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

Blood Cancer Journal 2022
Balducci E, et al

Estelle Balducci, Sophie Kaltenbach, Patrick Villarese, Eugénie Duroyon, Loria Zalmai, Chloé Friedrich, Felipe Suarez, Ambroise Marcais, Didier Bouscary, Justine Decroocq, Rudy Birsen, Michaëla Fontenay, Marie Templé, Chantal Brouzes, Aurore Touzart, Thomas Steimlé, Agata Cieslak, Ludovic Lhermitte, Carole Almire, Nicolas Chapuis, Olivier Hermine, Vahid Asnafi, Olivier Kosmider, Lucile Couronné Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are clinically and genetically heterogeneous myeloid malignancies associated with a broad range of recurring mutations and cytogenetic abnormalities. To date, their diagnostic workup includes a conventional karyotype to establish the IPSS-R (Revised International Prognostic Scoring System) and ELN (European Leukemia Net) prognostic scores in MDS and AML patients, respectively [1,2,3].

In recent years, many advances have been made in the development of methods for the detection of somatic cytogenetic abnormalities. In this regard, optical genome mapping (OGM) is a cutting-edge technology developed for genome-wide detection of structural variants (SVs) including balanced and unbalanced translocations, inversions, insertions, deletions, duplications as well as copy number variations (CNVs). This technology is based on the comparative analysis of optical genome maps obtained from high molecular weight DNA greater than 150 kb. OGM aims to address the limitations of existing cytogenetic techniques offering a higher resolution than karyotyping, allowing whole-genome analysis, unlike FISH, and the detection of balanced chromosomal abnormalities missed by CGH/SNP-array analysis [4]. Recently, its assessment in hematological malignancies including myeloid neoplasms has shown promising results as compared with standard cytogenetic techniques [5,6,7,8,9].

Given the scarce data available on this new technology, we conducted a study on a French series of 68 adult MDS and AML patients to evaluate its performance in the detection of somatic cytogenetic abnormalities and its clinical utility.

Sixty-eight samples (64 bone marrow samples and 4 peripheral blood samples) including 27 MDS cases and 41 AML cases were analyzed using OGM (Table S1). Twenty-six were retrospective cases collected between March 2010 and August 2020 and 42 were prospective cases sent to our laboratory for routine cytogenetic analysis between January 2021 and December 2021 (Fig. S1). Routine cytogenetic results were normal in 12/27 (44%) MDS cases and 19/41 (46%) AML cases, simple abnormal (<3 abnormalities) in 9/27 (33%) MDS cases and 12/41 (29%) AML cases, and complex (≥3 abnormalities) in 5/27 (18%) MDS cases and 8/41 (19%) AML cases. In the three remaining cases (1 MDS case and 2 AML cases), the karyotype was a failure. Patients’ routine cytogenetic and OGM results are presented in (Table S2).

OGM successfully detected most of the cytogenetic abnorma-lities seen on routine cytogenetics including aneuploidies as Y loss (Fig. S2A–C), monosomy 7, trisomy 8 (Fig. S2D–F), hyperdiploidy, and unbalanced SVs as 7q deletion (Fig. S2G–I), 5q deletion, ring of chromosome 7, 11q deletion, 20q deletion (Fig. 1). OGM also detected balanced SVs identifying partner genes of driver genes not routinely sought by other techniques such as t(6;11)/KMT2A::MLLT4 (UPN 19) (Fig. S3A–C), inv(3)/MECOM::RPN1 (UPN 87) (Fig. S3D–F), and t(2;3)/MECOM::BCL11A (UPN 134) (Fig. S3G-I and Fig. 1). Importantly, OGM provided successful analysis in the 3 cases of karyotype failure. Of note, in 10 patients, OGM missed cytogenetic abnormalities seen on routine cytogenetics in the following cases (Table S3): (1) low subclonal CNVs involving a whole chromosome as Y loss and trisomy 8, (2) clone with a gain of a whole batch of chromosomes as tetraploidy and near triploidy, (3) low subclones, (4) SVs which breakpoints are located in poorly covered areas by OGM (e.g. centromeric and telomeric regions) such as additional material on the short arm of acrocentric chromosomes. In two cases with available material (UPNs 1 and 112), we performed an interphase FISH analysis, known to display a low detection threshold. In UPN 112, interphase FISH detected trisomy 13 in 1.5% of the interphasic nuclei, confirming that OGM is not efficient to detect low subclonal trisomies. In UPN 1, interphase FISH failed to detect trisomy 5, indicating that a selective advantage of mitotic cells carrying aneuploidies under culture conditions cannot be fully ruled out. Overall, cytogenetic abnormalities seen on routine cytogenetics were successfully detected by OGM in 85% (58/68) of patients.

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