PMID- 36831635
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20230228
IS  - 2072-6694 (Print)
IS  - 2072-6694 (Electronic)
IS  - 2072-6694 (Linking)
VI  - 15
IP  - 4
DP  - 2023 Feb 17
TI  - Optical Genome Mapping as an Alternative to FISH-Based Cytogenetic Assessment in 
      Chronic Lymphocytic Leukemia.
LID - 10.3390/cancers15041294 [doi]
LID - 1294
AB  - 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.
FAU - Valkama, Andriana
AU  - Valkama A
AD  - Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research 
      Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland.
FAU - Vorimo, Sandra
AU  - Vorimo S
AD  - Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research 
      Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland.
FAU - Kumpula, Timo A
AU  - Kumpula TA
AUID- ORCID: 0000-0002-6124-8929
AD  - Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research 
      Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland.
FAU - Rasanen, Hannele
AU  - Rasanen H
AD  - Northern Finland Laboratory Centre Nordlab, 90220 Oulu, Finland.
FAU - Savolainen, Eeva-Riitta
AU  - Savolainen ER
AD  - Northern Finland Laboratory Centre Nordlab, 90220 Oulu, Finland.
FAU - Pylkas, Katri
AU  - Pylkas K
AUID- ORCID: 0000-0002-2449-0521
AD  - Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research 
      Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland.
AD  - Northern Finland Laboratory Centre Nordlab, 90220 Oulu, Finland.
FAU - Mantere, Tuomo
AU  - Mantere T
AUID- ORCID: 0000-0003-3284-4403
AD  - Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research 
      Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland.
LA  - eng
GR  - 338374/Academy of Finland/
GR  - 220111/Sigrid Juselius Foundation/
PT  - Journal Article
DEP - 20230217
PL  - Switzerland
TA  - Cancers (Basel)
JT  - Cancers
JID - 101526829
PMC - PMC9953986
OTO - NOTNLM
OT  - chromosomal aberration
OT  - chronic lymphocytic leukemia
OT  - cytogenetics
OT  - fluorescence in situ hybridization
OT  - optical genome mapping
COIS- The authors declare no conflict of interest.
EDAT- 2023/02/26 06:00
MHDA- 2023/02/26 06:01
PMCR- 2023/02/17
CRDT- 2023/02/25 01:41
PHST- 2023/01/15 00:00 [received]
PHST- 2023/02/08 00:00 [revised]
PHST- 2023/02/16 00:00 [accepted]
PHST- 2023/02/25 01:41 [entrez]
PHST- 2023/02/26 06:00 [pubmed]
PHST- 2023/02/26 06:01 [medline]
PHST- 2023/02/17 00:00 [pmc-release]
AID - cancers15041294 [pii]
AID - cancers-15-01294 [pii]
AID - 10.3390/cancers15041294 [doi]
PST - epublish
SO  - Cancers (Basel). 2023 Feb 17;15(4):1294. doi: 10.3390/cancers15041294.