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Patkar N, Kakirde C, Shaikh AF, Salve R, Bhanshe P, Chatterjee G, Rajpal S, Joshi S, Chaudhary S, Kodgule R, Ghoghale S, Deshpande N, Shetty D, Khizer SH, Jain H, Bagal B, Menon H, Khattry N, Sengar M, Tembhare P, Subramanian P, Gujral S. Clinical impact of panel-based error-corrected next generation sequencing versus flow cytometry to detect measurable residual disease (MRD) in acute myeloid leukemia (AML). Leukemia 2021; 35:1392-1404. [PMID: 33558666 PMCID: PMC8102181 DOI: 10.1038/s41375-021-01131-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/30/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
Abstract
We accrued 201 patients of adult AML treated with conventional therapy, in morphological remission, and evaluated MRD using sensitive error-corrected next generation sequencing (NGS-MRD) and multiparameter flow cytometry (FCM-MRD) at the end of induction (PI) and consolidation (PC). Nearly 71% of patients were PI NGS-MRD+ and 40.9% PC NGS-MRD+ (median VAF 0.76%). NGS-MRD+ patients had a significantly higher cumulative incidence of relapse (p = 0.003), inferior overall survival (p = 0.001) and relapse free survival (p < 0.001) as compared to NGS-MRD- patients. NGS-MRD was predictive of inferior outcome in intermediate cytogenetic risk and demonstrated potential in favorable cytogenetic risk AML. PI NGS-MRD- patients had a significantly improved survival as compared to patients who became NGS-MRD- subsequently indicating that kinetics of NGS-MRD clearance was of paramount importance. NGS-MRD identified over 80% of cases identified by flow cytometry at PI time point whereas FCM identified 49.3% identified by NGS. Only a fraction of cases were NGS-MRD- but FCM-MRD+. NGS-MRD provided additional information of the risk of relapse when compared to FCM-MRD. We demonstrate a widely applicable, scalable NGS-MRD approach that is clinically informative and synergistic to FCM-MRD in AML treated with conventional therapies. Maximum clinical utility may be leveraged by combining FCM and NGS-MRD modalities.
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Affiliation(s)
- Nikhil Patkar
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Chinmayee Kakirde
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Anam Fatima Shaikh
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rakhi Salve
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Prasanna Bhanshe
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Gaurav Chatterjee
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sweta Rajpal
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Swapnali Joshi
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Shruti Chaudhary
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rohan Kodgule
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Sitaram Ghoghale
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Nilesh Deshpande
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Dhanalaxmi Shetty
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Syed Hasan Khizer
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hasmukh Jain
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Bhausaheb Bagal
- grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hari Menon
- Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Navin Khattry
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Manju Sengar
- grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Prashant Tembhare
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Papagudi Subramanian
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sumeet Gujral
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
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Patkar N, Kakirde C, Bhanshe P, Joshi S, Chaudhary S, Badrinath Y, Ghoghale S, Deshpande N, Kadechkar S, Chatterjee G, Kannan S, Shetty D, Gokarn A, Punatkar S, Bonda A, Nayak L, Jain H, Bagal B, Menon H, Sengar M, Khizer SH, Khattry N, Tembhare P, Gujral S, Subramanian P. Utility of Immunophenotypic Measurable Residual Disease in Adult Acute Myeloid Leukemia-Real-World Context. Front Oncol 2019; 9:450. [PMID: 31263671 PMCID: PMC6584962 DOI: 10.3389/fonc.2019.00450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/13/2019] [Indexed: 01/10/2023] Open
Abstract
Introduction: One of the mainstays of chemotherapy in acute myeloid leukemia (AML) is induction with a goal to achieve morphological complete remission (CR). However, not all patients by this remission criterion achieve long-term remission and a subset relapse. This relapse is explained by the presence of measurable residual disease (MRD). Methods: We accrued 451 consecutive patients of adult AML (from March 2012 to December 2017) after informed consent. All patients received standard chemotherapy. MRD testing was done at post-induction and, if feasible, post-consolidation using 8- and later 10-color FCM. Analysis of MRD was done using a combination of difference from normal and leukemia-associated immunophenotype approaches. Conventional karyotyping and FISH were done as per standard recommendations, and patients were classified into favorable, intermediate, and poor cytogenetic risk groups. The presence of FLT3-ITD, NPM1, and CEBPA mutations was detected by a fragment length analysis-based assay. Results: As compared to Western data, our cohort of patients was younger with a median age of 35 years. There were 62 induction deaths in this cohort (13.7%), and 77 patients (17.1%) were not in morphological remission. The median follow-up was 26.0 months. Poor-risk cytogenetics and the presence of FLT3-ITD were significantly associated with inferior outcome. The presence of post-induction MRD assessment was significantly associated with adverse outcome with respect to OS (p = 0.01) as well as RFS (p = 0.004). Among established genetic subgroups, detection of MRD in intermediate cytogenetic and NPM1 mutated groups was also highly predictive of inferior outcome. On multivariate analysis, immunophenotypic MRD at the end of induction and FLT3-ITD emerged as independent prognostic factors predictive for outcome. Conclusion: This is the first data from a resource-constrained real-world setting demonstrating the utility of AML MRD as well as long-term outcome of AML. Our data is in agreement with other studies that determination of MRD is extremely important in predicting outcome. AML MRD is a very useful guide for guiding post-remission strategies in AML and should be incorporated into routine treatment algorithms.
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Affiliation(s)
- Nikhil Patkar
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Chinmayee Kakirde
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Prasanna Bhanshe
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Swapnali Joshi
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Shruti Chaudhary
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | | | - Sitaram Ghoghale
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Nilesh Deshpande
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Shraddha Kadechkar
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Gaurav Chatterjee
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Sadhana Kannan
- Biostatistics, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Dhanalaxmi Shetty
- Department of Cytogenetics, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Anant Gokarn
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Sachin Punatkar
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Avinash Bonda
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Lingaraj Nayak
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hasmukh Jain
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Bhausaheb Bagal
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hari Menon
- Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Manju Sengar
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Syed Hasan Khizer
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Navin Khattry
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Prashant Tembhare
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
| | - Sumeet Gujral
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Mumbai, India
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3
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Patkar N, Kodgule R, Kakirde C, Raval G, Bhanshe P, Joshi S, Chaudhary S, Badrinath Y, Ghoghale S, Kadechkar S, Khizer SH, Kannan S, Shetty D, Gokarn A, Punatkar S, Jain H, Bagal B, Menon H, Sengar M, Khattry N, Tembhare P, Subramanian P, Gujral S. Clinical impact of measurable residual disease monitoring by ultradeep next generation sequencing in NPM1 mutated acute myeloid leukemia. Oncotarget 2018; 9:36613-36624. [PMID: 30564301 PMCID: PMC6290958 DOI: 10.18632/oncotarget.26400] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/16/2018] [Indexed: 01/18/2023] Open
Abstract
Detection of measurable residual disease (MRD) by mutation specific techniques has prognostic relevance in NPM1 mutated AML (NPM1mut AML). However, the clinical utility of next generation sequencing (NGS) to detect MRD in AML remains unproven. We analysed the clinical significance of monitoring MRD using ultradeep NGS (NGS-MRD) and flow cytometry (FCM-MRD) in 137 samples obtained from 83 patients of NPM1mut AML at the end of induction (PI) and consolidation (PC). We could monitor 12 different types of NPM1 mutations at a sensitivity of 0.001% using NGS-MRD. We demonstrated a significant correlation between NGS-MRD and real time quantitative PCR (RQ-PCR). Based upon a one log reduction between PI and PC time points we could classify patients as NGS-MRD positive (<1log reduction) or negative (>1log reduction). NGS-MRD, FCM-MRD as well as DNMT3A mutations were predictive of inferior overall survival (OS) and relapse free survival (RFS). On a multivariate analysis NGS-MRD emerged as an independent, most important prognostic factor predictive of inferior OS (hazard ratio, 3.64; 95% confidence interval [CI] 1.58 to 8.37) and RFS (hazard ratio, 4.8; 95% CI:2.24 to 10.28). We establish that DNA based NPM1 NGS MRD is a highly useful test for prediction of relapse and survival in NPM1mut AML.
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Affiliation(s)
- Nikhil Patkar
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rohan Kodgule
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Chinmayee Kakirde
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Goutham Raval
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Prasanna Bhanshe
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Swapnali Joshi
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Shruti Chaudhary
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Y Badrinath
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Sitaram Ghoghale
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Shraddha Kadechkar
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Syed Hasan Khizer
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Sadhana Kannan
- Biostatistics, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Dhanalaxmi Shetty
- Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Anant Gokarn
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Sachin Punatkar
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hasmukh Jain
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Bhausaheb Bagal
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hari Menon
- Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Manju Sengar
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Navin Khattry
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Prashant Tembhare
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | | | - Sumeet Gujral
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
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