The Value of Next-Generation Sequencing in the Screening and Evaluation of Hematologic Neoplasms in Clinical Practice

Victoria Northrup, MSc; Allison Maybank, MSc; Nancy Carson, PhD; Tarek Rahmeh, MD

Disclosures

Am J Clin Pathol. 2020;153(5):639-645. 

In This Article

Abstract and Introduction

Abstract

Objectives: The implementation of next-generation sequencing (NGS) in routine clinical hematology practice remains limited. We evaluate the clinical value of NGS in the screening, diagnosis, and follow-up in hematologic neoplasms.

Methods: A targeted NGS panel was used to assess a total of 178 patients for questionable or previously diagnosed myeloid neoplasms.

Results: Gene variants were identified in 53% of patients. Novel variants were identified in 29% of patients and variants of unknown significance in 34%. Bone marrow samples yielded a higher number of variants than in peripheral blood. NGS is a more sensitive test than conventional cytogenetics. In several cases, NGS played a key role in the screening, diagnostics, prognostic stratification, and the clinical follow-up of a wide variety of myeloid neoplasms.

Conclusions: NGS is an effective tool in the evaluation of suspected and confirmed hematologic neoplasms and could become part of the routine workup of patients.

Introduction

Myeloid neoplasms are a heterogeneous group of disorders that include acute myeloid leukemia (AML), myelodysplastic syndromes (MDSs), myeloproliferative neoplasms (MPNs), and MDSs/MPNs. The identification of certain gene variants has become increasingly important in the diagnostic workup of myeloid neoplasms. This is evidenced by the 2016 World Health Organization classification of hematologic neoplasms incorporating several gene variants in its diagnostic criteria for myeloid neoplasms.[1] In addition to diagnostic value, several variants provide important prognostic information and/or guide patient management.[2] This has led to molecular testing becoming routine clinical practice for myeloid neoplasms.[3–5]

Next-generation sequencing (NGS) increasingly has been implemented in routine clinical diagnostics for myeloid malignancies.[2–5] The introduction of commercially available myeloid gene panels has aided in this increased uptake. Most commercially available myeloid gene panels include between 25 and 50 genes; panels containing upward of 400 genes have been developed.[6] However, for the purpose of routine hematology practice, panels with 25 to 50 genes cover all clinically actionable gene variants in hematologic malignancies, thus providing adequate medical information in a cost-effective manner. Genes included in these commercial panels are involved in various functional categories, including splicing machinery, epigenetic modifiers, cohesion, transcription factors, signaling molecules, and chromatin modifiers.[3] These gene panels have allowed multiple genes to be sequenced in parallel, which has begun to replace single-gene testing. This approach has resulted in an increase in genetic variants being identified, some of which are novel. Novel variants may be classified as likely pathogenic, likely benign, or as variants of unknown significance (VUSs), based on similarities to previously reported variants and in silico analysis.[7]

In 2017, the NGS Ion AmpliSeq Myeloid Panel (Thermo Fisher) was introduced for molecular diagnostics of myeloid malignancies at the Regional Hospital. This was replaced in 2018 with the Oncomine Myeloid Panel (Thermo Fisher). The Ion AmpliSeq Panel examines cancer hotspots in 30 genes and fusions involving 22 driver genes implicated in myeloid malignancies while the Oncomine Myeloid Panel includes an additional 10 cancer hotspot genes and fusion of eight additional driver genes. The clinical implementation of the Ion AmpliSeq Myeloid Panel and the Oncomine Myeloid Panel (Thermo Fisher) has increased the amount of genetic information available to physicians, including the discovery of some novel variants. Whereas other studies have focused on a small subset of myeloid malignancies[8] or previously diagnosed tumors,[9] we have examined randomly selected cases submitted for molecular diagnostics for a potential myeloid malignancy. This provides a better representation of the utility of our panel in routine clinical practice where molecular testing is used in a variety of clinical presentations. Herein we will examine the results found using both panels, including the reporting of novel variants discovered.

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