University of Oulu

Valkama A, Vorimo S, Kumpula TA, Räsänen H, Savolainen E-R, Pylkäs K, Mantere T. Optical Genome Mapping as an Alternative to FISH-Based Cytogenetic Assessment in Chronic Lymphocytic Leukemia. Cancers. 2023; 15(4):1294.

Optical genome mapping as an alternative to FISH-based cytogenetic assessment in chronic lymphocytic leukemia

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Author: Valkama, Andriana1; Vorimo, Sandra1; Kumpula, Timo A.1;
Organizations: 1Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
2Northern Finland Laboratory Centre Nordlab, 90220 Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 3.6 MB)
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Language: English
Published: Multidisciplinary Digital Publishing Institute, 2023
Publish Date: 2023-09-06


The fluorescence in situ hybridization (FISH) technique plays an important role in the risk stratification and clinical management of patients with chronic lymphocytic leukemia (CLL). For genome-wide analysis, FISH needs to be complemented with other cytogenetic methods, including karyotyping and/or chromosomal microarrays. However, this is often not feasible in a diagnostic setup. Optical genome mapping (OGM) is a novel technique for high-resolution genome-wide detection of structural variants (SVs), and previous studies have indicated that OGM could serve as a generic cytogenetic tool for hematological malignancies. Herein, we report the results from our study evaluating the concordance of OGM and standard-of-care FISH in 18 CLL samples. The results were fully concordant between these two techniques in the blinded comparison. Using in silico dilution series, the lowest limit of detection with OGM was determined to range between 3 and 9% variant allele fractions. Genome-wide analysis by OGM revealed additional (>1 Mb) aberrations in 78% of the samples, including both unbalanced and balanced SVs. Importantly, OGM also enabled the detection of clinically relevant complex karyotypes, undetectable by FISH, in three samples. Overall, this study demonstrates the potential of OGM as a first-tier cytogenetic test for CLL and as a powerful tool for genome-wide SV analysis.

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Series: Cancers
ISSN: 2072-6694
ISSN-E: 2072-6694
ISSN-L: 2072-6694
Volume: 15
Issue: 4
Article number: 1294
DOI: 10.3390/cancers15041294
Type of Publication: A1 Journal article – refereed
Field of Science: 3122 Cancers
Funding: This work was supported by the Sigrid Juselius Foundation (grant number 220111) and Academy of Finland (grant number 338374).
Academy of Finland Grant Number: 338374
Detailed Information: 338374 (Academy of Finland Funding decision)
Copyright information: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (