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Chaudhary P, Chaudhary S, Patel F, Patel S, Vaishnani T, Trivedi N, Patel D, Sonagara T, Hirapara A, Vyas K, Patel L, Kumar R, Chakraborty N, Sharma D, Suthar J, Kamdar P, Jajodia E, Ahmad F, Arora N. Validation of a novel NGS based BCR::ABL1 kinase domain mutation detection assay in Indian cohort. Sci Rep 2024; 14:15745. [PMID: 38977756 PMCID: PMC11231265 DOI: 10.1038/s41598-024-66310-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
The efficacy and treatment outcome of a CML patient are heavily dependent on BCR::ABL1 kinase domain (KD) mutation status. Next-generation sequencing technology is a bright alternative to the previously used sanger sequencing method due to its global presence in diagnostic setups, massive parallel sequencing ability, and far better sensitivity. In the present study, we have demonstrated a new protocol for kinase domain mutation analysis using the next-generation sequencing (NGS) method using the ion torrent sequencing platform. This protocol uses RNA as the starting material, followed by nested PCR to amplify the fusion transcript, which is subsequently used as a template for NGS. Initial validation and comparison of this assay with the sanger sequencing (SS) method yielded 95.23% agreement. CML samples (n = 121) with a failure to TKI response were subjected to this newly developed NGS-based assay to detect KD mutations, from which samples were found to have mutations with a sensitivity ranging from 2.32 to 93.41%. A total of 34.71% of samples (n = 42) were found to be positive for one or more KD mutations, whereas 65.29% of samples (n = 81) were found to be negative. Nine samples out of 42 positive samples, i.e., 21.42%, were found to have compound mutations. This is one of the first studies from India, which includes more than 160 samples and is analyzed by the NGS approach for KD mutation analysis.
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Affiliation(s)
- Pooja Chaudhary
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India.
| | - Spandan Chaudhary
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India.
| | - Falguni Patel
- Department of Biotechnology and Microbiology, Shri M.M. Patel Institute of Science and Research, Kadi Sarva Vishwavidyalaya, Gandhinagar, Gujarat, India
| | - Shiv Patel
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Toral Vaishnani
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Nikha Trivedi
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Dhiren Patel
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Tushar Sonagara
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Ashish Hirapara
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Kavisha Vyas
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Lokesh Patel
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Raja Kumar
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Nikkan Chakraborty
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Divya Sharma
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Jigar Suthar
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Payal Kamdar
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Ekta Jajodia
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Firoz Ahmad
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
| | - Neeraj Arora
- Molecular Department, Unipath Specialty Laboratory Ltd, Ahmedabad, Gujarat, India
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Benjamin C, Murugan S, Hoosen S, Rapiti N. Chronic myeloid leukemia kinase domain mutations: A retrospective descriptive study on the therapeutic and prognostic significance in patients at King Edward VIII Hospital, KwaZulu-Natal, South Africa. Health Sci Rep 2023; 6:e1376. [PMID: 37396560 PMCID: PMC10313909 DOI: 10.1002/hsr2.1376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/04/2023] Open
Abstract
Background Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm that harbors the Philadelphia chromosome. Tyrosine kinase inhibitor (TKI) therapy has dramatically improved the survival of patients with CML. Nevertheless, 20%-40% of CML patients require changes in TKI therapy due to intolerance or drug resistance. A total of 30%-60% of resistant cases result from kinase domain (KD) mutations. There is currently no published data on CML KD mutations in South Africa. Methods This retrospective, descriptive study collected data from 206 CML patients attending the King Edward Hospital Hematology clinic. Patient-based and mutation-based factors were analyzed using descriptive statistical analysis and Kaplan-Meier curves for survival analysis. Results KD mutations were detected in 29.1% (n = 60 of 206). A total of 40 different KD mutations were detected, with unknown responses to TKI therapy in 65% (n = 26 of 40). A total of 57.7% (n = 15 of 26) of mutations with an unknown response, showed a response to specific TKIs in our study. Four patients had A399T mutations, of which two showed good responses to Nilotinib. Patients with I293N and V280M mutations showed good responses to Imatinib. G250E was most frequently detected. Despite M351T being one of six most commonly reported KD mutations globally, this mutation was not detected in our patient cohort. A total of 20.9% (n = 43 of 206) human immunodeficiency virus (HIV) positive patients were identified, of which 25.6% (n = 11 of 43) had KD mutations. HIV status showed no significant effect on mutational status or overall survival. Conclusion The predicted response to TKI therapy was unknown in more than half of the KD mutations detected in our patient population. Additionally, eight patients with mutations with known responses to TKIs showed responses discordant to that expected. HIV status and KD mutations had no statistically significant effect on overall survival. Although some data were comparable to international publications, few notable differences warrant further investigation.
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Affiliation(s)
- Caryn Benjamin
- National Health Laboratory ServiceDurbanKwaZulu NatalSouth Africa
- University of KwaZulu NatalDurbanKwaZulu NatalSouth Africa
| | - Stephanie Murugan
- National Health Laboratory ServiceDurbanKwaZulu NatalSouth Africa
- University of KwaZulu NatalDurbanKwaZulu NatalSouth Africa
| | - Siddeeq Hoosen
- National Health Laboratory ServiceDurbanKwaZulu NatalSouth Africa
- University of KwaZulu NatalDurbanKwaZulu NatalSouth Africa
| | - Nadine Rapiti
- National Health Laboratory ServiceDurbanKwaZulu NatalSouth Africa
- University of KwaZulu NatalDurbanKwaZulu NatalSouth Africa
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Limsuwanachot N, Rerkamnuaychoke B, Niparuck P, Singdong R, Kongruang A, Hirunpatrawong P, Siriyakorn T, Yenchitsomanus PT, Siriboonpiputtana T. A customized mass array panel for BCR:: ABL1 tyrosine kinase domain mutation screening in chronic myeloid leukemia. J Mass Spectrom Adv Clin Lab 2023; 28:122-132. [PMID: 37128502 PMCID: PMC10148036 DOI: 10.1016/j.jmsacl.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/25/2023] [Accepted: 04/10/2023] [Indexed: 05/03/2023] Open
Abstract
Introduction The therapeutic strategy and management of chronic myeloid leukemia (CML) have rapidly improved with the discovery of effective tyrosine kinase inhibitors (TKIs) to target BCR::ABL1 oncoprotein. However, nearly 30% of patients develop TKI resistance due to acquired mutations on the tyrosine kinase domain (TKD) of BCR::ABL1. Methods We customized a mass array panel initially intended to detect and monitor the mutational burden of hotspot BCR::ABL1 TKD mutations accumulated in our database, including key mutations recently recommended by European LeukemiaNet. Additionally, we extended the feasibility of using the assay panel for the molecular classification of myeloproliferative neoplasms (MPNs) by incorporating primer sets specific for analyzing JAK2 V617F, MPL 515 K/L, and CALR types 1 and 2. Results We found that the developed mass array panel was superior for detecting and monitoring clinically significant BCR::ABL1 TKD mutations, especially in cases with low mutational burden and harboring compound/polyclonal mutations, compared with direct sequencing. Moreover, our customized mass array panel detected common genetic alterations in MPNs, and the findings were consistent with those of other comparable assays available in our laboratory. Conclusions Our customized mass array panel was practicably used as a routine robust assay for screening and monitoring BCR::ABL1 TKD mutations in patients with CML undergoing TKI treatment and feasible for analyzing common genetic mutations in MPNs.
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Affiliation(s)
- Nittaya Limsuwanachot
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Budsaba Rerkamnuaychoke
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pimjai Niparuck
- Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Roongrudee Singdong
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Adcharee Kongruang
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | | | - Pa-thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Teerapong Siriboonpiputtana
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Corresponding author at: Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand.
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Langabeer SE, Macleod S, Bhreathnach Ú, Fadalla K. Imatinib Resistance in Chronic Myeloid Leukemia Associated with a D363G BCR::ABL1 Kinase Domain Mutation. Case Rep Hematol 2023; 2023:6673144. [PMID: 37123466 PMCID: PMC10139808 DOI: 10.1155/2023/6673144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
Acquired resistance to tyrosine kinase inhibitors (TKIs) remains a therapeutic challenge in the treatment of chronic myeloid leukemia (CML). The most studied reason for TKI resistance is the acquisition of mutations within the BCR::ABL1 tyrosine kinase domain (KDM) and of which the majority of which occur at seven codons within this region. A case of CML is described in which presence of a rare D363G BCR::ABL1 KDM resulted in a suboptimal response to frontline imatinib. Switching to dasatinib resulted in achieving a sustained major molecular response that was maintained after a subsequent switch to bosutinib due to the side effects. Reporting of such cases is important for the future management of any CML patients with this rare mutation.
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Affiliation(s)
| | - Stuart Macleod
- Department of Haematology, St. Vincent's University Hospital, Dublin D04T6F4, Ireland
| | - Úna Bhreathnach
- Cancer Molecular Diagnostics, St. James's Hospital, Dublin D08W9RT, Ireland
| | - Kamal Fadalla
- Department of Haematology, St. Vincent's University Hospital, Dublin D04T6F4, Ireland
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Abulaiti D, Tuerxun N, Wang H, Abulizi P, Zhao F, Liu Y, Hao J. Differences in Variants in the Structural Domain of BCR-ABL1 Kinase between Chinese Han and Minority Patients with Chronic Myeloid Leukemia by Sanger Sequencing and Next-Generation Sequencing. Cytogenet Genome Res 2022; 162:201-206. [PMID: 36167055 DOI: 10.1159/000524706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/09/2022] [Indexed: 11/19/2022] Open
Abstract
This study aimed to detect differences in BCR-ABL1 kinase domain (KD) variants in patients with chronic myeloid leukemia (CML) who have been warned and failed in tyrosine kinase inhibitor (TKI) treatment among Chinese Han and ethnic minorities through Sanger sequencing (SS) and next-generation sequencing (NGS), and analyze the difference between SS and NGS detection. Peripheral blood samples from 51 CML patients with warning and failure of TKI therapy were analyzed using SS and NGS, and the detection differences between both sequencing types were compared. BCR-ABL1 KD variants were found in 23.53% of the cohort, including 7 Han Chinese (58.33%) and 5 ethnic minority cases (41.67%). Y253H, F317L, M244V, D276G, F359I, L387F, E459K, E255K, T315I, M351V, and heterozygous insertional mutated genes (ABL1 c.1068_1070dup) were detected. Comparison of the two sequencing assays revealed that NGS could detect compound variants and low frequency variants that were not detected by SS. More compound variants were detected in Han patients than in ethnic minority patients. In conclusion, there is no significant difference in BCR-ABL1 KD mutations between Han and ethnic minority patients. NGS has a higher mutation detection rate than SS, and can detect compound variants and genes with lower mutation frequency that are not detected by SS.
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Affiliation(s)
- Dilinazi Abulaiti
- Hematologic Disease Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Hematologic Disease Institute, Urumqi, China
| | - Niluopaer Tuerxun
- Hematologic Disease Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Hematologic Disease Institute, Urumqi, China
| | - Huan Wang
- Hematologic Disease Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Hematologic Disease Institute, Urumqi, China
| | - Patiguli Abulizi
- Hematologic Disease Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Hematologic Disease Institute, Urumqi, China
| | - Fang Zhao
- Hematologic Disease Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Hematologic Disease Institute, Urumqi, China
| | - Yang Liu
- Hematologic Disease Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Hematologic Disease Institute, Urumqi, China
| | - Jianping Hao
- Hematologic Disease Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Hematologic Disease Institute, Urumqi, China
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Romzova M, Smitalova D, Hynst J, Tom N, Loja T, Herudkova Z, Jurcek T, Stejskal L, Zackova D, Mayer J, Racil Z, Culen M. Hierarchical distribution of somatic variants in newly diagnosed chronic myeloid leukaemia at diagnosis and early follow-up. Br J Haematol 2021; 194:604-612. [PMID: 34212373 DOI: 10.1111/bjh.17659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/30/2022]
Abstract
There is an emerging body of evidence that patients with chronic myeloid leukaemia (CML) may carry not only breakpoint cluster region-Abelson murine leukaemia viral oncogene homologue 1 (BCR-ABL1) kinase domain mutations (BCR-ABL1 KD mutations), but also mutations in other genes. Their occurrence is highest during progression or at failure, but their impact at diagnosis is unclear. In the present study, we prospectively screened for mutations in 18 myeloid neoplasm-associated genes and BCR-ABL1 KD in the following populations: bulk leucocytes, CD34+ CD38+ progenitors and CD34+ CD38- stem cells, at diagnosis and early follow-up. In our cohort of chronic phase CML patients, nine of 49 patients harboured somatic mutations in the following genes: six ASXL1 mutations, one SETBP1, one TP53, one JAK2, but no BCR-ABL1 KD mutations. In seven of the nine patients, mutations were detected in multiple hierarchical populations including bulk leucocytes at diagnosis. The mutation dynamics reflected the BCR-ABL1 transcript decline induced by treatment in eight of the nine cases, suggesting that mutations were acquired in the Philadelphia chromosome (Ph)-positive clone. In one patient, the JAK2 V617F mutation correlated with a concomitant Ph-negative myeloproliferative neoplasm and persisted despite a 5-log reduction of the BCR-ABL1 transcript. Only two of the nine patients with mutations failed first-line therapy. No correlation was found between the mutation status and survival or response outcomes.
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Affiliation(s)
- Marianna Romzova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Dagmar Smitalova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jakub Hynst
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Nikola Tom
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Loja
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zdenka Herudkova
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Jurcek
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Lukas Stejskal
- Department of Hemato-Oncology, University Hospital, Ostrava, Czech Republic
| | - Daniela Zackova
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Jiri Mayer
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Zdenek Racil
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic.,Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Martin Culen
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
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