Optical Genome Mapping for Detection of -Another Tool in Our Toolbox

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2024 Nov 27

PMID 39596557

Authors

Zhenya Tang

Wei Wang

Gokce A Toruner

Shimin Hu

Hong Fang

Jie Xu

M James You

L Jeffrey Medeiros

Joseph D Khoury

Guilin Tang

Affiliations

Soon will be listed here.

Abstract

fusion is mostly derived from a reciprocal translocation t(9;22)(q34.1;q11.2) and is rarely caused by insertion. Various methods have been used for the detection of t(9;22)/, such as G-banded chromosomal analysis, fluorescence in situ hybridization (FISH), quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) and optical genome mapping (OGM). Understanding the strengths and limitations of each method is essential for the selection of appropriate method(s) of disease diagnosis and/or during the follow-up. We compared the results of OGM, chromosomal analysis, FISH, and/or RT-PCR in 12 cases with . was detected by FISH and RT-PCR in all 12 cases. One case with ins(22;9)/ was cryptic by chromosomal analysis and nearly missed by OGM. Atypical FISH signal patterns were observed in five cases, suggesting additional chromosomal aberrations involving chromosomes 9 and/or 22. RT-PCR identified the transcript isoforms p210 and p190 in seven and five cases, respectively. Chromosomal analysis revealed additional chromosomal aberrations in seven cases. OGM identified extra cytogenomic abnormalities in 10 cases, including chromoanagenesis and deletion, which were only detected by OGM. FISH offers rapid and definitive detection of fusion, while OGM provides a comprehensive cytogenomic analysis. In scenarios where OGM is feasible, chromosomal analysis and RT-PCR may not offer additional diagnostic value.

References

Gao Q, Liang W, Foltz S, Mutharasu G, Jayasinghe R, Cao S . Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018; 23(1):227-238.e3. PMC: 5916809. DOI: 10.1016/j.celrep.2018.03.050. View

Alaggio R, Amador C, Anagnostopoulos I, Attygalle A, de Oliveira Araujo I, Berti E . The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasms. Leukemia. 2022; 36(7):1720-1748. PMC: 9214472. DOI: 10.1038/s41375-022-01620-2. View

Hu X, Wang Q, Tang M, Barthel F, Amin S, Yoshihara K . TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Res. 2017; 46(D1):D1144-D1149. PMC: 5753333. DOI: 10.1093/nar/gkx1018. View

Zhen C, Wang Y . Molecular monitoring of chronic myeloid leukemia: international standardization of BCR-ABL1 quantitation. J Mol Diagn. 2013; 15(5):556-64. DOI: 10.1016/j.jmoldx.2013.05.010. View

Akkari Y, Baughn L, Dubuc A, Smith A, Mallo M, Dal Cin P . Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood. 2022; 139(15):2273-2284. PMC: 9710485. DOI: 10.1182/blood.2021014309. View

Mikhail F, Heerema N, Rao K, Burnside R, Cherry A, Cooley L . Section E6.1-6.4 of the ACMG technical standards and guidelines: chromosome studies of neoplastic blood and bone marrow-acquired chromosomal abnormalities. Genet Med. 2016; 18(6):635-42. DOI: 10.1038/gim.2016.50. View

Luhmann J, Stelter M, Wolter M, Kater J, Lentes J, Bergmann A . The Clinical Utility of Optical Genome Mapping for the Assessment of Genomic Aberrations in Acute Lymphoblastic Leukemia. Cancers (Basel). 2021; 13(17). PMC: 8431583. DOI: 10.3390/cancers13174388. View

Paolino J, Tsai H, Harris M, Pikman Y . Alterations and Therapeutic Targeting in B-Cell Acute Lymphoblastic Leukemia. Biomedicines. 2024; 12(1). PMC: 10813044. DOI: 10.3390/biomedicines12010089. View

Wierda W, Brown J, Abramson J, Awan F, Bilgrami S, Bociek G . NCCN Guidelines® Insights: Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma, Version 3.2022. J Natl Compr Canc Netw. 2022; 20(6):622-634. DOI: 10.6004/jnccn.2022.0031. View

10.

Fazio G, Bresolin S, Silvestri D, Quadri M, Saitta C, Vendramini E . PAX5 fusion genes are frequent in poor risk childhood acute lymphoblastic leukaemia and can be targeted with BIBF1120. EBioMedicine. 2022; 83:104224. PMC: 9403348. DOI: 10.1016/j.ebiom.2022.104224. View

11.

Tang Z, Toruner G, Tang G, Yin C, Wang W, Hu S . Chronic myeloid leukemia with insertion-derived BCR-ABL1 fusion: redefining complex chromosomal abnormalities by correlation of FISH and karyotype predicts prognosis. Mod Pathol. 2020; 33(10):2035-2045. DOI: 10.1038/s41379-020-0564-6. View

12.

Brandes D, Yasin L, Nebral K, Ebler J, Schinnerl D, Picard D . Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood and High Hyperdiploid Acute Lymphoblastic Leukemia. Hemasphere. 2023; 7(8):e925. PMC: 10353714. DOI: 10.1097/HS9.0000000000000925. View

13.

Mascarello J, Hirsch B, Kearney H, Ketterling R, Olson S, Quigley D . Section E9 of the American College of Medical Genetics technical standards and guidelines: fluorescence in situ hybridization. Genet Med. 2011; 13(7):667-75. DOI: 10.1097/GIM.0b013e3182227295. View

14.

Khoury J, Solary E, Abla O, Akkari Y, Alaggio R, Apperley J . The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Myeloid and Histiocytic/Dendritic Neoplasms. Leukemia. 2022; 36(7):1703-1719. PMC: 9252913. DOI: 10.1038/s41375-022-01613-1. View

15.

Campo E, Jaffe E, Cook J, Quintanilla-Martinez L, Swerdlow S, Anderson K . The International Consensus Classification of Mature Lymphoid Neoplasms: a report from the Clinical Advisory Committee. Blood. 2022; 140(11):1229-1253. PMC: 9479027. DOI: 10.1182/blood.2022015851. View

16.

Yang H, Garcia-Manero G, Sasaki K, Montalban-Bravo G, Tang Z, Wei Y . High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance. Leukemia. 2022; 36(9):2306-2316. PMC: 9417987. DOI: 10.1038/s41375-022-01652-8. View

17.

Smith A, Neveling K, Kanagal-Shamanna R . Optical genome mapping for structural variation analysis in hematologic malignancies. Am J Hematol. 2022; 97(7):975-982. DOI: 10.1002/ajh.26587. View

18.

Roberts K, Morin R, Zhang J, Hirst M, Zhao Y, Su X . Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell. 2012; 22(2):153-66. PMC: 3422513. DOI: 10.1016/j.ccr.2012.06.005. View

19.

Eckardt J, Stasik S, Rollig C, Petzold A, Sauer T, Scholl S . Mutated IKZF1 is an independent marker of adverse risk in acute myeloid leukemia. Leukemia. 2023; 37(12):2395-2403. PMC: 10681898. DOI: 10.1038/s41375-023-02061-1. View

20.

Soler G, Ouedraogo Z, Goumy C, Lebecque B, Aspas Requena G, Ravinet A . Optical Genome Mapping in Routine Cytogenetic Diagnosis of Acute Leukemia. Cancers (Basel). 2023; 15(7). PMC: 10093111. DOI: 10.3390/cancers15072131. View