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Analysis of institutional authors

Munté EAuthorRoca CAuthorDel Valle JAuthorPineda MAuthorMoreno VAuthor

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December 15, 2024
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Detection of germline CNVs from gene panel data: benchmarking the state of the art.

Publicated to:Briefings In Bioinformatics. 26 (1): bbae645- - 2024-11-22 26(1), DOI: 10.1093/bib/bbae645

Authors: Munté E; Roca C; Del Valle J; Feliubadaló L; Pineda M; Gel B; Castellanos E; Rivera B; Cordero D; Moreno V; Lázaro C; Moreno-Cabrera JM

Affiliations

Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Camí de les Escoles s/n, Badalona, Barcelona, Spain. - Author
Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Monforte de Lemos 5, 28029 Madrid, Spain. - Author
Hereditary Cancer Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Spain. - Author
Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL-ONCOBELL, Avinguda de la Granvia de l'Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Spain. - Author
Unit of Bioinformatics for Precision Oncology (UBOP), Catalan Institute of Oncology, Avinguda de la Granvia de l'Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain. - Author
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Abstract

Germline copy number variants (CNVs) play a significant role in hereditary diseases. However, the accurate detection of CNVs from targeted next-generation sequencing (NGS) gene panel data remains a challenging task. Several tools for calling CNVs within this context have been published to date, but the available benchmarks suffer from limitations, including testing on simulated data, testing on small datasets, and testing a small subset of published tools. In this work, we conducted a comprehensive benchmarking of 12 tools (Atlas-CNV, ClearCNV, ClinCNV, CNVkit, Cobalt, CODEX2, CoNVaDING, DECoN, ExomeDepth, GATK-gCNV, panelcn.MOPS, VisCap) on four validated gene panel datasets using their default parameters. We also assessed the impact of modifying 107 tool parameters and identified 13 parameter values that we suggest using to improve the tool F1 score. A total of 66 tool pair combinations were also evaluated to produce better meta-callers. Furthermore, we developed CNVbenchmarker2, a framework to help users perform their own evaluations. Our results indicated that in terms of F1 score, ClinCNV and GATK-gCNV were the best CNV callers. Regarding sensitivity, GATK-gCNV also exhibited particularly high performance. The results presented here provide an evaluation of the current state of the art in germline CNV detection from gene panel data and can be used as a reference resource when using any of the tools.

Keywords

BenchmarkingCnvsComputational biologyDatabases, geneticDna copy number variationsGene panelsGerm cellsGerm-line mutationGermlineHigh-throughput nucleotide sequencingHumansSoftware

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Briefings In Bioinformatics due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2024 there are still no calculated indicators, but in 2023, it was in position 4/66, thus managing to position itself as a Q1 (Primer Cuartil), in the category Mathematical & Computational Biology. Notably, the journal is positioned above the 90th percentile.

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-19:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 16.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 13 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 2.5.
  • The number of mentions on the social network X (formerly Twitter): 1 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (MUNTÉ ROCA, ELISABET) and Last Author (Moreno-Cabrera JM).