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Next-generation sequencing (NGS) is a high throughput analytical tool used for diagnosis of hereditary disorders such as myeloid malignancies. Copy number variants (CNVs) and genetic aberrations are used as a prognostic biomarker in myeloid malignancies. A targeted NGS assay is widely employed to identify targeted mutations, such as point mutations/single-nucleotide variants, insertions, and deletions. However, the potential use of the targeted NGS assay to detect common CNVs in myeloid malignancies compared with the traditional fluorescence in situ hybridization (FISH) panel, and conventional chromosome analysis (CCA) is still not completely determined.
In a recent proof-of-principle study, published in The Journal of Molecular Diagnostic, Liqun Jiang and colleagues1 compare the detection of myelodysplastic syndrome (MDS) CNVs by a targeted NGS with routine clinical methods (MDS FISH, and CCA). The study aimed to explore the possibility of using targeted NGS to identify somatic mutations and CNVs at the same time.
Samples of bone marrow or blood from 406 patients were analyzed using MDS FISH, targeted NGS, and CCA, and only 91 specimens with an abnormal MDS FISH panel were selected for the study. However, 315 normal samples were further characterized using CCA and targeted NGS. Figure 1 describes an outline of the methods employed in the study.
CCA, conventional chromosome analysis; CN-LOH, copy neutral-loss of heterozygosity; CNV, copy number variant; FISH, fluorescent in situ hybridization; NGS, next-generation sequencing.
*Adapted from L. Jiang et al.1
A succinct summary of the results is presented in Figure 2, and key outcomes are as follows:
Targeted NGS is a highly sensitive assay that provides a single platform to detect CNVs, relevant somatic mutations, and CN-LOH in myeloid malignancies in a single experiment. The assay offers a quick and prompt way of identification of critical regions, and can detect mutations missed by CCA or the MDS FISH panel.
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