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CORRECTION article

Front. Genet., 25 February 2022
Sec. Human and Medical Genomics
Volume 13 - 2022 | https://doi.org/10.3389/fgene.2022.868306
This article is part of the Research Topic Chromosome Structural Variants: Epidemiology, Identification and Contribution to Human Diseases View all 12 articles

Corrigendum: SVInterpreter: A Comprehensive Topologically Associated Domain Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants

This article is a correction to:

  1. SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants

    1. Read original article
Joana Fino Joana Fino1*Brbara MarquesBárbara Marques1Zirui Dong,,Zirui Dong2,3,4Dezso David Dezso David1*
  • 1Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal
  • 2Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
  • 3Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
  • 4Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China

A Corrigendum on
SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants

by Fino, J., Marques, B., Dong, Z., and David, D. (2021). Front. Genet. 12:757170. doi: 10.3389/fgene.2021.757170

In the original article, there was an error. The comparison with AnnotSV was made with its first version, which is currently out of date. Any remark made on this tool should not be considered.

The versions, commits and release dates of the tools used for comparison were not indicated.

Therefore, a correction has been made to Discussion, paragraph 11:

“Comparatively with other recent tools that support the evaluation of SVs, such as position_effect (commit: fced2c49, 13 June 2017), AnnotSV (Version 1.0, 21 December 2017) and ClinTAD (commit: 09b4925fb, 18 September 2019), SVInterpreter seems to be more comprehensive (Zepeda-Mendoza et al., 2017; Geoffroy et al., 2018; Spector and Wiita, 2019). First, SVInterpreter showed to be the one that allows more customization and adjustments, since, for example, AnnotSV and ClinTAD only work with one genome version, and ClinTAD only uses TAD boundaries of human embryonic stem cell data. Then, SVInterpreter shows a broader view of the affected regions, accounting for both gene disruption and position effects: AnnotSV is focused on the identification of genes directly affected by a breakpoint, and position_effect was designed to identify candidate genes essentially from position effect events. In regard to phenotypic comparison, as AnnotSV does not perform any, and ClinTAD is limited to the full HPO term overlap, position_effect is the only one with a similar functionality. Also, SVInterpreter is the one that retrieves the most information, including the position effect important data, GeneHancer cluster of interactions and chromatin loops, phenotypic data from DDG2P and clinGen, Gene-phenotype/disease associations in animal models, and GWAS data. Therefore, the existence of overlooked information by position_effect and AnnotSV, as shown in DGAP107, may contribute to limited results, biased candidate gene prioritization, and the need of additional resources.”

The authors apologize for the errors and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.

Publisher’s Note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

Keywords: SVInterpreter, bioinformatic web-tool, clinical outcome prediction, balanced structural variants, copy number variants, topologically associated domains, phenotypic comparison

Citation: Fino J, Marques B, Dong Z and David D (2022) Corrigendum: SVInterpreter: A Comprehensive Topologically Associated Domain Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants. Front. Genet. 13:868306. doi: 10.3389/fgene.2022.868306

Received: 02 February 2022; Accepted: 07 February 2022;
Published: 25 February 2022.

Approved by:

Frontiers Editorial Office, Frontiers Media SA, Switzerland

Copyright © 2022 Fino, Marques, Dong and David. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Joana Fino, joana.fino@insa.min-saude.pt; Dezso David, dezso.david@insa.min-saude.pt

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.