Next-Generation Sequencing of Immunoglobulin Heavy Chain Variable Region in Diagnostic Samples of Pediatric Acute Lymphoblastic Leukemia Identifies Hundreds of Clonal Subpopulations with Multiple Immunophenotypes

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1436-1436
Author(s):  
Charles Gawad ◽  
Malek Faham ◽  
Tom Willis ◽  
Martin Moorhead ◽  
Victoria Carlton ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Next Generation Sequencing ◽  
Acute Lymphoblastic Leukemia ◽  
High Risk ◽  
High Frequency ◽  
Lymphoblastic Leukemia ◽  
Variable Region ◽  
Employment Equity ◽  
Equity Ownership ◽  
Generation Sequencing

Abstract Abstract 1436 Background: The use of flow cytometry or real-time PCR-based methods to detect minimal residual disease (MRD) in children with Acute Lymphoblastic Leukemia (ALL) is a powerful tool for risk-adapted therapy stratification. However, current protocols for MRD detection incorrectly anticipate leukemia-free survival in 20–30% of low and intermediate risk patients. In this study, we present a new method for MRD detection using next-generation sequencing of the variable region of the immunoglobulin heavy chain (IgH) gene that can overcome two important limitations of current approaches as: (1) it detects lower levels of leukemia cells and (2) it identifies multiple evolved clones. Methods: To capture IgH sequences, we developed a set of multiplexed primers that allow the amplification of all known alleles of each V and J segment. We optimized the protocol to minimize amplification bias between primers. The products were then sequenced using the Illumina platform to obtain >1 million reads per sample. Using a streamlined algorithm, the data were used to calculate the frequency of clonotypes in each sample in a very sensitive and specific manner. Serial dilution experiments have also shown that this technology has a sensitivity of 0.0001%, or about 2 orders of magnitude better than flow cytometry. Results: To establish the ability to identify the leukemic clone, as well as the frequency of evolved clonotypes at diagnosis, we performed a pilot study with 24 diagnostic bone marrow samples (standard risk n=17, high risk n=6, very high risk n=1) from children with ALL. In these samples, single high-frequency clones were identified in 6 samples and multiple high-frequency clones were detected in 12 patients. Thus, we identified high-frequency clones in 75% (18/24) of samples. This is in agreement with previously published reports of PCR methods for VJ amplification. Next we compared the sequences of samples with multiple high-frequency clonotypes and found that, in all cases, the evolution was consistent with the previously described mechanism of V replacement. The evolved clones shared the same J segment allele, the number of bases deleted in the J segment, and at least part of the NDN sequence. Interestingly, in one patient there were 6 clonotypes with a frequency >1%. We then assessed whether the unique sequences present in these 6 clonal populations appeared in other lower frequency clonotypes from the same patient. We identified hundreds of distinct but related clones, consistent with active ongoing evolution of the leukemia. To further validate that the identified clonotypes in this patient were indeed leukemic, we sorted out the normal and malignant B cells, followed by repeat IgH sequencing. All the sequences suspected to have arisen by V replacement were enriched in the leukemic population and virtually absent from normal B cells. Finally, we sought to assess whether the evolved clones could have variable expression of surface markers used for MRD detection. In one patient, the different evolved clonotypes had variable CD38 expression based on IgH sequencing of blasts sorted by CD38. Further characterization of these clonotypes may reveal distinct underlying biology, as well as differing propensities for relapse. To further assess the associations between IgH sequence and immunophenotype, we are performing flow cytometry and sequencing of sorted subpopulations in additional diagnostic ALL samples (n=50). Conclusion: These findings suggest that this new technology may offer superior sensitivity and specificity for MRD detection, as well as more accurate stratification for risk-adapted therapies in children with ALL. Disclosures: Faham: Sequenta Inc: Employment, Equity Ownership. Willis:Sequenta Inc: Employment, Equity Ownership. Moorhead:Sequenta Inc.: Employment. Carlton:Sequenta Inc.: Employment. Zheng:Sequenta Inc.: Employment. Klinger:Sequenta Inc.: Employment.

Highly Sensitive Detection of Minimal Residual Disease in Acute Lymphoblastic Leukemia Using Next-Generation Sequencing of Immunoglobulin Heavy Chain Variable Region

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2540-2540
Author(s):  
Malek Faham ◽  
Tom Willis ◽  
Martin Moorhead ◽  
Victoria Carlton ◽  
Jianbiao Zheng ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Next Generation Sequencing ◽  
Lymphoblastic Leukemia ◽  
Patient Specific ◽  
Next Generation ◽  
Conventional Pcr ◽  
Employment Equity ◽  
Equity Ownership ◽  
Generation Sequencing

Abstract Abstract 2540 Background: Minimal Residual Disease (MRD) assessment is increasingly used for treatment stratification since it is a strong predictor of outcome in Acute lymphoblastic leukemia (ALL). The most widely used MRD assays include flow cytometric detection of aberrant immunophenotypes and PCR amplification of patient-specific antigen-receptor sequences. The latter approach has proven to provide reliable clinical information but requires the development of patient-specific reagents which is laborious, time-consuming, and generates assays with variable sensitivities. In addition, this methodology may miss clonal changes that can occur during the course of the disease, such as the emergence of subclones as well as genetic evolution. To overcome these limitations, we developed a universal amplification assay with a sequencing readout that eliminates the need for patient-specific reagents, allows the assay to detect leukemic cells that have genetically evolved, and has a higher sensitivity than conventional tests. Methods and Results: To amplify all the IgH sequences, we developed a PCR assay to amplify all alleles of all the V and J segments with very low amplfication bias. Amplified molecules were then subjected to clonal sequencing to obtain >1 million reads to measure the frequency of the different IgH clonotypes in the sample. It should be noted that current next generation sequencing costs of this deep sequencing are similar to those of an MRD test conducted by flow cytometry. We tested the sensitivity of the method by in serial dilutions of genomic DNA from a leukemia sample known to carry two IgH clonotypes with into genomic DNA obtained from peripheral blood sample from a healthy donor. The material from the dilution series was then sequenced and analyzed to measure the level of these clones. The leukemic clonotypes could be readily detected even when diluted 1 million fold. To directly compare the our method to established MRD assays in ALL, we studied diagnostic and follow-up samples from 10 ALL patients whose MRD levels have been previously assessed by both real-time PCR amplification of IgH genes and flow cytometry. The results of these tests were not disclosed until completion of the deep sequencing analysis. The follow up samples were collected during (n = 3) or at the end of remission induction therapy (n = 4), or during continuation therapy (n = 3). Samples were processed similarly to identify the leukemia-specific sequence in the diagnostic samples and determine the level of these sequences in the follow up samples. The sequencing-based method identified all 5 samples that were MRD-positive according to flow cytometry and PCR (Figure 2), with highly concordant estimates of MRD levels. Notably, among the remaining 5 samples, scored as MRD-negative by both flow cytometry and conventional PCR, the sequencing method detected residual leukemic sequences at a very low level (∼10−6) in one of the samples. The other 4 samples were MRD-negative by all three methods. Studies with a larger cohort of ALL samples are ongoing. Contrary to conventional PCR-based MRD testing, the sequencing technology allows for the detection of leukemic clones that evolve by V replacement or other mechanisms. In this study, we identified clonotypes in several of the diagnostic samples that appeared to be the result of V replacement. These and other newly appearing related clones can be monitored in subsequent samples using the generic amplification and sequencing assay. Conclusions: We developed a highly sensitive and specific MRD detection method based on next-generation sequencing of IgH genes. This method has substantial advantages over conventional PCR MRD in that it eliminates the need for patient-specific reagents, can follow genetic evolution, and has potential for higher sensitivity. Disclosures: Faham: Sequenta Inc: Employment, Equity Ownership. Willis:Sequenta Inc: Employment, Equity Ownership. Moorhead:Sequenta Inc: Employment, Equity Ownership. Carlton:Sequenta Inc: Employment, Equity Ownership. Zheng:Sequenta Inc: Employment, Equity Ownership.

scholarly journals Identification Rate of Myeloma-Specific Clonotypes in Multiple Diagnostic Sample Types from Patients with Multiple Myeloma Using Next-Generation Sequencing Method

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2036-2036 ◽  
Author(s):  
Hervé Avet-Loiseau ◽  
Jill Corre ◽  
Sabrina Maheo ◽  
Jianbiao Zheng ◽  
Malek Faham ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Bone Marrow ◽  
Next Generation Sequencing ◽  
High Frequency ◽  
Plasma Cells ◽  
Employment Equity ◽  
Myeloma Cells ◽  
Sequencing Method ◽  
Equity Ownership ◽  
Generation Sequencing

Abstract Background: Recent reports support the prognostic importance of minimal residual disease (MRD) levels in multiple myeloma (MM) patients and suggest that novel methods for MRD assessment can play a role in the evolving MM treatment paradigm (Martinez-Lopez et al., Blood 2014). The application of next-generation sequencing (NGS)-based MRD assessment has been previously demonstrated in multiple lymphoid malignancies (Faham et al., Blood 2012; Ladetto et al., Leukemia 2013). NGS-based MRD assessment requires a diagnostic sample for initial identification of the myeloma clonotype. In order for this MRD assessment approach to be clinically practical, it must allow for analysis of a diverse set of diagnostic samples. In this study, we assessed the rate of myeloma clonotype identification in 6 sample types at diagnosis: bone marrow (BM) aspirate slides, RNA extracted from CD138+ plasma cells, methanol-fixed BM cells, BM mononuclear cells, RBC-lysed BM cells, and DNA extracted from small numbers of CD138+ plasma cells. Methods: Baseline samples were collected from 606 patients with MM. The following samples were provided at baseline: bone marrow aspirate (BMA) slides (164), RNA extracted from CD138+ plasma cells (402), methanol-fixed BM cells (30), BMA cell preparations using a Ficoll protocol (13), BMA cell preparations using an RBC lysis protocol (19), and DNA extracted from small numbers of CD138+ plasma cells (5). Samples with sufficient input DNA (>15ng) were included in the analysis, although this requirement was waived for samples from CD138+ cells. The Ficoll BMA cell preparations were divided into the mononuclear cell fraction and the lower Ficoll fraction, which is typically comprised of granulocytes and erythrocytes. Identification of myeloma clonotypes was performed using Sequenta's LymphoSIGHT™ method. Briefly, using universal primer sets, we amplified immunoglobulin heavy chain (IGH) and light chain (IGK) variable, diversity, and joining gene segments from genomic DNA. Amplified products were sequenced and analyzed using standardized algorithms for clonotype determination. Myeloma-specific clonotypes were identified for each patient based on their high-frequency (>5%) within the B-cell repertoire. Results: The NGS assay identified a high-frequency myeloma clonotype in 555/606 (92%) of patients with MM. Myeloma clonotype identification rates were 141/164 (86%) in BMA slides, 375/402 (93%) in RNA extracted from CD138+ plasma cells, 30/30 (100%) in methanol cell preparations, 13/13 (100%) in Ficoll cell preparations, 18/19 (95%) in RBC lysis cell preparations, and 5/5 (100%) using small amounts of input CD138+ DNA (approximately 5000 cells). These applicability rates are consistent with previous reports of sequencing applicability in MM patients. In thirteen patients, we investigated the potential loss of myeloma-specific clonotypes due to Ficoll cell preparation. The variation in myeloma cell loss was typically low but ranged from essentially no loss to the loss of more than 90% of the myeloma cells in the PBMC of one patient compared to the RBC lysis preparation. The myeloma cells were detected in the typically discarded lower layer of the Ficoll preparation which explained the loss. Conclusions: These results suggest that sequencing based MRD analysis is applicable in >90% of patients with MM. Multiple sample types, including archived BMA slides, can be used for identification of the myeloma clonotype. Further evaluation and optimization of sample processing methods is ongoing to enable application of the sequencing method for clinical MRD assessment in MM patients. Disclosures Zheng: Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Munshi:Celgene: Consultancy; Onyx: Consultancy; Janssen: Consultancy; Sanofi-Aventi: Consultancy; Oncopep: Consultancy, Equity Ownership, Patents & Royalties.

Robust Detection Of Minimal Residual Disease In Unselected Patients With B-Cell Precursor Acute Lymphoblastic Leukemia By High-Throughput Sequencing Of IGH

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2550-2550
Author(s):  
David Wu ◽  
Ryan O Emerson ◽  
Anna Sherwood ◽  
Mignon L. Loh ◽  
Anne Angiolillo ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Acute Lymphoblastic Leukemia ◽  
B Cell ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Lymphoblastic Leukemia ◽  
Post Treatment ◽  
Employment Equity ◽  
Equity Ownership ◽  
Pre Treatment

Abstract High-throughput sequencing (HTS) of immunoglobulin heavy chain genes (IGH) may be useful for detecting minimal residual disease (MRD) in acute lymphoblastic leukemia. We previously demonstrated the first application of high-throughput sequencing for the detection of minimal residual disease in T-cell precursor acute lymphoblastic leukemia (TPC-ALL) (Sci. Transl. Med. 4(134):134ra63. 2012). Recently, Faham and colleagues considered deep sequencing for MRD detection in B-cell precursor acute lymphoblastic leukemia (BPC-ALL) (Blood 120(26):5173-80, 2012). As this prior analysis in BPC-ALL apparently focused only on samples known to have a clonal rearrangement in IGH, the potential applicability and wide-spread utility of sequencing of IGH in unselected clinical samples for MRD has not been tested. Here, we consider an unselected cohort of patients enrolled in Children Oncology Group AALL0932 trial and use residual material from 99 patient samples submitted for routine multi-parametric flow cytometry (mpFC) at U. of Washington. One sample failed in the initial DNA extraction step and was not further considered. We show using high-throughput sequencing that clonal IGH rearrangements can be identified in 92 of the remaining 98 pre-treatment samples, using a definition of a V-D-J or D-J rearrangement comprising at least 10% of total nucleated cells (Fig. 1A). Similar to our prior findings in TPC-ALL, we find three subsets of patients—1) those for whom MRD is not detected by either flow cytometry or HTS; 2) those for whom MRD is detected both by flow cytometry and HTS; and 3) those for whom MRD is detected only by HTS, but not flow cytometry (Fig. 1B). There were no false negative results by HTS as compared to flow cytometry.Figure 1Measurement of clonal IGH rearrangement by high-throughput sequencing (HTS) or immunphenotypically abnormal B lymphoblast population by multi-parametric flow cytometry in pre-treatment (A) or day 29 post-treatment (B) residual samples. Results are reported for both HTS (red) and mpFC (blue) as clone frequency per total nucleated cells.Figure 1. Measurement of clonal IGH rearrangement by high-throughput sequencing (HTS) or immunphenotypically abnormal B lymphoblast population by multi-parametric flow cytometry in pre-treatment (A) or day 29 post-treatment (B) residual samples. Results are reported for both HTS (red) and mpFC (blue) as clone frequency per total nucleated cells. In the third group (HTS+positive, flow cytometry-negative), a subset of these patients, (5 of 28) had MRD detectable by HTS at a level within the expected sensitivity of flow cytometry. We hypothesized that in these cases that post-treatment MRD sequences may be present within the maturing B cell compartment that is not immunophenotypically aberrant by flow cytometry. To test this hypothesis, we analyzed eight additional post-treatment samples that were negative for MRD by flow cytometry. The mature B-cell fraction was collected by triple, flow cytometry-sorting and then sequenced by HTS for IGH rearrangements to search for the index clone defined in the corresponding, paired pre-treatment samples. Although a limited finding, diagnostic index IGH sequence was indeed identified in one of eight samples, in only the mature B-cell fraction, which is consistent with the proportion of cases with high-level MRD detected by HTS but which was missed by flow cytometry. Taken together, our results provide additional support for assessment of MRD in acute lymphoblastic leukemia by high-throughput sequencing. Our findings argue that precise quantification of the level of MRD by HTS will be important, and suggest that clonal IGH rearrangement sequences may be detected in an immunophenotypically normal population of mature B cells that may not be detected by flow cytometry. Disclosures: Emerson: Adaptive Biotechnologies: Employment, Equity Ownership. Sherwood:Adaptive Biotechnologies: Employment, Equity Ownership. Kirsch:Adaptive Biotechnologies: Employment, Equity Ownership. Carlson:Adaptive Biotechnologies: Consultancy, Equity Ownership, Patents & Royalties. Williamson:Adaptive Biotechnologies: Employment, Equity Ownership. Wood:Becton Dickinson and Company, NJ, USA: Research Funding. Robins:Adaptive Biotechnologies: Consultancy, Equity Ownership, Patents & Royalties.

Use Of Rearranged Immune Receptor Sequencing To Measure Minimal Residual Disease (MRD) In Bone Marrow, Cerebrospinal Fluid and Testes In Relapsed Childhood Acute Lymphoblastic Leukemia

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 4984-4984
Author(s):  
Norman J. Lacayo ◽  
Li Weng ◽  
Charles Gawad ◽  
Malek Faham ◽  
Gary V Dahl
Keyword(s):  
Bone Marrow ◽  
Flow Cytometry ◽  
Cerebrospinal Fluid ◽  
Acute Lymphoblastic Leukemia ◽  
Deep Sequencing ◽  
Residual Disease ◽  
Lymphoblastic Leukemia ◽  
Employment Equity ◽  
Equity Ownership ◽  
Minimal Residual

Abstract Background Detection of minimal residual disease (MRD) in pediatric acute lymphoblastic leukemia (ALL) is a strong predictor of outcome. In addition, MRD testing prior to stem cell transplant for ALL can inform on the risk of relapse. The ClonoSIGHT test uses deep sequencing of immunoglobulin and T-cell receptors to identify and monitor MRD. In retrospective cohorts, we have previously shown this technology is highly correlated with flow cytometry and PCR-based MRD methods, but has even greater sensitivity than both technologies (Faham et al, Blood 2012; Gawad et al, Blood 2012).  Here we report on four clinical cases where we used the ClonoSIGHT assay to prospectively monitor MRD, in both the medullary and extramedullary compartments, to demonstrate the feasibility of this technology for MRD monitoring of children with relapsed ALL. Methods Universal primer sets were used to amplify rearranged variable (V), diversity (D), and joining (J) gene segments from the immunoglobulin heavy and kappa chain (IGH and IGK), as well as T-cell receptor beta, delta and gamma.  The assay was performed on genomic DNA isolated from cells from the bone marrow, cerebrospinal fluid, or testes.  The test was first done at the time of relapse to identify the malignant clonotype, which was monitored at subsequent time points. The patients were ineligible for clinical trials and concurrently underwent MRD testing using flow cytometry. The sequencing assays were performed to show feasibility of the approach. Results  Patient one was a 14 y/o ALL relapse patient who was not in morphologic remission after standard re-induction therapy. The malignant clonotype was identified on a bone marrow aspirate from relapse; follow-up MRD tests were done using both flow cytometry and deep sequencing five times throughout salvage therapy with 5-aza-2'-deoxycytidine, suberoylanilide hydroxamic acid and high dose cytarabine over 75 days; the last two MRD data points showed 0.6% and 6% by ClonoSIGHT MRD and 0.4% and 1.3% by flow cytometry MRD. Morphologic remission with count recovery was used as the criteria to direct this patient to SCT. Patient two was a 9 y/o with ALL, for whom MRD was used to test for relapsed disease in multiple tissues.  This patient experienced three isolated testicular relapses (M1 marrow and no CNS involvement) at the time of each relapse. The ClonoSIGHT assay was used on tissue from a testicular biopsy to identify the malignant clone(s).  Testing of the bone marrow and cerebrospinal fluid did not detect the malignant clones in those sites. This patient underwent therapeutic orchiectomy and 4-week systemic re-induction resulting in a fourth complete remission and now is under evaluation for consolidation therapy with a SCT. A third patient was an 8 y/o with a combined bone marrow and testicular ALL relapse, who was in morphologic remission in the marrow after re-induction therapy and testicular radiotherapy. Prior to undergoing SCT the patient had negative MRD by flow cytometry but had 0.008% MRD using the ClonoSIGHT MRD assay.  The fourth patient was a 15-yo with ALL relapse at 9 years from first remission, treated with a four-drug re-induction and Berlin-Frankfurt-Münster based consolidation and maintenance therapy.  This patient was MRD negative by both flow cytometry and ClonoSIGHT MRD at end of re-induction as well as end of consolidation and remains in remission. Conclusions We have shown the feasibility of using sequencing-based tests for monitoring MRD in children with relapsed ALL in medullary (bone marrow) and extramedullary compartments (testes and CSF).  Further studies are needed to establish the prognostic value of MRD detected by the ClonoSIGHT assay in both medullary and extramedullary sites that are below the limit of detection of PCR and flow cytometry. These sequencing-based tests may provide a useful tool to develop risk stratification schemas for drug development in relapsed childhood ALL. Disclosures: Weng: Sequenta, Inc.: Employment, Equity Ownership. Faham:Sequenta, Inc.: Employment, Equity Ownership, Membership on an entity’s Board of Directors or advisory committees.

scholarly journals Minimal Residual Disease Detection in Adults with Acute Lymphoblastic Leukemia By Next Generation Sequencing: Impact on Clinical Outcomes

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 9-9
Author(s):  
Lissette Cervantes ◽  
Lan Wang ◽  
George Yaghmour ◽  
Andrei Varnavski ◽  
Imran Siddiqi
Keyword(s):  
Flow Cytometry ◽  
Next Generation Sequencing ◽  
Acute Lymphoblastic Leukemia ◽  
Board Of Directors ◽  
Residual Disease ◽  
Lymphoblastic Leukemia ◽  
Advisory Committees ◽  
Post Induction ◽  
Generation Sequencing ◽  
Minimal Residual

Introduction: Measuring minimal residual disease (MRD) is an essential component of directing treatment and predicting outcomes in patients with acute lymphoblastic leukemia (ALL). Current methods used to detect MRD in patients with ALL include multiparameter flow cytometry (Flow), allele-specific and mutation-specific quantitative polymerase chain reaction, and more recently next-generation sequencing (NGS)-based methods. While flow cytometry remains standard of care for ALL MRD evaluation in most institutions, quantification of MRD with higher sensitivity assays could potentially improve early detection of clinical relapse resulting in better survival outcomes. The clonoSEQ NGS-based platform (Adaptive Biotechnologies, Seattle WA) tracks tumor specific V(D)J rearrangements in lymphoid malignancies and can detect MRD at less than 10-6 (0.0001%) level. Here we describe a real-world practice-based comparison of the impact of MRD testing by clonoSEQ and Flow on clinical outcomes in ALL. Methods: We retrospectively evaluated 45 adult patients with confirmed ALL admitted to the Norris Cancer Center (University of Southern California) between November 2017 and June 2020. In all patients, the presence/absence [(+)/(-)] of MRD was evaluated on bone marrow aspirates by both the clonoSEQ assay (clonoSEQ MRD) and by a flow cytometry-based COG ALL MRD assay (Flow). Descriptive statistics were used to characterize the cohort. The Fisher's exact test was used to describe groups with categorical outcomes. A p-value of < 0.05 was considered statistically significant. Results: Forty-five patients included in our study were aged 20 to 67 (median age 38), with 67% (30/45) males, 82% diagnosed with B-ALL (13% Ph-positive, 36% Ph-like, 51% Ph- negative),13% with T-ALL, and 5% with mixed-phenotype leukemia. Three patients were excluded from the analysis due to insufficient sampling. Among 38% (16/42) of patients with original Flow(-)/clonoSEQ(+) MRD, 31% (5/16) eventually became Flow(+) and later clinically relapsed, and 19% (3/16) received blinatumomab as a bridge to allogeneic hematopoietic cell transplantation (allo-HCT) and 2 remain in clinical remission (CR), 1 died from other medical complications. 11/14 Ph-like patients were analyzed post-induction. Post-induction clonoSEQ MRD status was used to direct these Ph-like B-ALL patients to allo-HCT (if positive, 8/11 patients) or to continue chemotherapy (if negative, 3/11 patients). Among 8/11 patients who underwent allo-HCT, 3/8 relapsed, while 5/8 remain in CR. All 3/11 patients who continued chemotherapy without allo-HCT, based on the clonoSEQ(-) MRD, remain in CR. Comparative post-induction clonoSEQ/Flow MRD data was available for 12 patients. Among these, 25% (3/12) were Flow(+)/clonoSEQ(+), 25% (3/12) were Flow(-)/clonoSEQ(+), and 50% (6/12) were Flow(-)/clonoSEQ(-), with the 12-month disease-free survival (DFS) rates of 33%, 100%, and 50%, respectively. Conclusions: Adult ALL is commonly associated with high relapse rates, often requiring therapy intensification with other agents or allo-HCT. We observed a trend towards a lower relapse rate and better outcomes with early treatment with blinatumomab and/or allo-HCT. Patients with post-induction clonoSEQ(-) MRD, who continued chemotherapy without allo-HCT or immunotherapy maintained molecular CR for > 1 year after diagnosis. Our data supports the clinical benefit of early molecular MRD evaluation with clonoSEQ to guide subsequent additional treatment (to reduce/eliminate MRD) or defer allo-HCT in MRD(-) patients. It is also important to note that a substantial subset of our unique adult population had high risk disease, whereas previous studies have focused on pediatric populations. Due to the small number of patients included, this analysis was mainly descriptive, and a larger patient cohort would be needed to better evaluate the clinical impact of MRD testing in adult ALL. Disclosures Yaghmour: Jazz:Consultancy, Speakers Bureau;Astellas:Consultancy, Speakers Bureau;Takeda:Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau;Alexion:Consultancy, Speakers Bureau;Agios:Consultancy, Membership on an entity's Board of Directors or advisory committees;Novartis:Consultancy, Membership on an entity's Board of Directors or advisory committees.Varnavski:Adaptive Biotechnologies:Current Employment.

scholarly journals BCR/ABL1-Like Acute Lymphoblastic Leukemia: From Diagnostic Approaches to Molecularly Targeted Therapy

2021 ◽  
pp. 1-9
Author(s):  
Anna Płotka ◽  
Krzysztof Lewandowski
Keyword(s):  
Flow Cytometry ◽  
Targeted Therapy ◽  
Acute Lymphoblastic Leukemia ◽  
High Risk ◽  
Lymphoblastic Leukemia ◽  
Genetic Alterations ◽  
Diagnostic Analysis ◽  
Cell Precursor ◽  
Molecularly Targeted Therapy ◽  
Diagnostic Approaches

<b><i>Background:</i></b> <i>BCR/ABL1</i>-like acute lymphoblastic leukemia is a newly recognized high-risk subtype of ALL, characterized by the presence of genetic alterations activating kinase and cytokine receptor signaling. This subtype is associated with inferior outcomes, compared to other B-cell precursor ALL. <b><i>Summary:</i></b> The recognition of <i>BCR/ABL1</i>-like ALL is challenging due to the complexity of underlying genetic alterations. Rearrangements of <i>CRLF2</i> are the most frequent alteration in <i>BCR/ABL1</i>-like ALL and can be identified by flow cytometry. The identification of <i>BCR/ABL1</i>-like ALL can be achieved with stepwise algorithms or broad-based testing. The main goal of the diagnostic analysis is to detect the underlying genetic alterations, which are critical for the diagnosis and targeted therapy. <b><i>Key Messages:</i></b> The aim of the manuscript is to review the available data on <i>BCR/ABL1</i>-like ALL characteristics, diagnostic algorithms, and novel, molecularly targeted therapeutic options.

scholarly journals Next-Generation Sequencing in Acute Lymphoblastic Leukemia

2019 ◽  
Vol 20 (12) ◽  
pp. 2929 ◽  
Author(s):  
Nicoletta Coccaro ◽  
Luisa Anelli ◽  
Antonella Zagaria ◽  
Giorgina Specchia ◽  
Francesco Albano
Keyword(s):  
Next Generation Sequencing ◽  
Acute Lymphoblastic Leukemia ◽  
Residual Disease ◽  
Age Of Onset ◽  
Lymphoblastic Leukemia ◽  
Genomic Analysis ◽  
Next Generation ◽  
Acute Leukemias ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.

scholarly journals Next-Generation Sequencing in Adult B Cell Acute Lymphoblastic Leukemia Patients

2017 ◽  
Vol 23 (4) ◽  
pp. 691-696 ◽  
Author(s):  
Olga Sala Torra ◽  
Megan Othus ◽  
David W. Williamson ◽  
Brent Wood ◽  
Ilan Kirsch ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acute Lymphoblastic Leukemia ◽  
B Cell ◽  
Lymphoblastic Leukemia ◽  
Next Generation ◽  
Cell Acute Lymphoblastic Leukemia ◽  
Generation Sequencing
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