Myeloma (MM). However, the disease distribution in the bone marrow (BM) is often heterogeneous. Functional imaging can be used to complement MRD detection at a single site, thereby accounting for asymmetrically distributed disease. Diffusion weighted MRI with background suppression (DWIBS) is a novel functional imaging method that can detect disease in a higher proportion of newly diagnosed MM (NDMM) patients than 18F-fluorodeoxyglucose positron emission tomography (PET), as it is independent of the tumor metabolism. Yet, its performance for monitoring of residual disease has not been described. The aims of this study were 1) to compare DWIBS to PET for the detection of residual disease in patients achieving complete remission (CR), and 2) to test whether DWIBS and PET could complement MRD flow cytometry with a sensitivity of 1x10-5. To address these aims, we investigated 168 NDMM and 33 relapsed patients for whom DWIBS, PET, and MRD were available at the onset of CR during first-line and salvage therapy, respectively.MethodsAll patients signed written consent in accordance with the Declaration of Helsinki. Residual focal lesions (FLs) were defined as well delineated focal intensities above the surrounding BM background. For DWIBS FLs were considered if restriction could be confirmed on ADC maps. 8-color MRD flow cytometry with a limit of detection of 1x10-5 was available for 83 NDMM and all 33 salvage therapy patients. The Kaplan-Meier method was used for survival analyses. PFS time was measured from onset of CR to relapse or death from any cause or censored at the date of last contact. Paired-end whole exome sequencing of CD138-enriched MM cells was performed on an Illumina HiSeq 2500. Mutations were called from BWA aligned sequencing reads using MuTect. Subclonal reconstruction was done using SciClone.ResultsCompared to PET, DWIBS detected more CR patients with residual FLs (21% vs. 6%), and the concordance between PET and DWIBS was low. Only 6 of the DWIBS-positive patients also presented with FLs in PET. Yet, 5 patients had PET+/DWIBS- FLs, suggesting that the two techniques are complementary. Both, DWIBS+ and PET+ FLs negatively impacted PFS (p<0.05).For 83 patients MRD data were available. Combining MRD and imaging, residual disease was detectable in 53 patients (64%). The best outcome was seen for 30 double negative (MRD-/Imaging-) patients (3 events with a median follow-up of 3.6 years), the worst outcome was seen for 10 double positive (MRD+/Imaging+) patients (median PFS: 2.1 years). Only 4 of 86 patients were MRD-/Imaging+, indicating that residual FLs are rare in MRD-negative NDMM patients at a sensitivity of 1x10-5.A heterogeneous disease distribution is a common feature of late-stage patients. To test if this increased heterogeneity confounded MRD, we investigated a set of 33 heavily pretreated patients who achieved CR during salvage therapy. Combining MRD and imaging data, we detected residual disease in 25 patients (76%). Of note, the proportion of patients, who were MRD-negative but had residual FLs on functional imaging was significantly higher compared to NDMM (8/16 vs 4/34 patients, p=0.01). At the same time, 10 patients (30%) were MRD+ but Imaging-, supporting the idea that a combined MRD/Imaging approach can improve detection of residual disease and should be used in late-stage patients.To obtain insights in the underlying biology, we performed longitudinal multi-region sequencing of a subset of these CR patients. Our findings support the concept of persistence and progression of multiple spatially separated clones in the BM irrespective of being in an MRD-negative CR. Thereby, focal residual disease could be shown to contribute to relapse.ConclusionDWIBS is a promising tool for detection of residual disease and complements PET. The combination of MRD diagnostics and functional imaging improves prediction of outcome, with double-negativity and double positivity defining groups with excellent and dismal PFS, respectively. Prospective trials using this information to tailor therapy are warranted. From a biological perspective, this study highlights the confounding effects of spatial heterogeneity and limited dissemination of clones within the BM on MRD diagnostics. This may especially be true for patients achieving deep responses during salvage therapies. DisclosuresRoy Choudhury:University of Arkansas for Medical Sciences: Employment, Research Funding. Epstein:University of Arkansas for Medical Sciences: Employment. Barlogie:International Workshop on Waldenström's Macroglobulinemia: Other: travel stipend; Millenium: Consultancy, Research Funding; Multiple Myeloma Research Foundation: Other: travel stipend; ComtecMed- World Congress on Controversies in Hematology: Other: travel stipend; Myeloma Health, LLC: Patents & Royalties: : Co-inventor of patents and patent applications related to use of GEP in cancer medicine licensed to Myeloma Health, LLC; European School of Haematology- International Conference on Multiple Myeloma: Other: travel stipend; Celgene: Consultancy, Research Funding; Dana Farber Cancer Institute: Other: travel stipend. Davies:Takeda: Consultancy, Honoraria; Abbvie: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Janssen: Consultancy, Honoraria. Morgan:Celgene: Consultancy, Honoraria, Research Funding; Bristol-Myers Squibb: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Janssen: Research Funding.

Duplex Sequencing Accurately Detects Variants below 1/100,000 in Genes Recurrently Mutated in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a challenging disease to treat: most patients achieve remission after induction chemotherapy, but the majority eventually relapse. Minimal residual disease (MRD) after initial treatment is the best predictor of relapse and is thus a critical metric around which to develop new treatments. However, conventional MRD diagnostics, including cytology and flow cytometry, are of variable sensitivity and often only perform well in specialty centers, and there is no gold standard. Molecular tests developed to measure trace MRD in other hematological malignancies (i.e. CML) are high-resolution but assay a single, universally-present mutation, while many different genetic drivers exist in AML and these are spread among dozens of genes. Virtually every AML patient harbors a unique combination of mutations, making it difficult to design an effective universal assay. As such, most reported molecular AML MRD assays are either sensitive for mutations that are only found in a narrow subset of patients, or can screen many potential sites of mutation, but with low sensitivity.Here we present a broadly applicable Duplex Sequencing-based AML MRD assay that can readily detect mutant allele frequencies (MAF) below 1/10,000 across a large panel of genes, and below 1/100,000 in a focused panel. Conventional next generation sequencing (NGS) introduces errors during amplification and sequencing, creating a background of artifactual noise that obscures true mutations present below ~1%. Duplex Sequencing improves accuracy >100,000-fold through a molecular tagging approach whereby both strands of each original DNA duplex are ligated with a unique molecular barcode and amplified such that the reads generated from each strand can be related back to their unique original duplex. Reads can also be distinguished from those of their mate strand, thus the two strands of each DNA duplex can be compared and any discrepant nucleotide positions are discounted as errors.Our complete AML panel targets 151 exons or hotspot codons in 29 genes with a 59 kilobase (kb) hybrid-capture footprint. This region comprises loci containing single-nucleotide and short indel mutations found in approximately 90% of adult AMLs. A mean Duplex error-corrected sequence depth of 10,837 and a maximum Duplex depth of 14,967 was obtained across these targets from a single library preparation using 250 ng of sheared leukocyte DNA (Fig. 1). Duplex depth can be readily increased by preparing additional Duplex libraries from the same source DNA to achieve proportionally higher sensitivity for rarer variants. This stands in contrast to conventional NGS where, beyond a modest level, an increase in depth simply increases the number of background errors identified (Fig. 2A).We simulated low-level residual disease by mixing control DNA from a healthy young blood donor with DNA from 9 human cell lines harboring known AML mutations at dilutions from 1:100 to 1:100,000 (Table 2). The genomic loci of these 9 mutations in NRAS, KRAS and TP53 were captured with a small 1 kb probe panel. This mixture was sequenced to a mean Duplex depth of >1,000,000-fold, with the highest and lowest MAFs shown in Fig. 2B. All were close to expected frequencies (r2=0.96) with MAF as low as 6x10-6 (Fig. 3). As proof of specificity, we examined all coding nucleotide positions (excluding the 9 expected variants) and identified only 241 background variant counts out of 414,452,402 total Duplex BP, for an aggregate mutation frequency of 5.8x10-7, consistent with the estimated background of normal human aging.Our Duplex Sequencing-based AML MRD assay is flexible, broadly applicable and extremely sensitive. The assay is easily implemented using standard NGS equipment and automated cloud-based analysis software. The ~90% of AML patients served by this SNV-focused panel can be expanded to nearly 100% with complementary indel detection via targeted NGS RT-PCR. Optionally, when a patient's mutation profile from time-of-diagnosis is known, MRD testing can focus exclusively on those targets using a subset of pre-validated probes to reduce sequencing cost. Improved MRD testing will facilitate accurate prognostication, better selection among treatment options, and could serve as a surrogate endpoint in clinical trials to bring new treatments to patients faster. We are currently evaluating Duplex Sequencing MRD tests in both retrospective and prospective clinical trials. [Display omitted] DisclosuresHiggins:TwinStrand Biosciences: Employment. Williams:TwinStrand Biosciences: Employment. Buckley:CTI Biopharma: Employment; TwinStrand Biosciences: Consultancy. Radich:TwinStrand Biosciences: Research Funding. Salk:TwinStrand Biosciences: Employment, Equity Ownership.

CD7 is expressed on a subset of normal CD34-positive myeloid precursors.

To improve monitoring of myeloid neoplasms by flow cytometry-based minimal residual disease (MRD) analysis, we analyzed the significance of leukemia-associated immunophenotype (LAIP) markers in 44 patients. In a pilot study cohort, peripheral blood or bone marrow samples from 13 patients with myeloid neoplasms and one case of B lymphoblastic leukemia in complete hematologic remission after allogeneic bone marrow or stem cell transplantation were subjected to selection for leukemia-specific phenotypes by fluorescence-activated cell sorting using individual marker combinations, followed by PCR-based chimerism analysis. The feasibility of this method could be demonstrated, with selection being successful in 12 cases, including two cases where mixed chimerism was found exclusively in sorted cells. Interestingly, four specimens displayed full donor chimerism in cells expressing the presumably aberrant combination CD34+ /CD7+ . Further analyses, including assessment of an independent cohort of 25 patients not affected by neoplastic bone marrow infiltration, revealed that normal myeloid precursors usually include a population coexpressing CD34, CD13, CD33, and CD7. We conclude that the combination CD34+ /CD7+ might not be suitable as an LAIP for MRD diagnostics and that a subset of normal myeloid precursors in the bone marrow expresses CD7.

Abstract 4878: Sensitive and specific DNA and RNA sequencing techniques for detecting minimal residual disease

Abstract The goal of this study was to assess the clinical applicability of molecular genetic techniques in the study of minimal residual disease (MRD) in pediatric acute myeloid leukemia (AML) via DNA and RNA-based methods. Currently, multi-parametric flow cytometry (MPFC) for surface immunophenotypes is the gold standard for MRD with a limit of detection between 0.001-0.002. However, approximately one-third of children with no detectable MRD by MPFC after first induction still relapse and suffer inferior outcomes. One potential reason is that a majority of refractory or recurrent AML clones will present with altered immunophenotypes compared to diagnostic specimens. In contrast, DNA mutations present at diagnosis will remain in refractory disease and therefore, a gene-based MRD platform surveying many genes could enable targeted, gene-specific therapy. Recently, the heterogeneous and unique genomic landscape of pediatric AML was characterized in the TARGET project and highlights the potential for leveraging companion molecular screens in the analysis of AML MRD. Contrary to adult AML, pediatric AML is not primarily characterized by single nucleotide variants (SNVs), but rather by complex structural variants (SV) that are difficult to detect using standard next generation sequencing techniques and analysis pipelines. The need to detect these complex SV and SNVs, all of which are at low allelic ratios (AR) at the remission state, demands assays that are capable of analyzing both DNA and RNA molecules at levels of detection comparable to MPFC. As proof of principal, we leveraged a unique capture technique (ArcherDx; CoreAML) to detect an important SV in pediatric AML, the internal tandem duplication in Fms related tyrosine Kinase (FLT3-ITD). Via a serial dilution of cells with known FLT3-ITD allelic ratio (MV4-11 cells), to determine a limit of detection, we were able to detect the mutation as low as 0.001. Next, we bench-marked the technique using diagnostic and relapse samples, and successfully detected FLT3-ITD at AR &amp;lt;0.01. To complement the DNA-based approach, we compared two error-corrected (EC) RNA assays (a Druley lab developed protocol and the ArcherDx; HemeV2 panel) to further assay SVs that cause novel gene fusions and aberrant exon usage, which are not detectable via DNA assays. Compared to existing cytogenetic and RNA-seq data, this new platform was capable of detecting known and novel cryptic translocations. Finally, we integrated the results from the FLT3-ITD assay and the RNA assay with our custom error-corrected sequencing data to create a novel bioinformatics workflow for assessing the biological implications of MRD clones detected. Collectively, our data support that EC sequencing, at both the DNA and RNA level, enable accurate detection of low allelic variants that could be used for improved clinical MRD diagnostics, prognostication and therapeutic selection. Citation Format: Erin L. Crowgey, Nitin Mahajan, Wing H. Wong, Edward A. Kolb, Todd Druley. Sensitive and specific DNA and RNA sequencing techniques for detecting minimal residual disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4878. doi:10.1158/1538-7445.AM2017-4878

The Clinical Impact of Macrofocal Disease in Multiple Myeloma Differs Between Presentation and Relapse

IntroductionFunctional imaging of Multiple Myeloma (MM) is redefining our knowledge of disease patterns. A pattern, termed macrofocal MM (macro MM), is defined by the presence of focal lesions and the absence of significant intervening bone marrow (BM) infiltration. At presentation, macro MM constitutes a distinct disease entity likely being associated with a favorable prognosis, although current evidence to support this is limited. Following first-line therapy, macrofocal patterns of disease emerge also in patients that initially presented with classical MM. In these patients the systemic BM involvement disappears in follow up examinations during treatment whereas focal lesions persist. In a third scenario, macrofocal patterns occur at overt relapse representing a patchy type of MM progression (Figure 1). The prognostic impact of a macrofocal pattern at these various disease stages is largely unknown. Therefore, we analyzed the clinical outcome and biological features of macro MM at different treatment stages.Patients and Methods279 patients met the criteria of macro MM. Of those, 56 were at initial presentation, 48 at restaging following first line therapy, and 175 at relapse. Generally, macrofocal lesions were present in both positron emission tomography and magnetic resonance imaging. All first-line patients were treated with multi-agent induction therapy, autologous stem cell transplantation and received maintenance within prospective trials. Outcome results were compared to a set of cases with classical MM matched for age, gene-expression based (GEP) risk group, and treatment protocol.ResultsMacro MM at presentation is rare, constituting 6% of patients in the time period examined. The vast majority showed GEP-based low risk (94%). Age, Ig-type, and sex were not significantly different between macro MM and classical MM. With a median follow up of 8.6 years, only 10 of the macro MM patients relapsed. Compared to a matched-pair MM group, progression-free survival (PFS) and overall survival (OS) were significantly better in the macro MM group (P= 0.01 and 0.04 for PFS and OS, respectively). Thus macro MM at presentation constitutes a low risk form of MM.Focusing on the 10 macro MM cases who relapsed, no specific risk profile could be identified except >26 focal lesions on MRI was associated with a shorter PFS (P=0.04) but not with OS. Of note, although focal lesions frequently responded slowly, the time to response was not associated with outcome.To elucidate whether there are biological differences between MM cells in focal lesions and at differentially involved BM sites, we analyzed a set of 16 patients with paired samples from macrofocal lesions and iliac crest BM aspirates. No difference in a GEP based proliferation index was seen between the two sites. After correction for multiple testing we did not observe gene expression differences between them. A candidate gene study including a set of 27, myeloma relevant, adhesion molecules also did not reveal expression differences.In contrast to the situation at presentation, macrofocal patterns at restaging during initial therapy showed a 70% cumulative 24 months relapse incidence. The outcome of these cases was significantly worse in comparison to matched controls (P=0.02 and 0.02 for PFS and OS, respectively). Of note, all patients with macro MM showed an objective response at the time of imaging with 9 of 46 cases meeting the IMWG criteria for CR.Performing a similar analysis of patients with macro MM at relapse showed that 25% of patients presented with that pattern; a surprisingly high proportion. Extramedullary involvement was common (41%). Of note, 36% of patients repeatedly showed macrofocal patterns at subsequent relapses. PFS and OS at 2 years from macrofocal relapse were 24% and 39%, respectively. A matched group OS comparison was not possible since number of relapses and treatments were too different among the patients.ConclusionsMacro MM at presentation seems to be an early stage of MM with an excellent prognosis. In contrast, a macrofocal pattern at restaging is associated with poor prognosis and early relapse. At this disease stage residual focal lesions may represent drug resistant clones. At overt relapse a macrofocal pattern was frequently seen, highlighting the need to integrate advanced imaging tools into the standard work up and indicating an important confounder of standard minimal residual disease diagnostics in MM. [Display omitted] DisclosuresBarlogie:Signal Genetics: Patents & Royalties. Davies:Janssen: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Celgene: Consultancy, Honoraria. Morgan:Celgene: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria; Bristol Meyers: Consultancy, Honoraria; Janssen: Research Funding; Univ of AR for Medical Sciences: Employment.

Real-time quantitative polymerase chain reaction detection of minimal residual disease in acute lymphoblastic leukemia: a single-center experience

Background Monitoring of minimal residual disease (MRD) has become a frontline clinical practice in the treatment of virtually all childhood acute lymphoblastic leukemia (ALL) cases and in many cases of adult patients with ALL. The MRD diagnostics has proven to be the strongest prognostic factor allowing for risk group assignment into different treatment arms. The MRD techniques need to be sensitive (≤10–4), which means, the ability to detect one malignant cell among 10 000 normal cells; broadly applicable; accurate; reliable; fast; and affordable. Aim The objective of this study is to evaluate the analysis of immunoglobulin heavy chain (IGH) or T-cell receptor (TCR) gene rearrangements as targets for MRD assessment in ALL, allowing early detection of relapsed cases, compare with the results of morphological evaluation of the same cases and to risk stratify patients with ALL according to the MRD assessment as a prognostic marker independent and superior to other conventional risk factors. Patients and methods Overall, 30 patients (15 males and 15 females) with age ranged from 1 to 25 years old were included in this study. Patients were subjected to full medical history, clinical examination, laboratory examinations such as complete blood count, bone marrow aspirate smear examination, cytochemistry, and immunophenotyping. The molecular studies done by real-time PCR were performed using consensus primers and allele-specific primers for (IGH) or (TCR) gene rearrangements as targets to detect MRD. The ALL cases were assessed by real-time quantitative PCR at the time of diagnosis and at the end of induction chemotherapy, and comparative cycle threshold (Ct) relative quantification method was used for quantitative gene expression. Results The results showed discrepancy between the morphologic examination for ALL assessment depending on the 5% blast index as an indicator of remission or nonremission; morphological nonremissions (>5% blast) were detected in eight (26.7%) cases whereas 22 (73.3%) cases showed morphological remissions ( Conclusion Approximately 81% of ALL cases previously diagnosed as being in the remission state depending on the morphologic assessment only tend to harbor MRD as evident by positive MRD assessment using real-time PCR. The molecular assessment of MRD allows early detection of relapse with chance of intervention and tailoring of treatment according to the patients' need. It was found that there was no relation between MRD results and risk stratification in ALL according to age and white blood cell at diagnosis; this confirms that detection of MRD of leukemic cells can be considered a superior prognostic marker of relapse, independent from conventional prognostic factors. The risk classification in ALL based on MRD results could be used to guide the final treatment strategy and predict early relapse; this should allow prediction of response and relapse while patients are still in the state of clinical remission and morphological remission too.

A Model for Predicting Effect of Treatment on Progression-Free Survival Using Minimal Residual Disease As a Surrogate Endpoint in Chronic Lymphocytic Leukemia

A Model for Predicting Effect of Treatment on Progression-Free Survival Using Minimal Residual Disease As a Surrogate Endpoint in Chronic Lymphocytic Leukemia

Next Generation Flow (NGF): A High Sensitive Technique to Detect Circulating Peripheral Blood (PB) Clonal Plasma Cells (cPC) in Patients with Newly Diagnosed of Plasma Cell Neoplasms (PCN)

Introduction: Previous studies have shown that cPC can be detected in PB by conventional flow cytometry (FC) in around 70% of multiple myeloma (MM) and 37% of monoclonal gammopathy of undetermined significance (MGUS) patients at diagnosis. Its presence in MGUS has been associated with a higher risk of malignant transformation. We here investigated the utility and sensitivity of the EuroFlow-IMF NGF-MM minimal residual disease (MRD) approach for detecting circulating cPC in PB of patients with PCN. Methods: A total of 137 samples (including 71 PB and 66 bone marrow -BM- paired samples) from 71 newly-diagnosed PCN patients (37 MGUS; 21 MM; 5 SMM and 8 solitary plasmacytomas -SP-), plus 6 PB samples from healthy controls, were studied. Samples were processed following the EuroFlow Bulk Lysis Standard Operating Protocol (SOP) and stained with the EuroFlow-IMF MM MRD panel (Tube 1:CD138BV421/CD27BV510/CD38FITC/CD56PE/CD45PerCP-Cy5.5/CD19PE-Cy7/CD117APC/CD81APC-C750, and; Tube 2: identical to Tube 1 except for CyKappaAPC/CyLambdaAPC-C750). A median of 10.6 x106 events (range: 1.7 x106 - 15.7x106) were measured for PB samples using a FACSCanto II (BD Biosciences, San Jose, USA) instrument. Data were analyzed using the Infinicyt software (version 1.8.0RC6; Cytognos SL, Salamanca, Spain). Risk stratification of MGUS patients was established by the Mayo Clinic index. ROC analysis was used to define a cut-off to distinguish between MM and MGUS cases according to the percentage and absolute number of circulating PB cPC. Results: Overall, cPC were detected in the PB of all MM and SMM cases studied (100%) and more than half of MGUS patients (60%; p=0.005), while constantly absent in the eight patients with SP. Upon classifying MGUS patients according to the Mayo Clinic Index (n=32), positive PB samples were found in 25%, 62% and 73% of cases with scores of 0, 1 and 2, respectively. Median (range) percentage and absolute cPC numbers (per µL) were of 13 to 16 and 10 to 200 times lower (p 60% of cPCs within the PC BM compartment (R2 = 0.75; n=66). The cut-off obtained to distinguish between MM and MGUS cases according to the percentage and absolute number of cPCs circulating in PB was of 0.0009% and 0.055 cPC/µL with a sensitivity of 93% and 86%, and a specificity of 75% and 75% for relative and absolute numbers, respectively. Conclusions: The EuroFlow-IMF NGF-MM MRD panel and approach are well-suited for high sensitive detection of circulating cPC in the PB of virtually every newly-diagnosed MM and SMM patient and the majority of MGUS cases, particularly among MGUS at higher risk of malignant progression; interestingly in both patients groups, the presence of PB involvement and its levels were closely associated with the degree of involvement of the BM PC compartment by cPC. * Both authors have contributed similarly to this work and they should both be considered as first author. Disclosures Paiva:EngMab AG: Research Funding; Celgene: Consultancy; Janssen: Consultancy; Millenium: Consultancy; Binding Site: Consultancy; Sanofi: Consultancy; BD Bioscience: Consultancy; Onyx: Consultancy. Puig:Janssen: Consultancy; The Binding Site: Consultancy. Mateos:Celgene: Consultancy, Honoraria; Takeda: Consultancy; Onyx: Consultancy; Janssen-Cilag: Consultancy, Honoraria. Durie:Celgene: Consultancy; Onyx: Consultancy; Takeda: Consultancy; Johnson and Johnson: Consultancy. van Dongen:BD Biosciences (cont9d): Other: Laboratory Services in the field of technical validation of EuroFlow-OneFlow antibody tubes in dried format. The Laboratory Services are provided by the Laboratory of Medical Immunology, Dept. of Immunology, Erasmus MC, Rotterdam, NL; Cytognos: Patents & Royalties: Licensing of IP on Infinicyt software, Patents on EuroFlow-based flowcytometric Diagnosis and Classification of hematological malignancies, Patents on MRD diagnostics, and Patents on PID diagnostics. ; Cytognos (continued): Patents & Royalties: Royalty income for EuroFlow Consortium. The Infinicyt software is provided to all EuroFlow members free-of-charge.Licensing of Patent on detection of IgE+ B-cells in allergic diseases. Royalties for Dept. of Immunology, Erasmus MC, Rotterdam, NL; DAKO: Patents & Royalties: Licensing of IP and Patent on Split-Signal FISH. Royalties for Dept. of Immunology, Erasmus MC, Rotterdam, NL; InVivoScribe: Patents & Royalties: Licensing of IP and Patent on BIOMED-2-based methods for PCR-based Clonality Diagnostics.. Royalty income for EuroClonality-BIOMED-2 Consortium ; Immunostep: Patents & Royalties: Licensing of IP and Patents on immunobead-based dection of fusion proteins in acute leukemias and other tumors. Royalties for Dept. of Immunology, Erasmus MC and for EuroFlow Consortium ; BD Biosciences: Other: Educational Services: Educational Lectures and Educational Workshops (+ related travelling costs). The lectures and workshops fully focus on the scientific achievements of the EuroFlow Consortium (No advertisement of products of BD Biosciences). , Patents & Royalties: Licensing of IP and Patent on EuroFlow-based flowcytometric Diagnosis and Classification of hematological malignancies; Royalty income for EuroFlow Consortium.; Roche: Consultancy, Other: Laboratory Services in the field of MRD diagnostics, provided by the Laboratory of Medical Immunology, Dept. of Immunology, Erasmus MC, Rotterdam, NL.. San Miguel:Janssen-Cilag: Honoraria; Onyx: Honoraria; Millennium: Honoraria; Bristol-Myers Squibb: Honoraria; Celgene: Honoraria; Novartis: Honoraria; Sanofi-Aventis: Honoraria.

Next Generation Flow (NGF) for High Sensitive Detection of Minimal Residual Disease (MRD) in Multiple Myeloma (MM)

Next Generation Flow (NGF) for High Sensitive Detection of Minimal Residual Disease (MRD) in Multiple Myeloma (MM)

Analytical Validation of Patient-Specific PCR-Based MRD Assessment for Use As a Primary Endpoint in CLL Clinical Trials

Analytical Validation of Patient-Specific PCR-Based MRD Assessment for Use As a Primary Endpoint in CLL Clinical Trials

Library Preparation Is the Major Factor Affecting Differences in Results of Immunoglobulin Gene Rearrangements Detection on Two Major Next-Generation Sequencing Platforms

Minimal residual disease (MRD) assessment via next generation sequencing (NGS) of immunoglobulin (Ig) and T-cell receptor (TR) gene rearrangements for lymphoid malignancies is currently under extensive development. NGS MRD has a potential to overcome the limitations of current techniques; laboriousness and difficult interpretation of qPCR for Ig/TR and low sensitivity of flow cytometry. However, amplicon-based NGS MRD has potential pitfalls that have to be addressed before it can be safely introduced for clinical decision making. Multi-center concordance in the experimental setting, quality control and interpretation of the results need to be achieved in order to surpass the advantages of qPCR, which is currently rigorously standardized within the EuroMRD consortium.Our aim was to test the stability and reproducibility of an optimized Ig heavy chain (IGH) based NGS approach for MRD assessment in a multi-center setting within the EuroClonality NGS Consortium on two different sequencing platforms.A one-step PCR library preparation approach was tested in seven institutions (Kiel, Salamanca, Milano, Bristol, London, Prague, Torino). Serial dilutions (10-1 to 10-5) of diagnostic DNA into polyclonal DNA as well as follow-up samples of 30 B-cell precursor ALLs with known complete IGH rearrangements were sequenced on the MiSeq. Serial dilutions of five different diagnostic ALL samples and libraries from polyclonal control were sequenced in parallel on both the MiSeq and Ion Torrent platforms. All samples were spiked with pre-defined copy numbers of five reference IGH sequences as a calibrator. FR2 primers, harboring platform-specific sequencing adapters, were used during the one-step PCR with 500ng of DNA per sample (75,000 copies). Negative and positive controls (27 pooled B-cell lines) were used for testing assay stability and reproducibility among the labs. Purpose-built bioinformatics methods were applied to analyze data. MRD results were compared to results of EuroMRD-based qPCR results.A total of 333 libraries were sequenced in 29 deep sequencing runs producing 194 million reads. The IGH gene rearrangements of all 27 pooled positive B-cell line controls were identified in all centers. NGS MRD analysis in 116 ALL follow-up samples revealed MRD positivity in 69/116 samples vs. 66/116 samples in qPCR, with discrepancies concerning samples with low MRD (R2=0.81). The dilution experiments gave similar results for both platforms, with a minimum sensitivity of 10-4 (as currently required by most treatment protocols using qPCR) for all tested assays. The correlation between MRD levels obtained by the two NGS platforms was good (R2=0.84). Ratios of reads containing reference IGH sequences were highly consistent in intra- and inter-laboratory analyses, independent of the total number of reads in the sample. When comparing platforms, in 10-1 dilution samples sequenced on MiSeq the ratio of reads harboring reference sequences was 2.1 to 2.7 times lower than in remaining dilutions, while on the Ion Torrent it was only 0.9 to 1.3 times, reflecting the competition with the leukemic clone. The correlation of the amounts of spiked-in sequences with the representation of reads harboring these sequences was slightly better for the Ion Torrent (R2=0.88) than for the MiSeq (R2=0.79). Amplification efficiency of each primer was checked by analyzing libraries from healthy polyclonal control. All primer sequences were present in all samples on both platforms, however, the differences between four libraries prepared from the same sample sequenced on the MiSeq were 2.6 times higher than in one library from this sample sequenced in five replicates on the Ion Torrent.The newly developed IGH assay shows robust intra and inter-laboratory reproducibility, which is the first step towards the safe use of this new MRD technique in a multi-center setting. The distribution of reference sequences and sequences of primers confirmed that the main source of differences between platform strategies is the library preparation and not the platform itself. Using the same amount of DNA, the sensitivity of the method is similar to qPCR. The performance and costs of the assay are similar for both the MiSeq and Ion Torrent. MRD analysis via NGS has therefore a great potential to replace qPCR as the gold standard for MRD-guided therapy in ALL, provided that thorough standardization can be achieved.Support: NV15-30626A, GBP302/12/G101. DisclosuresLangerak:Roche: Other: Lab services in the field of MRD diagnostics provided by Dept of Immunology, Erasmus MC (Rotterdam); DAKO: Patents & Royalties: Licensing of IP and Patent on Split-Signal FISH. Royalties for Dept. of Immunology, Erasmus MC, Rotterdam, NL; InVivoScribe: Patents & Royalties: Licensing of IP and Patent on BIOMED-2-based methods for PCR-based Clonality Diagnostics..

Monitoring of minimal residual disease in acute leukemia by multiparametric flow cytometry

In this review, we discuss methodological principles and clinical applications of minimal residual disease (MRD) assays based on multiparameter flow cytometry (MFC). The introduction of methods for MRD detection has revolutionized monitoring of treatment response in acute leukemia. Great progress has been made in the development of wide array of flow cytometric techniques for rare event detection. This advance was accompanied by increasingly greater understanding of the immunophenotypic features of leukemic and normal lymphoid cells, and of the antigenic differences that make MRD studies possible. Immunologic testing of MRD relies on "leukemia-associated" immunophenotypes which can be identified by MFC in the most of acute leukemia cases. The recent technical innovations in routine MFC (3 lasers and≥8 colors) and the new developments in software for data analysis make this technology the most attractive for MRD diagnostics. The importance of MFC methodology will be further strengthened by the ongoing international standardization efforts. Results of MRD testing provide unique and clinically important information. The systematic application of immunologic techniques to study MRD in clinical samples has demonstrated the prognostic significance of MRD in patients, leading to the use of MRD to regulate treatment intensity in many contemporary protocols. The identification of new markers of MRD should increase the sensitivity of MRD testing by MFC and is required to widen the applicability of MRD studies.

Next-Generation Sequencing and Real-Time Quantitative PCR For Quantification Of Low-Level Minimal Residual Disease In Acute Lymphoblastic Leukemia Of Adults

BackgroundDetection of minimal residual disease (MRD) in adult ALL is an independent risk parameter and early indicator of an impending relapse. MRD diagnostics have been incorporated in many ALL treatment protocols as a tool for pre-emptive treatment or risk group stratification. Currently, real-time quantitative (RQ)-PCR of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements is regarded as the most sensitive and standardized method to quantify MRD in BCR-ABL negative ALL. However, IG/TR oligoclonality and clonal evolution may lead to false negative results, while sensitivity varies depending on background amplification and is generally limited to 1E-05. Next-Generation Sequencing (NGS) of IG/TR gene rearrangements might overcome these limitations and potentially provide further increases in sensitivity, specificity, accuracy and reproducibility. We have performed a comparison of the two approaches on 130 diagnostic (DG), relapse (REL) and remission (FU) samples of 14 adult patients (pts) with B-cell precursor ALL. To test the NGS sensitivity, we partly selected follow-up samples for (low-level) RQ-PCR MRD positivity or a high pre-test probability of residual disease (either due to a later relapse or MRD detection in temporal relation to the analyzed sample). Patients and Methods130 samples (97 bone marrow, 31 peripheral blood, 2 stem cell apheresis; 15 DG, 107 FU, 8 REL samples) were analyzed from 14 pts with B-cell precursor ALL. IG/TR-based RQ-PCR was carried out within routine diagnostics in the context of prospective clinical trials [Brüggemann et al., Blood 2006], according to the EuroMRD criteria [van der Velden et al., Leukemia 2007] at the MRD reference laboratory in Kiel. NGS was performed at the Sequenta facilities in South San Francisco. Using universal primer sets, IGH, IGK, TRB, TRG, and TRD variable, (diversity), and joining gene segments were amplified from DG and REL DNA. PCR products were sequenced to obtain a high degree of coverage and analyzed using standardized algorithms for clonotype determination. Tumor-specific clonotypes were identified for each patient based on their high-frequency in DG samples. The presence of the tumor-specific clonotype was then quantitated in FU samples. A quantitative and standardized measure of clone level among all leukocytes was determined using internal reference DNA. Comparability of MRD results by RQ-PCR and NGS was assessed using bivariate correlations between methods analysis (software R 3.0.1 with cor.test). ResultsSanger sequencing of multiplex PCR detected 60 clonal IGH, IGK, TRB, TRG and/or TRD gene rearrangements at diagnosis (1-6/patient), NGS identified 57 index sequences (1-6/patient). Using NGS, relapse samples were analyzed for clonal evolution: 16/19 index rearrangements of relapsing pts were stable at relapse while 3/19 rearrangements (2 IGH VH-JH and 1 IGK) were lost at relapse.Based on Sanger sequence information of clonal rearrangements 1-3 RQ-PCR assays/patient were established while NGS focused on 1-4 clonal markers/patient.MRD was quantified in 107 FU in remission using both tools. A mean of 223,086±48,030 cells were analyzed per target using RQ-PCR, whereas NGS used 575,776±304,653 cells. An excellent concordance between the two methods was observed (p<0.0001, r2 = 0.974) with 46/107 samples being MRD positive and 45/107 MRD negative with both tools. Sequencing detected MRD in 13 samples that were negative by RQ-PCR whereas RQ-PCR revealed MRD in 3 NGS negative samples. All discrepancies affected samples with low MRD levels (below quantitative range (RQ-PCR) and levels below 8E-06 (NGS)) being consistent with Poisson sampling. In addition, both methods showed quantitative and qualitative inter-target differences with 11/49 RQ-PCR and 32/59 NGS positive samples being negative for at least one target illustrating the importance of focusing on more than one index sequence for RQ-PCR and NGS. ConclusionsSignificant concordance was observed between NGS and RQ-PCR, with NGS having similar or slightly better sensitivity compared to standardized RQ-PCR. This can be partly attributed to the higher number of cells analyzed by NGS and points out that sensitivity advantages afforded by the NGS platform may be achieved by higher input cell amounts. Prospective analyses of unselected cases must be performed to verify the clinical impact of low level NGS-based MRD detection. Disclosures:Pepin:Sequenta Inc.: Employment, Stockholder Other. Carlton:Sequenta Inc.: Employment, Stockholder Other. Faham:Sequenta Inc.: Employment, Stockholder Other.