Fellows' research : Ultra-sensitive gene sequencing technology for predicting relapse of Acute Myeloid Leukemia (AML)

26 Nov 2018

Fellows' research : Ultra-sensitive gene sequencing technology for predicting relapse of Acute Myeloid Leukemia (AML)


Dr. Nikhil Patkar, Intermediate Fellow

Tata Memorial Centre, Mumbai

Our team at Tata Memorial Centre, Mumbai, has developed an ultra-sensitive test, Next Generation Sequencing (NGS)- measurable residual disease (MRD) assay, for detecting molecular markers that can predict relapse of Nucleophosmin (NPM1) gene-mutated acute myeloid leukemia (AML), a life-threatening blood cancer requiring intense chemotherapy.

Mutations in the NPM1 gene are the most commonly found abnormality in AML. Within weeks of starting treatment, chemotherapy-resistant leukemic cells, called measurable residual disease or MRD, are detected. If MRD is present, it indicates relapse of blood cancer within a few months to a year. The prediction of relapse is problematic as the current tools available are not sensitive enough or precise in detecting MRD.

The assay developed by our team, offers an unparallel sensitivity in detecting one NPM1 mutant AML cell amongst one hundred thousand normal cells.Significant advantages over existing techniques such as real time PCR (qPCR) and multiparametric flow cytometry (FCM) were seen in terms of affordability, sensitivity and ease of testing. Although there are more than fifty different types of known NPM1 mutations, this single assay could potentially detect all of them.

The most important question here was to demonstrate the clinical significance of such an ultrasensitive assay. We tested 83 patients of NPM1 mutated AML and looked at their baseline characteristics as well as other mutations known to predict outcome. We performed MRD detection using NGS and orthogonal techniques such as flow cytometry and quantitative polymerase chain reaction (qPCR). MRD whether measured by genome sequencing or by flow cytometry as well as mutations in the DNMT3A gene were predictive of inferior outcome. On a multivariate analysis, MRD measured by NGS emerged as an independent, most important prognostic factor predictive of inferior overall survival (OS) and relapse free survival (RFS).

This research, published in Oncotarget, demonstrates that DNA based NPM1 NGS MRD is a highly useful test for prediction of relapse and survival in NPM1 mutated AML. Our research opens up several possibilities towards the detection of MRD. With an ultrasensitive assay we can simply monitor the blood sample over serial time points instead of a painful test that involves taking samples from the bone marrow of the patient. Additionally, our detection technique is simple enough to be used in laboratories without the need for complicated standardization or expert interpretation.


Clinical impact of measurable residual disease monitoring by ultradeep next generation sequencing in NPM1 mutated acute myeloid leukemia. Nikhil Patkar et al. Oncotarget. November 2018

Banner image credit: Peter Artymiuk. DNA double helix and sequencing output. Wellcome Images