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Bartram J, Wright G, Adams S, Archer P, Brooks T, Edwards D, Hancock J, Knecht H, Inglott S, Mountjoy E, Roynane M, Wakeman S, Moppett J, Hubank M, Goulden N. High-throughput sequencing of peripheral blood for minimal residual disease monitoring in childhood precursor B-cell acute lymphoblastic leukemia: A prospective feasibility study. Pediatr Blood Cancer 2022; 69:e29513. [PMID: 34971078 DOI: 10.1002/pbc.29513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/28/2021] [Accepted: 11/20/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND Minimal residual disease (MRD) measured on end-of-induction bone marrow (BM) is the most important biomarker for guiding therapy in pediatric acute lymphoblastic leukemia (ALL). Due to limited sensitivity of current approaches, peripheral blood (PB) is not a reliable source for identifying patients needing treatment changes. We sought to determine if high-throughput sequencing (HTS) (next-generation sequencing) of rearranged immunoglobulin and T-cell receptor genes can overcome this and be used to measure MRD in PB. PROCEDURE We employed a quantitative HTS approach to accurately measure MRD from one million cell equivalents of DNA from 17 PB samples collected at day 29 after induction therapy in patients with precursor B-cell ALL. We compared these results to the gold-standard real-time PCR result obtained from their paired BM samples, median follow-up 49 months. RESULTS With the increased sensitivity, detecting up to one abnormal cell in a million normal cells, we were able to detect MRD in the PB by HTS in all those patients requiring treatment intensification (MRD ≥ 0.005% in BM). CONCLUSION This is proof of principle that using the increased sensitivity of HTS, PB can be used to measure MRD and stratify children with ALL. The method is cost effective, rapid, accurate, and reproducible, with inherent advantages in children. Importantly, increasing the frequency testing by PB as opposed to intermittent BM sampling may allow extension of the dynamic range of MRD, giving a more complete picture of the kinetics of disease remission while improving relapse prediction and speed of detection.
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Affiliation(s)
- Jack Bartram
- Depatment of Haematology, Great Ormond Street Hospital for Children, London, UK.,Cancer Section, Institute of Child Health, University College London, UK
| | - Gary Wright
- Depatment of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Stuart Adams
- Depatment of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Paul Archer
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, UK
| | - Tony Brooks
- UCL Genomics, Institute of Child Health, University College London, UK
| | - Darren Edwards
- Cancer Section, Institute of Child Health, University College London, UK
| | - Jerry Hancock
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, UK
| | - Henrik Knecht
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sarah Inglott
- Depatment of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Edward Mountjoy
- School of Social and Community Medicine, University of Bristol, UK
| | - Marie Roynane
- Depatment of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Stephanie Wakeman
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, UK
| | - John Moppett
- Department of Paediatric Haematology/Oncology, Royal Hospital for Children, Bristol, UK
| | - Mike Hubank
- Centre for Molecular Pathology, The Royal Marsden, Sutton, UK
| | - Nick Goulden
- Depatment of Haematology, Great Ormond Street Hospital for Children, London, UK.,Trapehade, Monferran-Plavès, France
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2
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Park DJ, Cho HC, Kwon JH, Park JY. Utility of an immunoglobulin gene rearrangement assay based on multiplex PCR in detecting bone marrow involvement in B-cell non-Hodgkin lymphoma. Blood Res 2017; 52:141-143. [PMID: 28698854 PMCID: PMC5503895 DOI: 10.5045/br.2017.52.2.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/06/2016] [Accepted: 09/06/2016] [Indexed: 11/17/2022] Open
Affiliation(s)
- Dong Jin Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyoun Chan Cho
- Department of Laboratory Medicine, Hallym University College of Medicine, Kangdong Sacred Heart Hospital, Seoul, Korea
| | - Jung Hye Kwon
- Department of Internal Medicine, Hallym University College of Medicine, Kangdong Sacred Heart Hospital, Seoul, Korea
| | - Ji-Young Park
- Department of Laboratory Medicine, Hallym University College of Medicine, Kangdong Sacred Heart Hospital, Seoul, Korea
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3
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Sholl LM, Longtine J, Kuo FC. Molecular Analysis of Gene Rearrangements and Mutations in Acute Leukemias and Myeloid Neoplasms. ACTA ACUST UNITED AC 2017; 92:10.4.1-10.4.49. [PMID: 28075487 DOI: 10.1002/cphg.31] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A subset of acute leukemias and other myeloid neoplasms contains specific genetic alterations, many of which are associated with unique clinical and pathologic features. These alterations include chromosomal rearrangements leading to oncogenic fusion proteins or alteration of gene expression by juxtaposing oncogenes to enhancer elements, as well as mutations leading to aberrant activation of a variety of proteins critical to hematopoietic progenitor cell proliferation and differentiation. Molecular analysis is central to diagnosis and clinical management of leukemias, permitting genetic confirmation of a clinical and histologic impression, providing prognostic and predictive information, and facilitating detection of minimal residual disease. This unit will outline approaches to the molecular diagnosis of the most frequent and clinically relevant genetic alterations in acute leukemias and myeloid neoplasms. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | - Frank C Kuo
- Brigham and Women's Hospital, Boston, Massachusetts
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4
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Wu J, Jia S, Wang C, Zhang W, Liu S, Zeng X, Mai H, Yuan X, Du Y, Wang X, Hong X, Li X, Wen F, Xu X, Pan J, Li C, Liu X. Minimal Residual Disease Detection and Evolved IGH Clones Analysis in Acute B Lymphoblastic Leukemia Using IGH Deep Sequencing. Front Immunol 2016; 7:403. [PMID: 27757113 PMCID: PMC5048610 DOI: 10.3389/fimmu.2016.00403] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022] Open
Abstract
Acute B lymphoblastic leukemia (B-ALL) is one of the most common types of childhood cancer worldwide and chemotherapy is the main treatment approach. Despite good response rates to chemotherapy regiments, many patients eventually relapse and minimal residual disease (MRD) is the leading risk factor for relapse. The evolution of leukemic clones during disease development and treatment may have clinical significance. In this study, we performed immunoglobulin heavy chain (IGH) repertoire high throughput sequencing (HTS) on the diagnostic and post-treatment samples of 51 pediatric B-ALL patients. We identified leukemic IGH clones in 92.2% of the diagnostic samples and nearly half of the patients were polyclonal. About one-third of the leukemic clones have correct open reading frame in the complementarity determining region 3 (CDR3) of IGH, which demonstrates that the leukemic B cells were in the early developmental stage. We also demonstrated the higher sensitivity of HTS in MRD detection and investigated the clinical value of using peripheral blood in MRD detection and monitoring the clonal IGH evolution. In addition, we found leukemic clones were extensively undergoing continuous clonal IGH evolution by variable gene replacement. Dynamic frequency change and newly emerged evolved IGH clones were identified upon the pressure of chemotherapy. In summary, we confirmed the high sensitivity and universal applicability of HTS in MRD detection. We also reported the ubiquitous evolved IGH clones in B-ALL samples and their response to chemotherapy during treatment.
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Affiliation(s)
- Jinghua Wu
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Shan Jia
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Changxi Wang
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Sixi Liu
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xiaojing Zeng
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Huirong Mai
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xiuli Yuan
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Yuanping Du
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Xiaodong Wang
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xueyu Hong
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Xuemei Li
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Feiqiu Wen
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | | | - Changgang Li
- Hematology and Oncology Department, Shenzhen Children's Hospital , Shenzhen , China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark
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5
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Logan AC, Vashi N, Faham M, Carlton V, Kong K, Buño I, Zheng J, Moorhead M, Klinger M, Zhang B, Waqar A, Zehnder JL, Miklos DB. Immunoglobulin and T cell receptor gene high-throughput sequencing quantifies minimal residual disease in acute lymphoblastic leukemia and predicts post-transplantation relapse and survival. Biol Blood Marrow Transplant 2014; 20:1307-13. [PMID: 24769317 DOI: 10.1016/j.bbmt.2014.04.018] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 04/17/2014] [Indexed: 01/11/2023]
Abstract
Minimal residual disease (MRD) quantification is an important predictor of outcome after treatment for acute lymphoblastic leukemia (ALL). Bone marrow ALL burden ≥ 10(-4) after induction predicts subsequent relapse. Likewise, MRD ≥ 10(-4) in bone marrow before initiation of conditioning for allogeneic (allo) hematopoietic cell transplantation (HCT) predicts transplantation failure. Current methods for MRD quantification in ALL are not sufficiently sensitive for use with peripheral blood specimens and have not been broadly implemented in the management of adults with ALL. Consensus-primed immunoglobulin (Ig), T cell receptor (TCR) amplification and high-throughput sequencing (HTS) permit use of a standardized algorithm for all patients and can detect leukemia at 10(-6) or lower. We applied the LymphoSIGHT HTS platform (Sequenta Inc., South San Francisco, CA) to quantification of MRD in 237 samples from 29 adult B cell ALL patients before and after allo-HCT. Using primers for the IGH-VDJ, IGH-DJ, IGK, TCRB, TCRD, and TCRG loci, MRD could be quantified in 93% of patients. Leukemia-associated clonotypes at these loci were identified in 52%, 28%, 10%, 35%, 28%, and 41% of patients, respectively. MRD ≥ 10(-4) before HCT conditioning predicted post-HCT relapse (hazard ratio [HR], 7.7; 95% confidence interval [CI], 2.0 to 30; P = .003). In post-HCT blood samples, MRD ≥10(-6) had 100% positive predictive value for relapse with median lead time of 89 days (HR, 14; 95% CI, 4.7 to 44, P < .0001). The use of HTS-based MRD quantification in adults with ALL offers a standardized approach with sufficient sensitivity to quantify leukemia MRD in peripheral blood. Use of this approach may identify a window for clinical intervention before overt relapse.
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Affiliation(s)
- Aaron C Logan
- Division of Hematology and Blood and Marrow Transplantation, Department of Medicine, University of California, San Francisco, San Francisco, California.
| | - Nikita Vashi
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Malek Faham
- Sequenta Inc., South San Francisco, California
| | | | | | - Ismael Buño
- Department of Hematology, Hospital G.U. Gregorio Maranon, Madrid, Spain
| | | | | | | | - Bing Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Amna Waqar
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - David B Miklos
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, California
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6
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Vignetti M, Fazi P, la Sala A, Mandelli F. Treatment of Philadelphia-positive acute lymphoid leukemia. Int J Hematol Oncol 2014. [DOI: 10.2217/ijh.13.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY Philadelphia-positive (Ph+) acute lymphoblastic leukemia (ALL) represents approximately 15–30% of ALL in adults and is characterized by the expression of the fusion protein BCR–ABL with oncogenic activity. Remission and survival rates were lower whereas relapse risk was increased in Ph+ compared with Philadelphia-negative ALL, until remarkable improvements in the management of Ph+ ALL were achieved through the introduction of tyrosine kinase inhibitors that reduce the activity of the BCR–ABL protein. However, in patients achieving complete remission, allogeneic hematopoietic stem cell transplantation is in most cases a mandatory therapeutic step because rate of relapses are still high. This review will illustrate the current therapeutic options for the management of Ph+ ALL and indicate how better curative options may stem from appropriate implementation of tyrosine kinase inhibitors and novel antitumoral agents.
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Affiliation(s)
- Marco Vignetti
- Fondazione GIMEMA ONLUS, Central Office, Via Casilina, 5, 00182 Rome, Italy
- Hematology, Department of Cellular Biotechnologies & Hematology, “Sapienza” University, Rome, Italy
| | - Paola Fazi
- Fondazione GIMEMA ONLUS, Central Office, Via Casilina, 5, 00182 Rome, Italy
| | - Andrea la Sala
- Laboratory of Molecular & Cellular Immunology, IRCCS San Raffaele Pisana, Rome, Italy
| | - Franco Mandelli
- Fondazione GIMEMA ONLUS, Central Office, Via Casilina, 5, 00182 Rome, Italy.
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7
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Massive evolution of the immunoglobulin heavy chain locus in children with B precursor acute lymphoblastic leukemia. Blood 2012; 120:4407-17. [PMID: 22932801 DOI: 10.1182/blood-2012-05-429811] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability to distinguish clonal B-cell populations based on the sequence of their rearranged immunoglobulin heavy chain (IgH) locus is an important tool for diagnosing B-cell neoplasms and monitoring treatment response. Leukemic precursor B cells may continue to undergo recombination of the IgH gene after malignant transformation; however, the magnitude of evolution at the IgH locus is currently unknown. We used next-generation sequencing to characterize the repertoire of IgH sequences in diagnostic samples of 51 children with B precursor acute lymphoblastic leukemia (B-ALL). We identified clonal IgH rearrangements in 43 of 51 (84%) cases and found that the number of evolved IgH sequences per patient ranged dramatically from 0 to 4024. We demonstrate that the evolved IgH sequences are not the result of amplification artifacts and are unique to leukemic precursor B cells. In addition, the evolution often follows an allelic exclusion pattern, where only 1 of 2 rearranged IgH loci exhibit ongoing recombination. Thus, precursor B-cell leukemias maintain evolution at the IgH locus at levels that were previously underappreciated. This finding sheds light on the mechanisms associated with leukemic clonal evolution and may fundamentally change approaches for monitoring minimal residual disease burden.
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8
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Khaled SK, Thomas SH, Forman SJ. Allogeneic hematopoietic cell transplantation for acute lymphoblastic leukemia in adults. Curr Opin Oncol 2012; 24:182-90. [PMID: 22234252 PMCID: PMC3520484 DOI: 10.1097/cco.0b013e32834f5c41] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PURPOSE OF REVIEW Acute lymphoblastic leukemia (ALL) is a heterogeneous disease, for which treatment guidelines are still evolving. Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative therapeutic modality for ALL, and this review describes the recent studies and current practice patterns concerning the who, when, and how of allo-HCT in the management of ALL. RECENT FINDINGS Allogeneic stem cell transplantation is the treatment of choice for patients with ALL after first relapse and is also recommended for high-risk patients in first complete remission (CR1). Minimal residual disease evaluation and monitoring is developing as an important prognostic factor and could guide physicians in determining which patients, especially those with standard risk, might require transplant. Tyrosine kinase inhibitor (TKI) therapy allows a much higher proportion of Philadelphia-chromosome-positive ALL patients to attain remission and proceed to transplant with improved results; posttransplant TKI maintenance therapy may also provide survival benefit. Reduced-intensity conditioning regimens are a reasonable alternative for patients who would otherwise be ineligible for transplant because of age or comorbidity. SUMMARY For patients with high-risk features, there is general agreement that allo-HCT in CR1 is a potentially curative option; however, there is no consensus on early transplant for standard-risk patients.
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Affiliation(s)
- Samer K Khaled
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California, USA
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Eckert C, Flohr T, Koehler R, Hagedorn N, Moericke A, Stanulla M, Kirschner-Schwabe R, Cario G, Stackelberg A, Bartram CR, Henze G, Schrappe M, Schrauder A. Very early/early relapses of acute lymphoblastic leukemia show unexpected changes of clonal markers and high heterogeneity in response to initial and relapse treatment. Leukemia 2011; 25:1305-13. [DOI: 10.1038/leu.2011.89] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Sholl LM, Longtine J. Molecular analysis of gene rearrangements and mutations in acute leukemias and myeloproliferative neoplasms. CURRENT PROTOCOLS IN HUMAN GENETICS 2010; Chapter 10:Unit 10.4. [PMID: 20891029 DOI: 10.1002/0471142905.hg1004s67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A large subset of acute leukemias and other myeloproliferative neoplasms contain specific genetic alterations, many of which are associated with unique clinical and pathologic features. These alterations include chromosomal translocations leading to oncogenic fusion genes, as well as mutations leading to aberrant activation of a variety of proteins critical to hematopoietic progenitor cell proliferation and differentiation. Molecular analysis is central to diagnosis and clinical management of leukemias, permitting genetic confirmation of a clinical and histologic impression, providing prognostic and predictive information, and facilitating detection of minimal residual disease. This unit will outline approaches to the molecular diagnosis of the most frequent and clinically relevant genetic alterations in acute leukemias and myeloproliferative neoplasms.
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11
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Morley AA, Latham S, Brisco MJ, Sykes PJ, Sutton R, Hughes E, Wilczek V, Budgen B, van Zanten K, Kuss BJ, Venn NC, Norris MD, Crock C, Storey C, Revesz T, Waters K. Sensitive and specific measurement of minimal residual disease in acute lymphoblastic leukemia. J Mol Diagn 2009; 11:201-10. [PMID: 19324989 DOI: 10.2353/jmoldx.2009.080048] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A sensitive and specific quantitative real-time polymerase chain reaction method, involving three rounds of amplification with two allele-specific oligonucleotide primers directed against an rearrangement, was developed to quantify minimal residual disease (MRD) in B-lineage acute lymphoblastic leukemia (ALL). For a single sample containing 10 microg of good quality DNA, MRD was quantifiable down to approximately 10(-6), which is at least 1 log more sensitive than current methods. Nonspecific amplification was rarely observed. The standard deviation of laboratory estimations was 0.32 log units at moderate or high levels of MRD, but increased markedly as the level of MRD and the number of intact marker gene rearrangements in the sample fell. In 23 children with ALL studied after induction therapy, the mean MRD level was 1.6 x 10(-5) and levels ranged from 1.5 x 10(-2) to less than 10(-7). Comparisons with the conventional one-round quantitative polymerase chain reaction method on 29 samples from another 24 children who received treatment resulted in concordant results for 22 samples and discordant results for seven samples. The sensitivity and specificity of the method are due to the use of nested polymerase chain reaction, one segment-specific and two allele-specific oligonucleotide primers, and the use of a large amount of good quality DNA. This method may improve MRD-based decisions on treatment for ALL patients, and the principles should be applicable to DNA-based MRD measurements in other disorders.
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Affiliation(s)
- Alexander A Morley
- Department of Haematology and Genetic Pathology, Flinders University and Medical Centre, Adelaide, Australia.
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