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Optical Genome Mapping Enables Detection and Accurate Sizing of RFC1 Repeat Expansions

Facchini, Stefano; Dominik, Natalia; Manini, Arianna; Efthymiou, Stephanie; Currò, Riccardo; Rugginini, Bianca; Vegezzi, Elisa; ... Cortese, Andrea; + view all (2023) Optical Genome Mapping Enables Detection and Accurate Sizing of RFC1 Repeat Expansions. Biomolecules , 13 (10) , Article 1546. 10.3390/biom13101546. Green open access

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Abstract

A recessive Short Tandem Repeat expansion in RFC1 has been found to be associated with cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), and to be a frequent cause of late onset ataxia and sensory neuropathy. The usual procedure for sizing these expansions is based on Southern Blotting (SB), a time-consuming and a relatively imprecise technique. In this paper, we compare SB with Optical Genome Mapping (OGM), a method for detecting Structural Variants (SVs) based on the measurement of distances between fluorescently labelled probes, for the diagnosis of RFC1 CANVAS and disease spectrum. The two methods are applied to 17 CANVAS patients' blood samples and resulting sizes compared, showing a good agreement. Further, long-read sequencing is used for two patients to investigate the agreement of sizes with either SB or OGM. Our study concludes that OGM represents a viable alternative to SB, allowing for a simpler technique, a more precise sizing of the expansion and ability to expand analysis of SV in the entire genome as opposed to SB which is a locus specific method.

Type: Article
Title: Optical Genome Mapping Enables Detection and Accurate Sizing of RFC1 Repeat Expansions
Location: Switzerland
Open access status: An open access version is available from UCL Discovery
DOI: 10.3390/biom13101546
Publisher version: https://doi.org/10.3390/biom13101546
Language: English
Additional information: © 2023 by the Authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Keywords: CANVAS, RFC1, Southern Blotting, bionano, optical genome mapping, repeat expansion
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
URI: https://discovery.ucl.ac.uk/id/eprint/10180194
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