Next-Generation Sequencing in Adult B Cell Acute Lymphoblastic Leukemia Patients

Abstract

We used next generation sequencing (NGS) of the immunoglobulin genes to evaluate residual disease in 153 specimens from 32 patients with adult B cell ALL enrolled in a single, multi-center study. The sequencing results were compared to multi-parameter flow cytometry (MFC) data in 66 specimens (25 patients) analyzed by both methods. There was a strong concordance (82%) between the methods in the qualitative determination of the presence of disease. However, in 17% of cases leukemia was detected by sequencing, but not by MFC. In 54 bone marrow (BM) and peripheral blood (PB) paired specimens, the burden of leukemia detected by NGS was lower in PB than BM, although still detectable in 68% of the 28 paired specimens with positive BM. Lastly, patients without disease detected by NGS or MFC had a 5-year relapse free survival (RFS) of > 80%. The results suggest that residual disease detection by immunoglobulin gene sequencing is an extremely sensitive technique, and may identify patients that might benefit from transplant. Moreover, the increased sensitivity of the method may allow frequent peripheral blood testing to supplement marrow sampling to measure disease response.

Recommendations for the assessment and management of measurable residual disease in adults with acute lymphoblastic leukemia: A consensus of North American experts

“…The development of NGS as a tool to identify MRD may overcome some of the limitations of the current MFC and PCR methodologies described above. In ALL, the targets of NGS‐based MRD assays have thus far been the same leukemic clone‐specific IGH and TCR gene rearrangements as with PCR assays . NGS utilizes rapid, parallel sequencing using consensus primers.…”

“…This feature also makes standardization and performance characterization possible. The sensitivity achieved with NGS is up to 1–2 logs deeper than with other currently available methods of MRD detection in the United States, and there is evidence that NGS can identify clinically significant MRD in patients who are MRD negative by other MRD methodologies (ie, MFC or PCR) . It is important to note, however, that MFC and PCR can at least theoretically achieve similar levels of sensitivity as NGS if an adequate number of cells or DNA are analyzed, although this is not done in standard practice.…”

Description and prognostic significance of the kinetics of minimal residual disease status in adults with acute lymphoblastic leukemia treated with HyperCVAD

“…If a more sensitive assay is used to detect MRD, then fewer patients will be called MRD Neg . This is particularly important as newer and more sensitive assays using high‐throughput sequencing of IGH and TCR genes for MRD in B‐ and T‐ALL (respectively) are now available, potentially making our data more applicable in the near future. Another potential contributor is that patients included in these other analyses were largely enrolled on prospective clinical trials, whereas ours were not.…”

Advances in measurable residual disease monitoring for adult acute lymphoblastic leukemia

“…This technique relies on the high‐level multiplex PCR capability of NGS to allow the design of balanced primers that simultaneously amplify all possible combinations of the IGH/TR rearrangements . NGS has been compared to MFC as well as RT‐qPCR with NGS showing better sensitivities and discordant results favoring NGS. However, just like MFC, it is limited by the requirement of pretreatment diagnostic samples to obtain an index sequence for IGH/TR MRD detection.…”