IEIVariantFilter: a bioinformatics tool to speed up genetic diagnosis of inborn errors of immunity patients

Severe infectious diseases remain the leading cause of death in children and young adults worldwide. Monogenic inborn errors of immunity (IEIs) are traditionally defined as a heterogeneous group of rare inborn genetic diseases affecting the functioning of the immune system. Greater awareness has led to the clinical definition of 485 monogenic IEIs and whole exome sequencing (WES) is becoming increasingly relevant for IEI genetic diagnosis. The current protocol for IEI genetic studies includes manual filtering of the list of genes obtained as a WES read-out providing a short list of candidate genes. This procedure is time-consuming and can produce mistakes due to human error in manual filtering. IEIVariantFilter is a new web-based bioinformatics tool to speed up and refine the genetic diagnosis of IEI patients oriented for users in the biomedical field without needing bioinformatics expertise. IEIVariantFilter prioritizes genetic variants based on ranges of zygosity, the quality of reads, the predicted variant effect, and genes related to immunity, considering a consanguineous hypothesis whenever necessary. IEIVariantFilter facilitates gene and variant list prioritization, speeding up the identification of candidate disease-causing variants for validation by experimental studies. The software improves the genetic diagnosis of patients, thereby facilitating precision medicine and fast and proper treatment.

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Publication Details

Journal
NAR Genomics and Bioinformatics
Published
2025-03-29
DOI
https://doi.org/10.1093/nargab/lqaf069
Citations
1
Primary Topic
Immunodeficiency and Autoimmune Disorders
Type
article
Field-Weighted Citation Impact
0.80

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IEIVariantFilter: a bioinformatics tool to speed up genetic diagnosis of inborn errors of immunity patients

Fernando Corvillo, Rebeca Pérez de Diego, Lluís Quintana‐Murci, Silvia Sánchez‐Ramón et al.
1 citations
NAR Genomics and Bioinformatics
Immunodeficiency and Autoimmune Disorders
0.80
article

IEIVariantFilter: a bioinformatics tool to speed up genetic diagnosis of inborn errors of immunity patients

Fernando Corvillo, Rebeca Pérez de Diego, Lluís Quintana‐Murci, Silvia Sánchez‐Ramón, Rocío Mena, Yuval Itan, Ana Maria Van Den Rym, Carlos Rodríguez‐Gallego, Víctor Galán‐Gómez, Eduardo López‐Collazo, Antonio Pérez‐Martínez, Meltem Ece Kars, José M. Lorenzo-Salazar, Alberto López‐Lera, Carlos Flores, Rubén Martínez‐Barricarte, Blanca García‐Solis, José M. de Pereda, Rafael Villena Espinosa, Teresa Guerra-Galán, Ana de Andrés-Martín
article en
1 citations

Abstract

Severe infectious diseases remain the leading cause of death in children and young adults worldwide. Monogenic inborn errors of immunity (IEIs) are traditionally defined as a heterogeneous group of rare inborn genetic diseases affecting the functioning of the immune system. Greater awareness has led to the clinical definition of 485 monogenic IEIs and whole exome sequencing (WES) is becoming increasingly relevant for IEI genetic diagnosis. The current protocol for IEI genetic studies includes manual filtering of the list of genes obtained as a WES read-out providing a short list of candidate genes. This procedure is time-consuming and can produce mistakes due to human error in manual filtering. IEIVariantFilter is a new web-based bioinformatics tool to speed up and refine the genetic diagnosis of IEI patients oriented for users in the biomedical field without needing bioinformatics expertise. IEIVariantFilter prioritizes genetic variants based on ranges of zygosity, the quality of reads, the predicted variant effect, and genes related to immunity, considering a consanguineous hypothesis whenever necessary. IEIVariantFilter facilitates gene and variant list prioritization, speeding up the identification of candidate disease-causing variants for validation by experimental studies. The software improves the genetic diagnosis of patients, thereby facilitating precision medicine and fast and proper treatment.

NAR Genomics and BioinformaticsVol. 7(2)
Universidad de Las Palmas de Gran Canaria (ES), Centre National de la Recherche Scientifique (FR), Institut Pasteur (FR), Instituto Cajal (ES), Hospital Universitario de Canarias (ES), Hospital Universitario La Paz (ES), Instituto de Salud Carlos III (ES), Hospital Clínico San Carlos (ES), Universidad Fernando Pessoa Canarias (ES), Hospital Universitario de Gran Canaria Doctor Negrín (ES), Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (ES), Instituto Tecnológico y de Energías Renovables (ES), Hospital La Paz Institute for Health Research (ES), Centre for Biomedical Network Research on Rare Diseases (ES), Universidad Autónoma de Madrid (ES), Vanderbilt University Medical Center (US), Icahn School of Medicine at Mount Sinai (US)
European Commission, European Society for Immunodeficiencies, National Institutes of Health, Instituto de Salud Carlos III, National Institute of Allergy and Infectious Diseases
Good health and well-being
Openalex Percentile: Top 28%
Immunodeficiency and Autoimmune Disorders
0.80
DOIOpen Access PDFOpenAlex
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