Research

​We actively collaborate with adult and pediatric hematolymphoid disease management groups and the bone marrow transplantation team at the Tata Memorial Centre and ACTREC.

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Our Research can broadly be divided into the following areas:

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1. Measurable Residual Disease Detection for Acute Myeloid Leukemia

 

Our group has led pioneering clinical work comparing multiparameter flow cytometry and error-corrected panel-based next-generation sequencing for the detection of MRD in acute myeloid leukemia.

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• Nikhil Patkar*, Chinmayee Kakirde, Anam Fatima Shaikh et al. 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 (Impact Factor: 11.528) 

• Nikhil Patkar*, Rohan Kodgule , Chinmayee Kakirde , et al. Clinical impact of measurable residual disease monitoring by ultradeep next generation sequencing in NPM1 mutated acute myeloid leukemia. Oncotarget. 2018 Nov 27;9(93):36613-36624 (Impact Factor: 5.168)  

• Nikhil Patkar*, Chinmayee Kakirde, Prasanna Bhanshe, et al. Utility of Immunophenotypic MRD in AML– Real-World Context. Front Oncol. 2019 Jun 13;9:450

• Molecular Measurable Residual Disease Detection in Acute Myeloid Leukemia Using Error Corrected Next Generation Sequencing. Nikhil Patkar et al. Platform Presentation : 62nd American Society of Hematology Annual Meeting and Exposition. 2020

 

We are taking this research further by trying to improve MRD detection using cutting edge techniques such as duplexed sequencing and we are also trying to understand the biology of chemotherapy resistance and clonal evolution using single-cell genomics. 

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2. Development of Novel Next-Generation Sequencing Methods for Genomics of Blood Cancers

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We develop next-generation sequencing-based molecular methods for diagnosis, prognostication and monitoring of blood cancers. Also we are developing nanopore sequencing based methods to diagnose and classify blood cancers

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• Nikhil Patkar*, Prasanna Bhanshe, Sweta Rajpal, et al. NARASIMHA: Novel Assay based on Targeted RNA Sequencing to Identify ChiMeric Gene Fusions in Hematological Malignancies. Blood Cancer Journal 2020 (Impact Factor: 11.977)

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3. Artificial Intelligence and its Application to Blood Cancers

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 Machine Learning and Deep Learning have revolutionized so many aspects of our life including research. We are using ML/DL approaches to change the way diagnostics of leukemia is being performed. This includes development of methylation based classifiers for ultrarapid diagnosis of acute leukemia, image based classification of blood cancers using whole slide imaging and lastly graph neural networks for identification of novel therapies of acute myeloid leukemia

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• Nikhil Patkar*, Anam Fatima Shaikh, Chinmayee Kakirde, et al. A Novel Machine Learning Derived Genetic Score Correlates with Measurable Residual Disease and is Highly Predictive of Outcome in Acute Myeloid Leukemia with Mutated NPM1. Blood Cancer Journal 2019 ;9(10):79 (Impact Factor: 11.977) 

• Shaikh AF, Kakirde C, .., Patkar N* Machine learning derived genomics driven prognostication for acute myeloid leukemia with RUNX1-RUNX1T1. Leuk Lymphoma. 2020 ;1-7 *Corresponding Author (Impact Factor:3.093) 

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4. Genomics of Acute Leukemia

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We are currently sequencing a large cohort of pediatric leukemia samples using whole transcriptome sequencing to comprehensively characterize their genetic abnormalities.

In parallel, we are developing adaptive whole genome sequencing assays leveraging nanopore technology for rapid diagnosis and classification of acute leukemia. To expand clinical accessibility, we are evaluating the implementation of targeted RNA sequencing across major public hospitals in India, utilizing our patented library preparation approach combined with nanopore sequencing for rapid diagnosis of childhood leukemia. Additionally, we are developing ultra-sensitive next-generation sequencing assays specifically designed for minimal residual disease (MRD) detection in childhood lymphoblastic leukemia.

 

Research Funding: 

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We are generously funded by these agencies:

1. Indian Council of Medical Research - Center for Advanced Research Grant (2025 - 2030)

2. Indian Council of Medical Research - Intermediate Grant (2025 - 2029)

3. Illumina Inc Medical Research Grant (2023 - 2026)

4. St Jude Global Alliance(2024-2026)

5. ThermoFisher Scientific : Oncomine Global Grant (2024-2026)

6. Wellcome Trust DBT India Alliance Senior Fellowship (2023 - 2028)

7. Completed: India Cancer Research Consortium - Indian Council of Medical Research (2020 - 2023)

8. Completed: Lady Tata Memorial Trust (2021 - 2024)

9. Completed: Wellcome Trust DBT India Alliance Intermediate Fellowship (2015-2021)