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Douillard V, Dos Santos Brito Silva N, Bourguiba-Hachemi S, Naslavsky MS, Scliar MO, Duarte YAO, Zatz M, Passos-Bueno MR, Limou S, Gourraud PA, Launay É, Castelli EC, Vince N. Optimal population-specific HLA imputation with dimension reduction. HLA 2024; 103:e15282. [PMID: 37950640 DOI: 10.1111/tan.15282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/29/2023] [Accepted: 10/14/2023] [Indexed: 11/13/2023]
Abstract
Human genomics has quickly evolved, powering genome-wide association studies (GWASs). SNP-based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP-genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data as a reference panel for imputing HLA from admixed individuals of African and European ancestries, focusing on (a) the full dataset, (b) 10 replications from 6 populations, and (c) 19 conditions for the custom reference panels. The full dataset outperformed smaller models, with a good F1-score of 0.66 for HLA-B. However, custom models outperformed the multiethnic or population models of similar size (F1-scores up to 0.53, against up to 0.42). We demonstrated the importance of using genetically specific models for imputing populations, which are currently underrepresented in public datasets, opening the door to HLA imputation for every genetic population.
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Affiliation(s)
- Venceslas Douillard
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Nayane Dos Santos Brito Silva
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Sonia Bourguiba-Hachemi
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Yeda A O Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, Brazil
- Epidemiology Department, Public Health School, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Sophie Limou
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Pierre-Antoine Gourraud
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Élise Launay
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- Department of Pediatrics and Pediatric Emergency, Hôpital Femme Enfant Adolescent, CHU de Nantes, Nantes, France
| | - Erick C Castelli
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Nicolas Vince
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
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Le Guen C, Leroy E, Pennetier M, Launay É, Bichali S, Prot-Labarthe S. [Illustrated case study of a patient with pediatric multisystem inflammatory syndrome]. Soins Pediatr Pueric 2023; 44:42-47. [PMID: 37980161 DOI: 10.1016/j.spp.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
Between November 2020 and June 2021, twelve children were treated at a university hospital in western France for pediatric multisystem inflammatory syndrome (PIMS). While the clinical presentation may have been reminiscent of Kawasaki disease, PIMS, a new nosological entity, was mentioned in the media in the context of the Covid-19 pandemic. In 2023, research into this syndrome will continue in France and Europe.
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Affiliation(s)
- Camille Le Guen
- Pharmacie clinique, centre hospitalier universitaire de Nantes, 1 place Alexis-Ricordeau, 44093 Nantes, France.
| | - Estelle Leroy
- Pharmacie clinique, centre hospitalier universitaire de Nantes, 1 place Alexis-Ricordeau, 44093 Nantes, France
| | - Martine Pennetier
- Pharmacie clinique, centre hospitalier universitaire de Nantes, 1 place Alexis-Ricordeau, 44093 Nantes, France
| | - Élise Launay
- Pédiatrie générale, centre hospitalier universitaire de Nantes, 1 place Alexis-Ricordeau, 44093 Nantes, France; Faculté de médecine, université de Nantes, 1 rue Gaston-Veil, 44000 Nantes, France
| | - Saïd Bichali
- Maladies chroniques de l'enfant et unité de soins continus, centre hospitalier universitaire de Nantes, 1 place Alexis-Ricordeau, 44093 Nantes, France
| | - Sonia Prot-Labarthe
- Pharmacie clinique, centre hospitalier universitaire de Nantes, 1 place Alexis-Ricordeau, 44093 Nantes, France; Faculté de pharmacie, université de Nantes, 9 rue Bias, 44000 Nantes, France; Inserm U1123, Eceve, site Villemin, 10 avenue de Verdun, 75010 Paris, France
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Launay É, Picherot G. [What is new in pediatry]. Rev Prat 2017; 67:63-69. [PMID: 30512439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Élise Launay
- Service de pédiatrie, CHU de Nantes, Nantes, France
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Gras-Le Guen C, Launay É. [Acute fever in children]. Rev Prat 2015; 65:649-652. [PMID: 26165100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Fever in children is a very common symptom associated most of the time with a viral infection. However, in 7% of children, fever without source is the first symptom of a serious bacterial infection such as pneumonia, meningitis, pyelonephritis or bacteremia. The key point in clinical examination of these children is the early identification of toxic signs. Because SBI prevalence is higher in very young children (1-3 month-aged), they required a specific management with some systematic complementary investigations and a broad indication of probabilistic antibiotherapy treatment.
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