Ann Lab Med.  2024 Jul;44(4):324-334. 10.3343/alm.2023.0339.

Comparison of Optical Genome Mapping With Conventional Diagnostic Methods for Structural Variant Detection in Hematologic Malignancies

• Shim Y
• Koo YK
• Shin S
• Lee ST
• Lee KA
• Choi JR

• KMID: 2557931
• DOI: http://doi.org/10.3343/alm.2023.0339

Abstract

Background
Structural variants (SVs) are currently analyzed using a combination of conventional methods; however, this approach has limitations. Optical genome mapping (OGM), an emerging technology for detecting SVs using a single-molecule strategy, has the potential to replace conventional methods. We compared OGM with conventional diagnostic methods for detecting SVs in various hematologic malignancies.
Methods
Residual bone marrow aspirates from 27 patients with hematologic malignancies in whom SVs were observed using conventional methods (chromosomal banding analysis, FISH, an RNA fusion panel, and reverse transcription PCR) were analyzed using OGM. The concordance between the OGM and conventional method results was evaluated.
Results
OGM showed concordance in 63% (17/27) and partial concordance in 37% (10/27) of samples. OGM detected 76% (52/68) of the total SVs correctly (concordance rate for each type of SVs: aneuploidies, 83% [15/18]; balanced translocation, 80% [12/15] unbalanced translocation, 54% [7/13] deletions, 81% [13/16]; duplications, 100% [2/2] inversion 100% [1/1]; insertion, 100% [1/1]; marker chromosome, 0% [0/1]; isochromosome, 100% [1/1]). Sixteen discordant results were attributed to the involvement of centromeric/telomeric regions, detection sensitivity, and a low mapping rate and coverage. OGM identified additional SVs, including submicroscopic SVs and novel fusions, in five cases.
Conclusions
OGM shows a high level of concordance with conventional diagnostic methods for the detection of SVs and can identify novel variants, suggesting its potential utility in enabling more comprehensive SV analysis in routine diagnostics of hematologic malignancies, although further studies and improvements are required.

Keyword

Copy number variations; Gene fusion; Hematologic neoplasms; Optical genome mapping; Structural variations

Figure

• 

  Fig. 1 Results of conventional laboratory tests and OGM for S4. (A) CBA revealed an insertion in the long arm of chromosome 9. (B) Whole-genome circos plot obtained by OGM showing MYC amplification. (C) FISH was performed using Vysis probes (Abbott Molecular). (D) NGS CNV analysis showing amplification of the q24.21 band in chromosome 8. Abbreviations: OGM, optical genome mapping; CBA, chromosomal banding analysis; chr, chromosome; CNV, copy number variant.

• 

  Fig. 2 Additional finding of EP300::ZNF384 fusion by OGM in S18. (A) Genome map view showing the EP300::ZNF384 fusion. Map of S18 (blue) aligned to reference maps of chromosome 12 and chromosome 22 (green), with breakpoints in ZNF384 and EP300, respectively. Label alignments between the reference and sample genome maps are indicated by gray lines. Translocation breakpoints are indicated by pink lines. (B) Confirmation of the EP300::ZNF384 fusion using Sanger sequencing. The red arrow indicates the breakpoint. Abbreviations: OGM, optical genome mapping; chr, chromosome.

Reference

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