Optical genome mapping refines cytogenetic diagnostics, prognostic stratification and provides new molecular insights in adult MDS/AML patients

Balducci, Estelle; Kaltenbach, Sophie; Villarèse, Patrick; Duroyon, Eugénie; Zalmai, Loria; Friedrich, Chloé; Suarez, Félipe; Marçais, Ambroise; Bouscary, Didier; Decroocq, Justine; Birsen, Rudy; Fontenay, Michaëla; Templé, Marie; Brouzes, Chantal; Touzart, Aurore; Steimlé, Thomas; Cieślak, Agata; Lhermitte, Ludovic; Almire, Carole; Chapuis, Nicolas; Hermine, Olivier; Asnafi, Vahid; Kosmider, Olivier; Couronné, Lucile

doi:10.1038/s41408-022-00718-1

Cited by 23 publications

(32 citation statements)

References 14 publications

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“…Balducci et al published a study with 41 AML and 27 MDS patients. In 88% of the AML cases, concordance with standard diagnostics was reached [ 31 ]. Notably, apart from CBA, the percentage of patients analyzed with FISH was higher than in the study by Levy and co-workers (63% vs. 19%).…”

Section: Optical Genome Mapping In Aml—concordance With Standard Diag...mentioning

confidence: 99%

“…Balducci et al published a study with 68 patients, 27 of whom were MDS patients, reaching a 94% concordance rate and gaining additional information in 19% of cases. In 22%, a change in IPSS-R was obtained [ 31 ]. Notably, these MDS cases were heterogenic, including only cases with excessive blasts in our work, but also other subtypes of MDS in other cohorts.…”

Section: Optical Genome Mapping In Aml—concordance With Standard Diag...mentioning

confidence: 99%

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Optical Genome Mapping for Cytogenetic Diagnostics in AML

Nilius‐Eliliwi

Gerding

Schroers

et al. 2023

Cancers

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The classification and risk stratification of acute myeloid leukemia (AML) is based on reliable genetic diagnostics. A broad and expanding variety of relevant aberrations are structural variants beyond single-nucleotide variants. Optical Genome Mapping is an unbiased, genome-wide, amplification-free method for the detection of structural variants. In this review, the current knowledge of Optical Genome Mapping (OGM) with regard to diagnostics in hematological malignancies in general, and AML in specific, is summarized. Furthermore, this review focuses on the ability of OGM to expand the use of cytogenetic diagnostics in AML and perhaps even replace older techniques such as chromosomal-banding analysis, fluorescence in situ hybridization, or copy number variation microarrays. Finally, OGM is compared to amplification-based techniques and a brief outlook for future directions is given.

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Section: Optical Genome Mapping In Aml—concordance With Standard Diag...mentioning

confidence: 99%

Section: Optical Genome Mapping In Aml—concordance With Standard Diag...mentioning

confidence: 99%

Optical Genome Mapping for Cytogenetic Diagnostics in AML

Nilius‐Eliliwi

Gerding

Schroers

et al. 2023

Cancers

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“…The performance of OGM in hematological malignancies compared to SOC testing regimens has now been well established with OGM showing equal or better sensitivity and resolution for the detection of diagnostic and prognostic abnormalities malignancies 8,10–12,33 . Consequently, there has been a rapid interest in adopting OGM in clinical laboratories for detection of sentinel cytogenomic abnormalities in patients with hematological neoplasms.…”

Section: Discussionmentioning

confidence: 99%

A framework for the clinical implementation of optical genome mapping in hematologic malignancies

Levy,

Kanagal‐Shamanna,

Sahajpal

et al. 2024

American J Hematol

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Optical Genome Mapping (OGM) is rapidly emerging as an exciting cytogenomic technology both for research and clinical purposes. In the last 2 years alone, multiple studies have demonstrated that OGM not only matches the diagnostic scope of conventional standard of care cytogenomic clinical testing but it also adds significant new information in certain cases. Since OGM consolidates the diagnostic benefits of multiple costly and laborious tests (e.g., karyotyping, fluorescence in situ hybridization, and chromosomal microarrays) in a single cost‐effective assay, many clinical laboratories have started to consider utilizing OGM. In 2021, an international working group of early adopters of OGM who are experienced with routine clinical cytogenomic testing in patients with hematological neoplasms formed a consortium (International Consortium for OGM in Hematologic Malignancies, henceforth “the Consortium”) to create a consensus framework for implementation of OGM in a clinical setting. The focus of the Consortium is to provide guidance for laboratories implementing OGM in three specific areas: validation, quality control and analysis and interpretation of variants. Since OGM is a complex technology with many variables, we felt that by consolidating our collective experience, we could provide a practical and useful tool for uniform implementation of OGM in hematologic malignancies with the ultimate goal of achieving globally accepted standards.

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“…Thus, identification of P2RY8::CRLF2 fusion is critical in clinical practice. Though OGM has been shown to have the potential to be a routine tool in hematology malignancies [26,27], some technical limitations remain to be further addressed by anticipated software improvements, especially in PAR regions. However, it is also possible that P2RY8::CRLF2 fusion can be missed by VAF which is lower than 5%.…”

Section: Discussionmentioning

confidence: 99%

Optical Genome Mapping for Comprehensive Assessment of Chromosomal Aberrations and Discovery of New Fusion Genes in Pediatric B-Acute Lymphoblastic Leukemia

Gao

Wang

et al. 2022

Cancers

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Purpose: To assess the potential added value of Optical Genomic Mapping (OGM) for identifying chromosomal aberrations. Methods: We utilized Optical Genomic Mapping (OGM) to determine chromosomal aberrations in 46 children with B-cell Acute lymphoblastic leukemia ALL (B-ALL) and compared the results of OGM with conventional technologies. Partial detection results were verified by WGS and PCR. Results: OGM showed a good concordance with conventional cytogenetic techniques in identifying the reproducible and pathologically significant genomic SVs. Two new fusion genes (LMNB1::PPP2R2B and TMEM272::KDM4B) were identified by OGM and verified by WGS and RT-PCR for the first time. OGM has a greater ability to detect complex chromosomal aberrations, refine complicated karyotypes, and identify more SVs. Several novel fusion genes and single-gene alterations, associated with definite or potential pathologic significance that had not been detected by traditional methods, were also identified. Conclusion: OGM addresses some of the limitations associated with conventional cytogenomic testing. This all-in-one process allows the detection of most major genomic risk markers in one test, which may have important meanings for the development of leukemia pathogenesis and targeted drugs.

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Optical genome mapping refines cytogenetic diagnostics, prognostic stratification and provides new molecular insights in adult MDS/AML patients

Cited by 23 publications

References 14 publications

Optical Genome Mapping for Cytogenetic Diagnostics in AML

Optical Genome Mapping for Cytogenetic Diagnostics in AML

A framework for the clinical implementation of optical genome mapping in hematologic malignancies

Optical Genome Mapping for Comprehensive Assessment of Chromosomal Aberrations and Discovery of New Fusion Genes in Pediatric B-Acute Lymphoblastic Leukemia

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