NGS better discriminates true MRD positivity for the risk stratification of childhood ALL treated on MRD-based protocol

Abstract

We compared minimal residual disease (MRD) levels evaluated by routinely used real-time quantitative PCR (qPCR) patient-specific assays and by next generation sequencing (NGS) approach in 780 immunoglobulin/T-cell receptor (IG/TR) markers in 432 children with B-cell precursor acute lymphoblastic leukemia (ALL) treated on the AIEOP-BFM ALL 2009 protocol. Our aim was to compare the MRD-based risk stratification at the end of induction (EOI). The results were concordant in 639/780 (81.9%) of these markers, 37/780 (4.7%) markers were detected only by NGS. In 104/780 (13.3%) markers positive only by qPCR, a large fraction (23/104; 22.1%) was detected also by NGS, however, due to the presence of identical IG/TR rearrangements in unrelated samples, we classified those as nonspecific/falsely-positive. Risk group stratification based on the MRD results by qPCR and NGS at EOI was concordant in 76% of the patients, 19% of the patients would be assigned to a lower-risk group by NGS, largely due to the elimination of false-positive qPCR results, and 5% of patients would be assigned to a higher risk group by NGS. NGS MRD is highly concordant with qPCR while providing more specific results and can be an alternative in the frontline MRD evaluation in forthcoming MRD-based protocols.