The impact of next-generation sequencing for diagnosis and disease understanding of myeloid malignancies

ABSTRACT

Introduction

Defining the chromosomal and molecular changes associated with myeloid neoplasms (MNs) optimizes clinical care through improved diagnosis, prognosis, treatment planning, and patient monitoring. This review will concisely describe the techniques used to profile MNs clinically today, with descriptions of challenges and emerging approaches that may soon become standard-of-care.

Areas covered

In this review, the authors discuss molecular assessment of MNs using non-sequencing techniques, including conventional cytogenetic analysis, fluorescence in situ hybridization, chromosomal genomic microarray testing; as well as DNA- or RNA-based next-generation sequencing (NGS) assays; and sequential monitoring via digital PCR or measurable residual disease assays. The authors explain why distinguishing somatic from germline alleles is critical for optimal management. Finally, they introduce emerging technologies, such as long-read, whole exome/genome, and single-cell sequencing, which are reserved for research purposes currently but will become clinical tests soon.

Expert opinion

The authors describe challenges to the adoption of comprehensive genomic tests for those in resource-constrained environments and for inclusion into clinical trials. In the future, all aspects of patient care will likely be influenced by the adaptation of artificial intelligence and mathematical modeling, fueled by rapid advances in telecommunications.

KEYWORDS:

• Next-generation sequencing
• molecular profiling
• somatic allele
• germline variant

Article highlights

• Myeloid neoplasms are a heterogeneous group of diseases with many molecular markers relevant for diagnosis, prognosis, treatment decisions, and patient monitoring that change throughout a patient’s disease course and are monitored sequentially over time using a variety of assays, many of which are now based on next generation sequencing (NGS).

• The main types of molecular markers followed in myeloid neoplasms are structural DNA aberrations and gene mutations.

• Non-sequencing-based techniques that reveal DNA structural rearrangements include conventional cytogenetic analysis, fluorescence in situ hybridization, chromosomal genomic and microarray testing, with optical genome mapping emerging with rapid uptake by clinical laboratories.

• DNA-based NGS molecular profiling panels provide multi-gene testing into a single test with rapid turn-around-times.

• Because many panel-based sequencing assays designed to detect acquired DNA mutations in MNs for diagnostic and prognostic purposes cover genes that can also be altered in the germline state, it is possible to identify patients with likely germline alleles incidentally from tumor-based molecular profiling, especially by calculating the change in the variant allele frequency (VAF) using the coefficient of variance in the VAF.

• RNA-based NGS assays are most sensitive for the detection of transcribed products of gene fusions of diagnostic and prognostic significance in myeloid neoplasms.

Declaration of interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewer disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

This paper was not funded.