A framework for the clinical implementation of optical genome mapping in hematologic malignancies.
Journal
American journal of hematology
ISSN: 1096-8652
Titre abrégé: Am J Hematol
Pays: United States
ID NLM: 7610369
Informations de publication
Date de publication:
Apr 2024
Apr 2024
Historique:
revised:
09
10
2023
received:
12
08
2023
accepted:
22
11
2023
pubmed:
2
1
2024
medline:
2
1
2024
entrez:
2
1
2024
Statut:
ppublish
Résumé
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.
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
642-661Subventions
Organisme : Generalitat de Catalunya
ID : SGR00560
Organisme : Generalitat de Catalunya
ID : SGR288
Organisme : CERCA Programme
Organisme : Fundació Internacional Josep Carreras
Informations de copyright
© 2024 The Authors. American Journal of Hematology published by Wiley Periodicals LLC.
Références
Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006;7:85-97.
Nowell P, Hungerford D. A minute chromosome in chronic granulocytic leukemia. Science. 1979;1960(132):1488-1501.
Rowley JD. Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature. 1973;243:290-293.
Khoury JD, Solary E, Abla O, et al. The 5th edition of the World Health Organization classification of haematolymphoid tumours: myeloid and histiocytic/dendritic neoplasms. Leukemia. 2022;36:1703-1719.
Arber DA, Orazi A, Hasserjian RP, et al. International consensus classification of myeloid neoplasms and acute leukemias: integrating morphologic, clinical, and genomic data. Blood. 2022;140:1200-1228.
Döhner H, Wei AH, Appelbaum FR, et al. Diagnosis and management of AML in adults: 2022 recommendations from an international expert panel on behalf of the ELN. Blood. 2022;140:1345-1377.
Smith AC, Neveling K, Kanagal-Shamanna R. Optical genome mapping for structural variation analysis in hematologic malignancies. Am J Hematol. 2022;97:975-982.
Neveling K, Mantere T, Vermeulen S, et al. Next-generation cytogenetics: comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping. Am J Hum Genet. 2021;108:1423-1435.
Sahajpal NS, Mondal AK, Singh H, et al. Clinical utility of combined optical genome mapping and 523-gene next generation sequencing panel for comprehensive evaluation of myeloid cancers. Cancers. 2023:15(12):3214. doi:10.3390/cancers15123214
Gerding WM, Tembrink M, Nilius-Eliliwi V, et al. Optical genome mapping reveals additional prognostic information compared to conventional cytogenetics in AML/MDS patients. Int J Cancer. 2022;150:1998-2011. doi:10.1002/ijc.33942
Balducci E, Kaltenbach S, Villarese P, et al. Optical genome mapping refines cytogenetic diagnostics, prognostic stratification and provides new molecular insights in adult MDS/AML patients. Blood Cancer J. 2022;12:58-61.
Levy B, Baughn LB, Akkari YMN, et al. Optical genome mapping in acute myeloid leukemia: a multicenter evaluation. Blood Adv. 2022;7:1297-1307.
Suttorp J, Lühmann JL, Behrens YL, et al. Optical genome mapping as a diagnostic tool in pediatric acute myeloid leukemia. Cancers (Basel). 2022;14:1-20.
Yang H, Garcia-Manero G, Sasaki K, et al. High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance. Leukemia. 2022;36:2306-2316.
Lestringant V, Duployez N, Penther D, et al. Optical genome mapping, a promising alternative to gold standard cytogenetic approaches in a series of acute lymphoblastic leukemias. Genes Chromosomes Cancer. 2021;60:657-667.
Lühmann JL, Stelter M, Wolter M, et al. The clinical utility of optical genome mapping for the assessment of genomic aberrations in acute lymphoblastic leukemia. Cancers (Basel). 2021;13:13.
Rack K, Bie J, Ameye G, et al. Optimizing the diagnostic workflow for acute lymphoblastic leukemia by optical genome mapping. Am J Hematol. 2022;97:548-561.
Puiggros A, Ramos-Campoy S, Kamaso J, et al. Optical genome mapping: a promising new tool to assess genomic complexity in chronic lymphocytic leukemia (CLL). Cancers (Basel). 2022;14:1-21.
Valkama A, Vorimo S, Kumpula TA, et al. Optical genome mapping as an alternative to FISH-based cytogenetic assessment in chronic lymphocytic leukemia. Cancers (Basel). 2023;15:1-12.
Jennings LJ, Arcila ME, Corless C, et al. Guidelines for validation of next-generation sequencing-based oncology panels: a joint consensus recommendation of the Association for Molecular Pathology and College of American pathologists. J Mol Diagn. 2017;19:341-365.
Sahajpal NS, Mondal AK, Tvrdik T, et al. Clinical validation and diagnostic utility of optical genome mapping for enhanced cytogenomic analysis of hematological neoplasms. J Mol Diagn. 2022;24:1279-1291.
Iqbal MA, Broeckel U, Levy B, et al. Multisite assessment of optical genome mapping for analysis of structural variants in constitutional postnatal cases. J Mol Diagn. 2023;25:175-188.
Stevens-Kroef M, Olde Weghuis DEM, Hoischen A, Vissers LELM, Neveling K. Next generation cytogenetics': ‘Optical Genome Mapping’ verbetert detectie van cytogenetische afwijkingen bij hematologische maligniteiten. Ned Tijdschr Tandheelkd Hematol. 2023;20:208-216.
Sabatella M, Mantere T, Waanders E, et al. Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors. J Pathol. 2021;255:202-211.
Kanagal-Shamanna R, Loghavi S, Dinardo CD, et al. Bone marrow pathologic abnormalities in familial platelet disorder with propensity for myeloid malignancy and germline RUNX1 mutation. Haematologica. 2017;102:1661-1670.
Li MM, Datto M, Duncavage EJ, et al. Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017;19:4-23.
Mikhail FM, Biegel JA, Cooley LD, et al. Technical laboratory standards for interpretation and reporting of acquired copy-number abnormalities and copy-neutral loss of heterozygosity in neoplastic disorders: a joint consensus recommendation from the American College of Medical Genetics and Genom. Genet Med. 2019;21:1903-1915.
Schoumans J, Suela J, Hastings R, et al. Guidelines for genomic array analysis in acquired haematological neoplastic disorders. Genes Chromosomes Cancer. 2016;55:480-491.
Akkari YMN, Baughn LB, Dubuc AM, et al. Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood. 2022;139:2273-2284.
Holland AJ, Cleveland DW. Chromoanagenesis and cancer: mechanisms and consequences of localized, complex chromosomal rearrangements. Nat Med. 2012;18:1630-1638.
Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet. 2019;12:1-12.
Moore S, McGowan-Jordan J, Smith AC, et al. Genome Mapping Nomenclature. Cytogenet Genome Res. Published online December 8, 2023. doi: 10.1159/000535684
Sahajpal NS, Mondal AK, Singh H, et al. Clinical utility of optical genome mapping and 523-gene next generation sequencing panel for comprehensive evaluation of myeloid cancers. Cancers (Basel). 2023;15:3214.
Mateo J, Chakravarty D, Dienstmann R, et al. A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO scale for clinical actionability of molecular targets (ESCAT). Ann Oncol. 2018;29:1895-1902.
Horak P, Klink B, Heining C, et al. Precision oncology based on omics data: the NCT Heidelberg experience. Int J Cancer. 2017;141:877-886.
Vago L, Perna SK, Zanussi M, et al. Loss of mismatched HLA in leukemia after stem-cell transplantation. N Engl J Med. 2009;361:478-488.
Berry NK, Scott RJ, Rowlings P, Enjeti AK. Clinical use of SNP-microarrays for the detection of genome-wide changes in haematological malignancies. Crit Rev Oncol Hematol. 2019;142:58-67.
Chun K, Hagemeijer A, Iqbal A, Slovak ML. Implementation of standardized international karyotype scoring practices is needed to provide uniform and systematic evaluation for patients with myelodysplastic syndrome using IPSS criteria: an international working group on MDS cytogenetics study. Leuk Res. 2010;34:160-165.
Grimwade D, Hills RK, Moorman AV, et al. Refinement of cytogenetic classification in acute myeloid leukemia: determination of prognostic significance of rare recurring chromosomal abnormalities among 5876 younger adult patients treated in the United Kingdom Medical Research Council trials. Blood. 2010;116:354-365.
Baliakas P, Jeromin S, Iskas M, et al. Cytogenetic complexity in chronic lymphocytic leukemia: definitions, associations, and clinical impact. Blood. 2019;133:1205-1216.
Nguyen-Khac F, Bidet A, Daudignon A, et al. The complex karyotype in hematological malignancies: a comprehensive overview by the francophone Group of Hematological Cytogenetics (GFCH). Leukemia. 2022;36:1451-1466.
Leeksma AC, Taylor J, Wu B, et al. Clonal diversity predicts adverse outcome in chronic lymphocytic leukemia. Leukemia. 2019;33:390-402.
Ramos-Campoy S, Puiggros A, Beà S, et al. Chromosome banding analysis and genomic microarrays are both useful but not equivalent methods for genomic complexity risk stratification in chronic lymphocytic leukemia patients. Haematologica. 2022;107:593-603.
Scarpelli I, Stalder VB, Tsilimidos G, et al. Refined cytogenetic IPSS-R evaluation by the use of SNP array in a cohort of 290 MDS patients. Genes Chromosomes Cancer. 2023;62:721-731.