Optical Genome Mapping as an Alternative to FISH-Based Cytogenetic Assessment in Chronic Lymphocytic Leukemia

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...

Full description

Saved in:
Bibliographic Details
Published in:Cancers 2023-02, Vol.15 (4), p.1294
Main Authors: Valkama, Andriana, Vorimo, Sandra, Kumpula, Timo A, Räsänen, Hannele, Savolainen, Eeva-Riitta, Pylkäs, Katri, Mantere, Tuomo
Format: Article
Language:English
Subjects:
Biobanks
Cancer
Cell division
Chromosome aberrations
Chronic lymphocytic leukemia
Cytogenetics
Data analysis
Fluorescence in situ hybridization
Gene mapping
Genetic aspects
Genome-wide association studies
Genomes
Genomics
Karyotypes
Labeling
Leukemia
Malignancy
Oncology, Experimental
Software
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:2072-6694
2072-6694
DOI:10.3390/cancers15041294