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Use of Optical Genome Mapping to Detect Structural Variants in Neuroblastoma

Lookup NU author(s): Ruby Barford, Fang Fong, Hannah Hartley, Dr Lisa Allinson, Professor Deborah Tweddle

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© 2023 by the authors.Background: Neuroblastoma is the most common extracranial solid tumour in children, accounting for 15% of paediatric cancer deaths. Multiple genetic abnormalities have been identified as prognostically significant in neuroblastoma patients. Optical genome mapping (OGM) is a novel cytogenetic technique used to detect structural variants, which has not previously been tested in neuroblastoma. We used OGM to identify copy number and structural variants (SVs) in neuroblastoma which may have been missed by standard cytogenetic techniques. Methods: Five neuroblastoma cell lines (SH-SY5Y, NBLW, GI-ME-N, NB1691 and SK-N-BE2(C)) and two neuroblastoma tumours were analysed using OGM with the Bionano Saphyr® instrument. The results were analysed using Bionano Access software and compared to previous genetic analyses including G-band karyotyping, FISH (fluorescent in situ hybridisation), single-nucleotide polymorphism (SNP) array and RNA fusion panels for cell lines, and SNP arrays and whole genome sequencing (WGS) for tumours. Results: OGM detected copy number abnormalities found using previous methods and provided estimates for absolute copy numbers of amplified genes. OGM identified novel SVs, including fusion genes in two cell lines of potential clinical significance. Conclusions: OGM can reliably detect clinically significant structural and copy number variations in a single test. OGM may prove to be more time- and cost-effective than current standard cytogenetic techniques for neuroblastoma.

Publication metadata

Author(s): Barford RG, Whittle E, Weir L, Fong FC, Goodman A, Hartley HE, Allinson LM, Tweddle DA

Publication type: Article

Publication status: Published

Journal: Cancers

Year: 2023

Volume: 15

Issue: 21

Print publication date: 01/11/2023

Online publication date: 31/10/2023

Acceptance date: 23/10/2023

Date deposited: 28/11/2023

ISSN (electronic): 2072-6694

Publisher: Multidisciplinary Digital Publishing Institute (MDPI)

URL: https://doi.org/10.3390/cancers15215233

DOI: 10.3390/cancers15215233

Data Access Statement: The data shown in this study are available in this manuscript and the supplementary material.

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