ArticleFrontiers in immunology2015
Novel primary immunodeficiency candidate genes predicted by the human gene connectome.
Article in Frontiers in immunology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 54 citations in OpenAlex.
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- Contribution of next generation sequencing to the diagnosis of inborn errors of immunity in a pediatric cohort.Frontiers in immunology · 2025Article
- Genetic Evaluation of the Patients with Clinically Diagnosed Inborn Errors of Immunity by Whole Exome Sequencing: Results from a Specialized Research Center for Immunodeficiency in Türkiye.Journal of clinical immunology · 2024Article
- Current understanding of ELF4 deficiency: a novel inborn error of immunity.World journal of pediatrics : WJP · 2024Review
- Who's your data? Primary immune deficiency differential diagnosis prediction via machine learning and data mining of the USIDNET registry.Clinical immunology (Orlando, Fla.) · 2023Article
- Inborn errors of immunity caused by defects in the DNA damage response pathways: Importance of minimizing treatment-related genotoxicity.Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2022Review
- Novel brown adipose tissue candidate genes predicted by the human gene connectome.Scientific reports · 2022Article
- Leveraging Systems Immunology to Optimize Diagnosis and Treatment of Inborn Errors of Immunity.Frontiers in systems biology · 2022Article
- Added Value of Reanalysis of Whole Exome- and Whole Genome Sequencing Data From Patients Suspected of Primary Immune Deficiency Using an Extended Gene Panel and Structural Variation Calling.Frontiers in immunology · 2022Review
- Review
- Beyond monogenetic rare variants: tackling the low rate of genetic diagnoses in predominantly antibody deficiency.Cellular & molecular immunology · 2021Review
- Identifying disease-causing mutations in genomes of single patients by computational approaches.Human genetics · 2020Review
- Screening for primary immunodeficiency diseases by next-generation sequencing in early life.Clinical & translational immunology · 2020Article
- A rare case of acquired immunodeficiency associated with myelodysplastic syndrome.Molecular genetics & genomic medicine · 2019Article
- Review
- The histone methyltransferase Setd2 is indispensable for V(D)J recombination.Nature communications · 2019Article
- Primary immunodeficiency diseases in a tuberculosis endemic region: challenges and opportunities.Genes and immunity · 2019Review
- Targeted NGS Platforms for Genetic Screening and Gene Discovery in Primary Immunodeficiencies.Frontiers in immunology · 2019Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
Germline genetic mutations underlie various primary immunodeficiency (PID) diseases. Patients with rare PID diseases (like most non-PID patients and healthy individuals) carry, on average, 20,000 rare and common coding variants detected by high-throughput sequencing. It is thus a major challenge to select only a few candidate disease-causing variants for experimental testing. One of the tools commonly used in the pipeline for estimating a potential PID-candidate gene is to test whether the specific gene is included in the list of genes that were already experimentally validated as PID-causing in previous studies. However, this approach is limited because it cannot detect the PID-causing mutation(s) in the many PID patients carrying causal mutations of as yet unidentified PID-causing genes. In this study, we expanded in silico the list of potential PID-causing candidate genes from 229 to 3,110. We first identified the top 1% of human genes predicted by the human genes connectome to be biologically close to the 229 known PID genes. We then further narrowed down the list of genes by retaining only the most biologically relevant genes, with functionally enriched gene ontology biological categories similar to those for the known PID genes. We validated this prediction by showing that 17 of the 21 novel PID genes published since the last IUIS classification fall into this group of 3,110 genes (p < 10(-7)). The resulting new extended list of 3,110 predicted PID genes should be useful for the discovery of novel PID genes in patients.
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