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Urbaneja E, Bonet N, Solis-Moruno M, Mensa-Vilaro A, de Landazuri IO, Tormo M, Lara R, Plaza S, Fabregat V, Yagüe J, Casals F, Arostegui JI. Case report: Novel compound heterozygous IL1RN mutations as the likely cause of a lethal form of deficiency of interleukin-1 receptor antagonist. Front Immunol 2024; 15:1381447. [PMID: 38646532 PMCID: PMC11026629 DOI: 10.3389/fimmu.2024.1381447] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 03/04/2024] [Indexed: 04/23/2024] Open
Abstract
Undiagnosed monogenic diseases represent a challenging group of human conditions highly suspicious to have a genetic origin, but without conclusive evidences about it. We identified two brothers born prematurely from a non-consanguineous healthy couple, with a neonatal-onset, chronic disease characterized by severe skin and bone inflammatory manifestations and a fatal outcome in infancy. We conducted DNA and mRNA analyses in the patients' healthy relatives to identify the genetic cause of the patients' disease. DNA analyses were performed by both Sanger and next-generation sequencing, which identified two novel heterozygous IL1RN variants: the intronic c.318 + 2T>G variant in the father and a ≈2,600-bp intragenic deletion in the mother. IL1RN mRNA production was markedly decreased in both progenitors when compared with healthy subjects. The mRNA sequencing performed in each parent identified two novel, truncated IL1RN transcripts. Additional experiments revealed a perfect intrafamilial phenotype-genotype segregation following an autosomal recessive inheritance pattern. The evidences shown here supported for the presence of two novel loss-of-function (LoF) IL1RN pathogenic variants in the analyzed family. Biallelic LoF variants at the IL1RN gene cause the deficiency of interleukin-1 receptor antagonist (DIRA), a monogenic autoinflammatory disease with marked similarities with the patients described here. Despite the non-availability of the patients' samples representing the main limitation of this study, the collected evidences strongly suggest that the patients described here suffered from a lethal form of DIRA likely due to a compound heterozygous genotype at IL1RN, thus providing a reliable genetic diagnosis based on the integration of old medical information with currently obtained genetic data.
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Affiliation(s)
- Elena Urbaneja
- Department of Immunology and Pediatric Rheumatology, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Nuria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Manuel Solis-Moruno
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Anna Mensa-Vilaro
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Iñaki Ortiz de Landazuri
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Marc Tormo
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Scientific Computing Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Rocio Lara
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | - Susana Plaza
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | | | - Jordi Yagüe
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Juan I. Arostegui
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
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Vega M, Barrios R, Fraile R, de Castro Cogle K, Castillo D, Anglada R, Casals F, Ayté J, Lowy-Gallego E, Hidalgo E. Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery. Nucleic Acids Res 2023; 51:12161-12173. [PMID: 37956308 PMCID: PMC10711424 DOI: 10.1093/nar/gkad1066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Chromatin remodeling is essential to allow full development of alternative gene expression programs in response to environmental changes. In fission yeast, oxidative stress triggers massive transcriptional changes including the activation of hundreds of genes, with the participation of histone modifying complexes and chromatin remodelers. DNA transcription is associated to alterations in DNA topology, and DNA topoisomerases facilitate elongation along gene bodies. Here, we test whether the DNA topoisomerase Top1 participates in the RNA polymerase II-dependent activation of the cellular response to oxidative stress. Cells lacking Top1 are resistant to H2O2 stress. The transcriptome of Δtop1 strain was not greatly affected in the absence of stress, but activation of the anti-stress gene expression program was more sustained than in wild-type cells. Top1 associated to stress open reading frames. While the nucleosomes of stress genes are partially and transiently evicted during stress, the chromatin configuration remains open for longer times in cells lacking Top1, facilitating RNA polymerase II progression. We propose that, by removing DNA tension arising from transcription, Top1 facilitates nucleosome reassembly and works in synergy with the chromatin remodeler Hrp1 as opposing forces to transcription and to Snf22 / Hrp3 opening remodelers.
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Affiliation(s)
- Montserrat Vega
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rubén Barrios
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rodrigo Fraile
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | | | - Roger Anglada
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Ferran Casals
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Ernesto Lowy-Gallego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona 08003, Spain
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Mascaro JM, Rodriguez-Pinto I, Poza G, Mensa-Vilaro A, Fernandez-Martin J, Caminal-Montero L, Espinosa G, Hernández-Rodríguez J, Diaz M, Rita-Marques J, Sanmarti R, Castañeda S, Colunga D, Coto-Hernández R, Fanlo P, Elejalde JI, Bujan S, Figueras I, Marco FM, Andrés M, Suárez S, Gonzalez-Garcia A, Fustà-Novell X, Garcia-Belando C, Granados A, Fernandez-Figueras MT, Quilis N, Orriols-Caba M, Gómez de la Torre R, Cid MC, Espígol-Frigolé G, Alvarez-Abella A, Labrador E, Rozman M, Lopez-Guerra M, Castillo P, Alamo-Moreno JR, Gonzalez-Roca E, Plaza S, Fabregat V, Lara R, Vicente-Rabaneda EF, Tejedor-Vaquero S, Magri G, Bonet N, Solis-Moruno M, Cerutti A, Fornas O, Casals F, Yagüe J, Aróstegui JI. Spanish cohort of VEXAS syndrome: clinical manifestations, outcome of treatments and novel evidences about UBA1 mosaicism. Ann Rheum Dis 2023; 82:1594-1605. [PMID: 37666646 PMCID: PMC10646843 DOI: 10.1136/ard-2023-224460] [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: 06/07/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND The vacuoles, E1-enzyme, X linked, autoinflammatory and somatic (VEXAS) syndrome is an adult-onset autoinflammatory disease (AID) due to postzygotic UBA1 variants. OBJECTIVES To investigate the presence of VEXAS syndrome among patients with adult-onset undiagnosed AID. Additional studies evaluated the mosaicism distribution and the circulating cytokines. METHODS Gene analyses were performed by both Sanger and amplicon-based deep sequencing. Patients' data were collected from their medical charts. Cytokines were quantified by Luminex. RESULTS Genetic analyses of enrolled patients (n=42) identified 30 patients carrying UBA1 pathogenic variants, with frequencies compatible for postzygotic variants. All patients were male individuals who presented with a late-onset disease (mean 67.5 years; median 67.0 years) characterised by cutaneous lesions (90%), fever (66.7%), pulmonary manifestations (66.7%) and arthritis (53.3%). Macrocytic anaemia and increased erythrocyte sedimentation rate and ferritin were the most relevant analytical abnormalities. Glucocorticoids ameliorated the inflammatory manifestations, but most patients became glucocorticoid-dependent. Positive responses were obtained when targeting the haematopoietic component of the disease with either decitabine or allogeneic haematopoietic stem cell transplantation. Additional analyses detected the UBA1 variants in both haematopoietic and non-haematopoietic tissues. Finally, analysis of circulating cytokines did not identify inflammatory mediators of the disease. CONCLUSION Thirty patients with adult-onset AID were definitively diagnosed with VEXAS syndrome through genetic analyses. Despite minor interindividual differences, their main characteristics were in concordance with previous reports. We detected for the first time the UBA1 mosaicism in non-haematopoietic tissue, which questions the previous concept of myeloid-restricted mosaicism and may have conceptual consequences for the disease mechanisms.
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Affiliation(s)
- Jose Manuel Mascaro
- Department of Dermatology, Hospital Clínic, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | | | - Gabriela Poza
- Department of Internal Medicine, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Anna Mensa-Vilaro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | | | - Luis Caminal-Montero
- Department of Internal Medicine, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Gerard Espinosa
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Department of Autoimmune Diseases, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Jose Hernández-Rodríguez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Department of Autoimmune Diseases, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Marina Diaz
- Department of Haematology, Hospital Clínic, Barcelona, Spain
| | - Joana Rita-Marques
- Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Raimon Sanmarti
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Department of Rheumatology, Hospital Clínic, Barcelona, Spain
| | - Santos Castañeda
- Department of Rheumatology, Hospital Universitario La Princesa, Madrid, Spain
- Instituto de Investigaciones Sanitarias Princesa (IIS-Princesa), Madrid, Spain
- Cátedra UAM-Roche, EPID-Future, Department of Medicine, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Dolores Colunga
- Department of Internal Medicine, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Rubén Coto-Hernández
- Department of Internal Medicine, Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Patricia Fanlo
- Department of Internal Medicine, Hospital Universitario de Navarra, Pamplona, Spain
| | | | - Segundo Bujan
- Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ignasi Figueras
- Department of Dermatology, Hospital de Bellvitge, Barcelona, Spain
| | - Francisco Manuel Marco
- Department of Immunology, Hospital General Universitario de Alicante Dr Balmis, Alicante, Spain
- Alicante Institute for Health and Biomedical Research, Alicante, Spain
| | - Mariano Andrés
- Alicante Institute for Health and Biomedical Research, Alicante, Spain
- Seccion de Reumatologia, Hospital General Universitario de Alicante, Alicante, Spain
- Department of Clinic Medicine, Universidad Miguel Hernandez de Elche, Elche, Spain
| | - Silvia Suárez
- Department of Internal Medicine, Hospital Valle del Nalón, Langreo, Spain
| | - Andres Gonzalez-Garcia
- Systemic Autoimmune Diseases Unit, Department of Internal Medicine, Hospital Universitario Ramón y Cajal | IRYCIS, Madrid, Spain
| | | | - Clara Garcia-Belando
- Department of Rheumatology, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Ana Granados
- Department of Internal Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | | | - Neus Quilis
- Department of Rheumatology, Hospital Universitari de Vinalopo, Elche, Spain
| | - Maria Orriols-Caba
- Department of Internal Medicine, Hospital comarcal Alt Penedès, Consorci Sanitari Alt Penedès-Garraf, Vilafranca del Penedès, Spain
| | | | - Maria Cinta Cid
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Department of Autoimmune Diseases, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Georgina Espígol-Frigolé
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Department of Autoimmune Diseases, Hospital Clinic de Barcelona, Barcelona, Spain
| | | | | | - Maria Rozman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Department of Haematology, Hospital Clínic, Barcelona, Spain
| | - Monica Lopez-Guerra
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Pathology, Hospital Clínic, Barcelona, Spain
| | - Paola Castillo
- Department of Pathology, Hospital Clínic, Barcelona, Spain
| | | | - Eva Gonzalez-Roca
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | - Susana Plaza
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | | | - Rocio Lara
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | - Esther F Vicente-Rabaneda
- Department of Rheumatology, Hospital Universitario La Princesa, Madrid, Spain
- Instituto de Investigaciones Sanitarias Princesa (IIS-Princesa), Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Giuliana Magri
- Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
- Immunology Unit, Department of Biomedical Sciences, Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain
| | - Nuria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Solis-Moruno
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Andrea Cerutti
- Hospital del Mar Medical Research Institute, PRBB, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Oscar Fornas
- Flow Cytometry Unit, Universitat Pompeu Fabra - Center of Genomic Regulation, Barcelona, Spain
| | - Ferran Casals
- Departament de Genètica, Microbiologia i Estadística, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Jordi Yagüe
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | - Juan I Aróstegui
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Department of Immunology, Hospital Clínic, Barcelona, Spain
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Aizpurua-Iraola J, Rasal R, Prieto L, Comas D, Bonet N, Casals F, Calafell F, Vásquez P. Population analysis of complete mitogenomes for 334 samples from El Salvador. Forensic Sci Int Genet 2023; 66:102906. [PMID: 37364481 DOI: 10.1016/j.fsigen.2023.102906] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
The use of mitochondrial DNA (mtDNA) in the field of forensic genetics is widely spread mainly due to its advantages when identifying highly degraded samples. In this sense, massive parallel sequencing has made the analysis of the whole mitogenome more accessible, noticeably increasing the informativeness of mtDNA haplotypes. The civil war (1980-1992) in El Salvador caused many deaths and disappearances (including children) all across the country and the economic and social instability after the war forced many people to emigration. For this reason, different organizations have collected DNA samples from relatives with the aim of identifying missing people. Thus, we present a dataset containing 334 complete mitogenomes from the Salvadoran general population. To the best of our knowledge, this is the first publication of a nationwide forensic-quality complete mitogenome database of any Latin American country. We found 293 different haplotypes, with a random match probability of 0.0041 and 26.6 mean pairwise differences, which is similar to other Latin American populations, and which represent a marked improvement from the values obtained with just control region sequences. These haplotypes belong to 54 different haplogroups, being 91% of them of Native American origin. Over a third (35.9%) of the individuals carried at least a heteroplasmic site (excluding length heteroplasmies). Ultimately, the present database aims to represent mtDNA haplotype diversity in the general Salvadoran populations as a basis for the identification of people that disappeared during or after the civil war.
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Affiliation(s)
- Julen Aizpurua-Iraola
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Lourdes Prieto
- Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Comisaría General de Policía Científica. DNA Laboratory, Madrid, Spain
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Departament de Medicina i Ciències de la Vida, Barcelona, Spain
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, San Salvador, El Salvador
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Solís-Moruno M, Batlle-Masó L, Bonet N, Aróstegui JI, Casals F. Somatic genetic variation in healthy tissue and non-cancer diseases. Eur J Hum Genet 2023; 31:48-54. [PMID: 36289407 PMCID: PMC9823099 DOI: 10.1038/s41431-022-01213-8] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 09/19/2022] [Accepted: 10/03/2022] [Indexed: 02/08/2023] Open
Abstract
Somatic genetic variants have been studied for several years mostly concerning cancer, where they contribute to its origin and development. It is also clear that the somatic variants load is greater in aged individuals in comparison to younger ones, pointing to a cause/consequence of the senescence process. More recently, researchers have focused on the role of this type of variation in healthy tissue and its dynamics in cell lineages and different organs. In addition, somatic variants have been described to contribute to monogenic diseases, and the number of evidences of their role in complex disorders is also increasing. Thanks to recent advances in next-generation sequencing technologies, this type of genetic variation can be now more easily studied than in the past, although we still face some important limitations. Novel strategies for sampling, sequencing and filtering are being investigated to detect these variants, although validating them with an orthogonal approach will most likely still be needed. In this review, we aim to update our knowledge of somatic variation detection and its relation to healthy tissue and non-cancer diseases.
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Affiliation(s)
- Manuel Solís-Moruno
- grid.5612.00000 0001 2172 2676Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain ,grid.410458.c0000 0000 9635 9413Department of Immunology, Hospital Clínic, Barcelona, Spain ,grid.10403.360000000091771775Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Batlle-Masó
- grid.7080.f0000 0001 2296 0625Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Núria Bonet
- grid.5612.00000 0001 2172 2676Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain
| | - Juan I. Aróstegui
- grid.410458.c0000 0000 9635 9413Department of Immunology, Hospital Clínic, Barcelona, Spain ,grid.10403.360000000091771775Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ,grid.5841.80000 0004 1937 0247Universitat de Barcelona, Barcelona, Spain
| | - Ferran Casals
- grid.5612.00000 0001 2172 2676Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain ,grid.5841.80000 0004 1937 0247Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain ,grid.5841.80000 0004 1937 0247Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
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González-González E, Galván-Román JM, García-Sanz Í, Casals F, Fernández-Bueno J, Real de Asúa D. Healthcare workers' perception of the usefulness of a healthcare ethics consultation service. Rev Clin Esp 2023; 223:10-16. [PMID: 36528057 DOI: 10.1016/j.rceng.2022.10.004] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/05/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Clinical ethics consultation services (CEC) have arisen from Healthcare Ethics Committees (HEC) to address ethical conflicts in real-time. Our aim was to determine the perception of usefulness of a CEC service among healthcare workers one year after its creation as well as to assess changes in trends in the use of the CEC and HEC between 2015 and 2021. MATERIALS AND METHODS This observational, cross-sectional study was based on a standardized survey of healthcare workers at an urban tertiary care hospital. The results were also compared to those from an identical survey conducted in the same population in 2015. RESULTS A total of 213 professionals participated (mean age 44 ± 11 years, 69% women). The professionals were more familiar with the HEC than the CEC service (94% vs 61%; p < 0.001). Forty-five individuals (21%) had consulted the CEC since its implementation; 95% of them found the consultation useful. Physicians knew about and used the CEC more than other groups of professionals. The degree of knowledge of the HEC increased significantly by 2021 compared to 2015 (94% v. 76%; p < 0.001). Some areas for improvement identified were the need for greater dissemination of the service, guaranteeing institutional resources to maintain the service, and encouraging greater participation from different professional groups. CONCLUSIONS Knowledge of the institutional HEC and CEC services has increased in recent years among healthcare workers, who considered the CEC service to be useful for addressing ethical conflicts in daily practice.
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Affiliation(s)
- E González-González
- Servicio de Medicina Interna, Hospital Universitario de La Princesa, Madrid, Spain
| | - J M Galván-Román
- Servicio de Medicina Interna, Hospital Universitario de La Princesa, Madrid, Spain; Servicio de Consultoría en Ética Clínica, Comité de Ética para la Asistencia Sanitaria, Hospital Universitario de La Princesa, Madrid, Spain; Grupo de Trabajo en Bioética y Profesionalismo, Sociedad Española de Medicina Interna, Madrid, Spain
| | - Í García-Sanz
- Servicio de Consultoría en Ética Clínica, Comité de Ética para la Asistencia Sanitaria, Hospital Universitario de La Princesa, Madrid, Spain; Servicio de Cirugía General y del Aparato Digestivo, Hospital Universitario de La Princesa, Madrid, Spain
| | - F Casals
- Servicio de Consultoría en Ética Clínica, Comité de Ética para la Asistencia Sanitaria, Hospital Universitario de La Princesa, Madrid, Spain; Servicio de Aparato Digestivo, Hospital Universitario de La Princesa, Madrid, Spain
| | - J Fernández-Bueno
- Servicio de Consultoría en Ética Clínica, Comité de Ética para la Asistencia Sanitaria, Hospital Universitario de La Princesa, Madrid, Spain; Unidad de Cuidados Paliativos Hospitalarios, Hospital Universitario de La Princesa, Madrid, Spain
| | - D Real de Asúa
- Servicio de Medicina Interna, Hospital Universitario de La Princesa, Madrid, Spain.
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Moreno-Ruiz N, Lao O, Aróstegui JI, Laayouni H, Casals F. Assessing the digenic model in rare disorders using population sequencing data. Eur J Hum Genet 2022; 30:1439-1443. [PMID: 36192439 PMCID: PMC9712436 DOI: 10.1038/s41431-022-01191-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/18/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022] Open
Abstract
An important fraction of patients with rare disorders remains with no clear genetic diagnostic, even after whole-exome or whole-genome sequencing, posing a difficulty in giving adequate treatment and genetic counseling. The analysis of genomic data in rare disorders mostly considers the presence of single gene variants in coding regions that follow a concrete monogenic mode of inheritance. A digenic inheritance, with variants in two functionally-related genes in the same individual, is a plausible alternative that might explain the genetic basis of the disease in some cases. In this case, digenic disease combinations should be absent or underrepresented in healthy individuals. We develop a framework to evaluate the significance of digenic combinations and test its statistical power in different scenarios. We suggest that this approach will be relevant with the advent of new sequencing efforts including hundreds of thousands of samples.
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Affiliation(s)
- Nerea Moreno-Ruiz
- Servei de Genòmica, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Institut de Biologia Evolutiva (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | | | - Oscar Lao
- Institut de Biologia Evolutiva (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Juan Ignacio Aróstegui
- Departament d'Immunologia, Hospital Clínic - Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Escola de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.
- Bioinformatics Studies, ESCI-UPF, Barcelona, Spain.
| | - Ferran Casals
- Servei de Genòmica, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain.
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8
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Calls A, Torres‐Espin A, Tormo M, Martínez‐Escardó L, Bonet N, Casals F, Navarro X, Yuste VJ, Udina E, Bruna J. A transient inflammatory response contributes to oxaliplatin neurotoxicity in mice. Ann Clin Transl Neurol 2022; 9:1985-1998. [PMID: 36369764 PMCID: PMC9735376 DOI: 10.1002/acn3.51691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/14/2022] [Accepted: 10/16/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Peripheral neuropathy is a relevant dose-limiting adverse event that can affect up to 90% of oncologic patients with colorectal cancer receiving oxaliplatin treatment. The severity of neurotoxicity often leads to dose reduction or even premature cessation of chemotherapy. Unfortunately, the limited knowledge about the molecular mechanisms related to oxaliplatin neurotoxicity leads to a lack of effective treatments to prevent the development of this clinical condition. In this context, the present work aimed to determine the exact molecular mechanisms involved in the development of oxaliplatin neurotoxicity in a murine model to try to find new therapeutical targets. METHODS By single-cell RNA sequencing (scRNA-seq), we studied the transcriptomic profile of sensory neurons and satellite glial cells (SGC) of the Dorsal Root Ganglia (DRG) from a well-characterized mouse model of oxaliplatin neurotoxicity. RESULTS Analysis of scRNA-seq data pointed to modulation of inflammatory processes in response to oxaliplatin treatment. In this line, we observed increased levels of NF-kB p65 protein, pro-inflammatory cytokines, and immune cell infiltration in DRGs and peripheral nerves of oxaliplatin-treated mice, which was accompanied by mechanical allodynia and decrease in sensory nerve amplitudes. INTERPRETATION Our data show that, in addition to the well-described DNA damage, oxaliplatin neurotoxicity is related to an exacerbated pro-inflammatory response in DRG and peripheral nerves, and open new insights in the development of anti-inflammatory strategies as a treatment for preventing peripheral neuropathy induced by oxaliplatin.
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Affiliation(s)
- Aina Calls
- Department of Cell Biology, Physiology, and Immunology, Institute of NeuroscienceUniversitat Autònoma de BarcelonaBellaterraSpain,Biomedical Research Center Network on Neurodegenerative Diseases (CIBERNED)BellaterraSpain
| | - Abel Torres‐Espin
- Department of Neurological Surgery, Brain and Spinal Injury CenterUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Marc Tormo
- Genomics Core Facility, Departament de Ciències Experimentals i de la SalutUniversitat Pompeu Fabra, Parc de Recerca Biomèdica de BarcelonaBarcelonaSpain,Scientific IT Core Facility, Departament de Ciències Experimentals i de la SalutUniversitat Pompeu Fabra, Parc de Recerca Biomèdica de BarcelonaBarcelonaSpain
| | - Laura Martínez‐Escardó
- Department of Biochemistry, Institute of NeuroscienceUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Núria Bonet
- Genomics Core Facility, Departament de Ciències Experimentals i de la SalutUniversitat Pompeu Fabra, Parc de Recerca Biomèdica de BarcelonaBarcelonaSpain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la SalutUniversitat Pompeu Fabra, Parc de Recerca Biomèdica de BarcelonaBarcelonaSpain,Departament de Genètica, Microbiologia i Estadística, Facultat de BiologiaUniversitat de BarcelonaBarcelonaSpain
| | - Xavier Navarro
- Department of Cell Biology, Physiology, and Immunology, Institute of NeuroscienceUniversitat Autònoma de BarcelonaBellaterraSpain,Biomedical Research Center Network on Neurodegenerative Diseases (CIBERNED)BellaterraSpain
| | - Víctor J. Yuste
- Department of Biochemistry, Institute of NeuroscienceUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Esther Udina
- Department of Cell Biology, Physiology, and Immunology, Institute of NeuroscienceUniversitat Autònoma de BarcelonaBellaterraSpain,Biomedical Research Center Network on Neurodegenerative Diseases (CIBERNED)BellaterraSpain
| | - Jordi Bruna
- Department of Cell Biology, Physiology, and Immunology, Institute of NeuroscienceUniversitat Autònoma de BarcelonaBellaterraSpain,Biomedical Research Center Network on Neurodegenerative Diseases (CIBERNED)BellaterraSpain,Unit of Neuro‐Oncology, Hospital Universitari de BellvitgeBellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de LlobregatBarcelonaSpain
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9
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López-Urrutia E, Sancha A, Useros D, Galván-Román J, García-Sanz Í, Casals F, Fernández-Bueno J, Real de Asúa D. Descripción de la experiencia de un servicio de consultoría en ética clínica en el período 2019-2021. Revista Clínica Española 2022. [DOI: 10.1016/j.rce.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Reula AJTI, Cochino AV, Martins AL, Angosto-Bazarra D, de Landazuri IO, Mensa-Vilaro A, Cabral M, Baroja-Mazo A, Baños MC, Lobato-Salinas Z, Fabregat V, Plaza S, Yagüe J, Casals F, Oliva B, Figueiredo AE, Pelegrín P, Aróstegui JI. Correction to: Characterization of Novel Pathogenic Variants Leading to Caspase-8 Cleavage-Resistant RIPK1-Induced Autoinflammatory Syndrome. J Clin Immunol 2022; 42:1433. [PMID: 35802274 PMCID: PMC9674752 DOI: 10.1007/s10875-022-01322-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
| | - Alexis-Virgil Cochino
- University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania.,National Institute for Mother and Child Health, "Alessandrescu-Rusescu", Bucharest, Romania
| | - Andreia L Martins
- Department of Pediatrics, Hospital Prof. Doutor Fernando Fonseca, Amadora, Portugal
| | - Diego Angosto-Bazarra
- Instituto Murciano de Investigacion Biosanitaria IMIB-Arrixaca, Hospital Clinico Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain
| | - Iñaki Ortiz de Landazuri
- Department of Immunology, Hospital Clinic, Barcelona, Spain.,Institut d'Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Anna Mensa-Vilaro
- Department of Immunology, Hospital Clinic, Barcelona, Spain.,Institut d'Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Marta Cabral
- Unit of Pediatric Rheumatology, Hospital Prof. Doutor Fernando Fonseca, Amadora, Portugal
| | - Alberto Baroja-Mazo
- Instituto Murciano de Investigacion Biosanitaria IMIB-Arrixaca, Hospital Clinico Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain
| | - María C Baños
- Instituto Murciano de Investigacion Biosanitaria IMIB-Arrixaca, Hospital Clinico Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain
| | | | | | - Susana Plaza
- Department of Immunology, Hospital Clinic, Barcelona, Spain
| | - Jordi Yagüe
- Department of Immunology, Hospital Clinic, Barcelona, Spain.,Institut d'Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain.,School of Medicine, University of Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Department of Experimental and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomedica de Barcelona, Barcelona, Spain.,Departament of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Baldomero Oliva
- Structural Bioinformatics Lab GRIB-IMIM, Department of Experimental and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomedica de Barcelona, Barcelona, Spain
| | - Antonio E Figueiredo
- Unit of Pediatric Immunology, Hospital Prof. Doutor Fernando Fonseca, Amadora, Portugal
| | - Pablo Pelegrín
- Instituto Murciano de Investigacion Biosanitaria IMIB-Arrixaca, Hospital Clinico Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain.,Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - Juan I Aróstegui
- Department of Immunology, Hospital Clinic, Barcelona, Spain. .,Institut d'Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain. .,School of Medicine, University of Barcelona, Barcelona, Spain.
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11
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Lobon I, Solís-Moruno M, Juan D, Muhaisen A, Abascal F, Esteller-Cucala P, García-Pérez R, Martí MJ, Tolosa E, Ávila J, Rahbari R, Marques-Bonet T, Casals F, Soriano E. Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes. Front Aging 2022; 3:851039. [PMID: 35821807 PMCID: PMC9261316 DOI: 10.3389/fragi.2022.851039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
The role of somatic mutations in complex diseases, including neurodevelopmental and neurodegenerative disorders, is becoming increasingly clear. However, to date, no study has shown their relation to Parkinson disease’s phenotype. To explore the relevance of embryonic somatic mutations in sporadic Parkinson disease, we performed whole-exome sequencing in blood and four brain regions of ten patients. We identified 59 candidate somatic single nucleotide variants (sSNVs) through sensitive calling and a careful filtering strategy (COSMOS). We validated 27 of them with amplicon-based ultra-deep sequencing, with a 70% validation rate for the highest-confidence variants. The identified sSNVs are in genes with synaptic functions that are co-expressed with genes previously associated with Parkinson disease. Most of the sSNVs were only called in blood but were also found in the brain tissues with ultra-deep amplicon sequencing, demonstrating the strength of multi-tissue sampling designs.
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Affiliation(s)
- Irene Lobon
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
- *Correspondence: Irene Lobon, ; Eduardo Soriano,
| | - Manuel Solís-Moruno
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Ashraf Muhaisen
- Department of Cell Biology, Physiology and Immunology and Institute of Neurosciences, Universitat de Barcelona (UB), Barcelona, Spain
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Federico Abascal
- Cancer, Ageing, and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | | | - Maria Josep Martí
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Department of Neurology, Hospital Clínic de Barcelona, Institut d’Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain
| | - Eduardo Tolosa
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Department of Neurology, Hospital Clínic de Barcelona, Institut d’Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain
| | - Jesús Ávila
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, Madrid, Spain
| | - Raheleh Rahbari
- Cancer, Ageing, and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology and Institute of Neurosciences, Universitat de Barcelona (UB), Barcelona, Spain
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- *Correspondence: Irene Lobon, ; Eduardo Soriano,
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12
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Casals F, Rasal R, Anglada R, Tormo M, Bonet N, Rivas N, Vásquez P, Calafell F. A forensic population database in El Salvador: 58 STRs and 94 SNPs. Forensic Sci Int Genet 2021; 57:102646. [PMID: 34875492 DOI: 10.1016/j.fsigen.2021.102646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/31/2022]
Abstract
We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in a sample of 248 men and 143 women from El Salvador, Central America. Regional division (Centro, Oriente, Occidente) showed in almost all cases FST values not significantly different from 0, and further analyses were applied only to the undivided, country-wide population. The overall random match probability (RMP) decreased from 6.79 × 10-31 in length-based genotypes in the 27 autosomal STRs to 1.47 × 10-34 in repeat-sequence based genotypes. Combining the autosomal loci in this set, RMP reaches 2.97 × 10-70. In a population genetic analysis, El Salvador showed the lowest FST values with US Hispanics both for autosomal and X-STRs; however, it was much closer to Native Americans for the latter than for the former, in accordance with the well-known gender-biased admixture that created most Latin American populations.
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Affiliation(s)
- Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadísitca, Universitat de Barcelona, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Roger Anglada
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Marc Tormo
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Scientific IT Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Nury Rivas
- Instituto de Medicina Legal Dr. Roberto Masferrer, San Salvador, El Salvador
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, 27 calle Pnte. No.1329 Colonia Layco, San Salvador, El Salvador
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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13
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Ionescu D, Peñín-Franch A, Mensa-Vilaró A, Castillo P, Hurtado-Navarro L, Molina-López C, Romero-Chala S, Plaza S, Fabregat V, Buján S, Marques J, Casals F, Yagüe J, Oliva B, Fernández-Pereira LM, Pelegrín P, Aróstegui JI. First Description of Late-Onset Autoinflammatory Disease Due to Somatic NLRC4 Mosaicism. Arthritis Rheumatol 2021; 74:692-699. [PMID: 34672126 DOI: 10.1002/art.41999] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/01/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022]
Abstract
INTRODUCTION Autoinflammatory diseases (AIDs) are inherited disorders of innate immunity that usually start during childhood. However, several studies have recently reported an increasing number of patients with AID starting in adulthood. OBJECTIVE This study was undertaken to characterize the cause underlying a patient with late-onset uncharacterized AID. METHODS Genetic studies were performed using Sanger sequencing and next-generation sequencing (NGS) methods. In silico, in vitro and ex vivo analyses were performed to determine the functional consequences of the detected variant. RESULTS We studied a 57 years-old woman who started at the age of 47 years with recurrent episodes of fever, myalgias, arthralgias, diffuse abdominal pain, diarrhea, adenopathies and systemic inflammation, which were relatively well controlled with anti-IL-1 drugs. NGS analyses did not detect germline variants in any of the known AID-associated genes, but they identified the p.Ser171Phe NLRC4 variant in unfractionated blood, with an allele fraction (2-4%) compatible with gene mosaicism. Structural modeling analyses suggest that this missense variant might favor the open, active conformation of the NLRC4 protein, and in vitro and ex vivo analyses confirmed its trend to oligomerize and activate the NLRC4-inflammasome, with a subsequent IL-18 overproduction. CONCLUSION We have identified the post-zygotic p.Ser171Phe NLRC4 variant as a plausible cause of the disease in the enrolled patient. Functional and structural studies clearly support for the first time its gain-of-function behavior consistent with previously reported NLRC4 pathogenic variants. These novel evidences should be considered in the diagnostic workup of patients with uncharacterized AID starting during adulthood.
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Affiliation(s)
- Daniela Ionescu
- Department of Immunology and Molecular Genetics, Hospital San Pedro de Alcántara, Cáceres, Spain
| | - Alejandro Peñín-Franch
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, Hospital Clínico Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain
| | | | - Paola Castillo
- Department of Pathology, Hospital Clínic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Laura Hurtado-Navarro
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, Hospital Clínico Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain
| | - Cristina Molina-López
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, Hospital Clínico Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain
| | - Silvia Romero-Chala
- Department of Immunology and Molecular Genetics, Hospital San Pedro de Alcántara, Cáceres, Spain
| | - Susana Plaza
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | | | - Segundo Buján
- Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Joana Marques
- Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Department of Experimental and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Jordi Yagüe
- Department of Immunology, Hospital Clínic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Baldomero Oliva
- Structural Bioinformatics Lab GRIB-IMIM, Department of Experimental and Life Sciences, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | | | - Pablo Pelegrín
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, Hospital Clínico Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain.,Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - Juan I Aróstegui
- Department of Immunology, Hospital Clínic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,School of Medicine, Universitat de Barcelona, Barcelona, Spain
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14
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Solís-Moruno M, Mensa-Vilaró A, Batlle-Masó L, Lobón I, Bonet N, Marquès-Bonet T, Aróstegui JI, Casals F. Publisher Correction: Assessment of the gene mosaicism burden in blood and its implications for immune disorders. Sci Rep 2021; 11:17030. [PMID: 34404866 PMCID: PMC8371119 DOI: 10.1038/s41598-021-96172-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Manuel Solís-Moruno
- Institut de Biologia Evolutiva (CSIC UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, Spain.,Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Anna Mensa-Vilaró
- Department of Immunology, Hospital Clínic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Batlle-Masó
- Institut de Biologia Evolutiva (CSIC UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, Spain.,Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Irene Lobón
- Institut de Biologia Evolutiva (CSIC UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (CSIC UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.,CNAG CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifci ICTA ICP, C/Columnes S/N, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Juan I Aróstegui
- Department of Immunology, Hospital Clínic, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain. .,Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain.
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15
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Vullo CM, Catelli L, Ibarra Rodriguez AA, Papaioannou A, Merino JCÁ, Lopez-Parra AM, Gaviria A, Baeza-Richer C, Romanini C, González-Moya E, Casals F, Calafell F, Berardi G, Iannacone GC, Vicuña Giraldo GC, Zorba GK, Boschi I, Olarte JV, Ruiz Gomez JE, Acierno JP, Soto ML, Miranda MV, García King MD, Marrucci MA, Porto MJ, Piñero MH, Aler M, Stephenson Ojea MM, Navarrete SC, Toscanini U, Saragoni VG, Bozzo W, Posada Posada YC, Bajunovic Z, Solla LP, Parsons T. Second GHEP-ISFG exercise for DVI: "DNA-led" victims' identification in a simulated air crash. Forensic Sci Int Genet 2021; 53:102527. [PMID: 34034006 DOI: 10.1016/j.fsigen.2021.102527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/22/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
The Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) has organized a second collaborative exercise on a simulated case of Disaster Victim Identification (DVI), with the participation of eighteen laboratories. The exercise focused on the analysis of a simulated plane crash case of medium-size resulting in 66 victims with varying degrees of fragmentation of the bodies (with commingled remains). As an additional difficulty, this second exercise included 21 related victims belonging to 6 families among the 66 missings to be identified. A total number of 228 post-mortem samples were represented with aSTR and mtDNA profiles, with a proportion of partial aSTR profiles simulating charred remains. To perform the exercise, participants were provided with aSTR and mtDNA data of 51 reference pedigrees -some of which deficient-including 128 donors for identification purposes. The exercise consisted firstly in the comparison of the post-mortem genetic profiles in order to re-associate fragmented remains to the same individual and secondly in the identification of the re-associated remains by comparing aSTR and mtDNA profiles with reference pedigrees using pre-established thresholds to report a positive identification. Regarding the results of the post-mortem samples re-associations, only a small number of discrepancies among participants were detected, all of which were from just a few labs. However, in the identification process by kinship analysis with family references, there were more discrepancies in comparison to the correct results. The identification results of single victims yielded fewer problems than the identification of multiple related victims within the same family groups. Several reasons for the discrepant results were detected: a) the identity/non-identity hypotheses were sometimes wrongly expressed in the likelihood ratio calculations, b) some laboratories failed to use all family references to report the DNA match, c) In families with several related victims, some laboratories firstly identified some victims and then unnecessarily used their genetic information to identify the remaining victims within the family, d) some laboratories did not correctly use "prior odds" values for the Bayesian treatment of the episode for both post-mortem/post-mortem re-associations as well as the ante-mortem/post-mortem comparisons to evaluate the probability of identity. For some of the above reasons, certain laboratories failed to identify some victims. This simulated "DNA-led" identification exercise may help forensic genetic laboratories to gain experience and expertize for DVI or MPI in using genetic data and comparing their own results with the ones in this collaborative exercise.
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Affiliation(s)
- Carlos M Vullo
- Argentine Forensic Anthropology Team (EAAF), Córdoba, Argentina.
| | - Laura Catelli
- Argentine Forensic Anthropology Team (EAAF), Córdoba, Argentina.
| | | | | | - J Carlos Álvarez Merino
- Laboratorio de Identificación Genética, Facultad de Medicina, Universidad de Granada, Granada, Spain.
| | - A M Lopez-Parra
- Laboratory of Forensic and Population Genetics, Dept of Toxicology and Health Legislation, Madrid, Spain.
| | - Aníbal Gaviria
- Lab de Genética Molecular Cruz Vital - Cruz Roja Ecuatoriana, Quito, Ecuador.
| | - Carlos Baeza-Richer
- Laboratory of Forensic and Population Genetics, Dept of Toxicology and Health Legislation, Madrid, Spain.
| | - Carola Romanini
- Argentine Forensic Anthropology Team (EAAF), Córdoba, Argentina.
| | | | - Ferran Casals
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain.
| | | | | | - Gian Carlo Iannacone
- Laboratorio De Biología Molecular y Genética Del Instituto De Medicina Legal, Lima, Peru.
| | | | - Gulbanu K Zorba
- Committee on Missing Persons Cyprus (CMP) Anthropological Laboratory, Nicosia, Cyprus.
| | - Ilaria Boschi
- Istituto di Sanità Pubblica-Medicina Legale Policlinico Gemelli, Roma, Italy.
| | - Jane Valdivia Olarte
- Laboratorio De Biología Molecular y Genética Del Instituto De Medicina Legal, Lima, Peru.
| | | | | | - Manuel López Soto
- Instituto Nacional de Toxicología y Ciencias Forenses (INTCF), Madrid, Spain.
| | | | | | | | - Maria J Porto
- Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal.
| | | | - Mercedes Aler
- Instituto de Medicina Legal y Ciencias Forenses, Valencia, Spain.
| | | | | | | | - Victor G Saragoni
- Unidad de Genética Forense, Servicio Médico Legal, Santiago de Chile, Chile.
| | - Walter Bozzo
- Banco Nacional De Datos Genéticos, CABA, Argentina.
| | | | | | - Lourdes Prieto Solla
- Grupo de Medicina Xenómica, Instituto de Ciencias Forenses, USC, Santiago de Compostela, Spain; Comisaría General de Policía Científica. Madrid.
| | - Thomas Parsons
- International Commission for Missing Persons (ICMP), USA.
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16
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Costa D, Bonet N, Solé A, González de Aledo-Castillo JM, Sabidó E, Casals F, Rovira C, Nadal A, Marin JL, Cobo T, Castelo R. Genome-wide postnatal changes in immunity following fetal inflammatory response. FEBS J 2020; 288:2311-2331. [PMID: 33006196 PMCID: PMC8049052 DOI: 10.1111/febs.15578] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/22/2020] [Accepted: 09/28/2020] [Indexed: 11/29/2022]
Abstract
The fetal inflammatory response (FIR) increases the risk of perinatal brain injury, particularly in extremely low gestational age newborns (ELGANs, < 28 weeks of gestation). One of the mechanisms contributing to such a risk is a postnatal intermittent or sustained systemic inflammation (ISSI) following FIR. The link between prenatal and postnatal systemic inflammation is supported by the presence of well‐established inflammatory biomarkers in the umbilical cord and peripheral blood. However, the extent of molecular changes contributing to this association is unknown. Using RNA sequencing and mass spectrometry proteomics, we profiled the transcriptome and proteome of archived neonatal dried blood spot (DBS) specimens from 21 ELGANs. Comparing FIR‐affected and unaffected ELGANs, we identified 782 gene and 27 protein expression changes of 50% magnitude or more, and an experiment‐wide significance level below 5% false discovery rate. These expression changes confirm the robust postnatal activation of the innate immune system in FIR‐affected ELGANs and reveal for the first time an impairment of their adaptive immunity. In turn, the altered pathways provide clues about the molecular mechanisms triggering ISSI after FIR, and the onset of perinatal brain injury. Databases EGAS00001003635 (EGA); PXD011626 (PRIDE).
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Affiliation(s)
- Daniel Costa
- Department of Pediatrics, Hospital de Figueres, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Núria Bonet
- Genomics Core Facility, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Amanda Solé
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain.,Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Eduard Sabidó
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain.,Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Alfons Nadal
- Department of Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Spain
| | - Jose Luis Marin
- Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre for Biomedical Research on Rare Diseases (CIBER-ER), University of Barcelona, Spain
| | - Teresa Cobo
- Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centre for Biomedical Research on Rare Diseases (CIBER-ER), University of Barcelona, Spain
| | - Robert Castelo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Research Programme on Biomedical Informatics, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
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17
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Martín-Nalda A, Fortuny C, Rey L, Bunney TD, Alsina L, Esteve-Solé A, Bull D, Anton MC, Basagaña M, Casals F, Deyá A, García-Prat M, Gimeno R, Juan M, Martinez-Banaclocha H, Martinez-Garcia JJ, Mensa-Vilaró A, Rabionet R, Martin-Begue N, Rudilla F, Yagüe J, Estivill X, García-Patos V, Pujol RM, Soler-Palacín P, Katan M, Pelegrín P, Colobran R, Vicente A, Arostegui JI. Severe Autoinflammatory Manifestations and Antibody Deficiency Due to Novel Hypermorphic PLCG2 Mutations. J Clin Immunol 2020; 40:987-1000. [PMID: 32671674 PMCID: PMC7505877 DOI: 10.1007/s10875-020-00794-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/20/2020] [Indexed: 01/28/2023]
Abstract
Autoinflammatory diseases (AIDs) were first described as clinical disorders characterized by recurrent episodes of seemingly unprovoked sterile inflammation. In the past few years, the identification of novel AIDs expanded their phenotypes toward more complex clinical pictures associating vasculopathy, autoimmunity, or immunodeficiency. Herein, we describe two unrelated patients suffering since the neonatal period from a complex disease mainly characterized by severe sterile inflammation, recurrent bacterial infections, and marked humoral immunodeficiency. Whole-exome sequencing detected a novel, de novo heterozygous PLCG2 variant in each patient (p.Ala708Pro and p.Leu845_Leu848del). A clear enhanced PLCγ2 activity for both variants was demonstrated by both ex vivo calcium responses of the patient's B cells to IgM stimulation and in vitro assessment of PLC activity. These data supported the autoinflammation and PLCγ2-associated antibody deficiency and immune dysregulation (APLAID) diagnosis in both patients. Immunological evaluation revealed a severe decrease of immunoglobulins and B cells, especially class-switched memory B cells, with normal T and NK cell counts. Analysis of bone marrow of one patient revealed a reduced immature B cell fraction compared with controls. Additional investigations showed that both PLCG2 variants activate the NLRP3-inflammasome through the alternative pathway instead of the canonical pathway. Collectively, the evidences here shown expand APLAID diversity toward more severe phenotypes than previously reported including dominantly inherited agammaglobulinemia, add novel data about its genetic basis, and implicate the alternative NLRP3-inflammasome activation pathway in the basis of sterile inflammation.
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Affiliation(s)
- Andrea Martín-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Institut de Recerca, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Claudia Fortuny
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Institut de Recerca, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Department of Pediatrics, Hospital Sant Joan de Deu, Esplugues, Spain
- Institut de Recerca Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Spain
| | - Lourdes Rey
- Department of Pediatrics, Hospital Alvaro Cunqueiro, Vigo, Spain
| | - Tom D Bunney
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Laia Alsina
- Institut de Recerca Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Spain
- Department of Allergy and Clinical Immunology Clinical Immunology and Primary, Immunodeficiencies Unit, Hospital Sant Joan de Déu, Esplugues, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic, Barcelona, Spain
| | - Ana Esteve-Solé
- Institut de Recerca Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Spain
- Department of Allergy and Clinical Immunology Clinical Immunology and Primary, Immunodeficiencies Unit, Hospital Sant Joan de Déu, Esplugues, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic, Barcelona, Spain
| | - Daniel Bull
- ARUK Drug Discovery Institute, University College London, London, UK
| | - Maria Carmen Anton
- Department of Immunology-CDB (esc 4-pl 0), Hospital Clínic, Villarroel, 170, 08036, Barcelona, Spain
| | - María Basagaña
- Allergy Section, Hospital Universitari Germans Trias i Pujol, Autonomous University of Barcelona, Badalona, Spain
| | - Ferran Casals
- Genomics Core Facility, Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain
| | - Angela Deyá
- Institut de Recerca Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Spain
- Department of Allergy and Clinical Immunology Clinical Immunology and Primary, Immunodeficiencies Unit, Hospital Sant Joan de Déu, Esplugues, Spain
- Clinical Immunology Unit, Hospital Sant Joan de Déu-Hospital Clínic, Barcelona, Spain
| | - Marina García-Prat
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Institut de Recerca, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Ramon Gimeno
- Department of Immunology, Hospital del Mar, Institut Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Manel Juan
- Department of Immunology-CDB (esc 4-pl 0), Hospital Clínic, Villarroel, 170, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Helios Martinez-Banaclocha
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Juan J Martinez-Garcia
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Anna Mensa-Vilaró
- Department of Immunology-CDB (esc 4-pl 0), Hospital Clínic, Villarroel, 170, 08036, Barcelona, Spain
| | - Raquel Rabionet
- Institut de Recerca Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues, Spain
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRJSD, CIBERER, Barcelona, Spain
| | - Nieves Martin-Begue
- Department of Pediatric Ophthalmology, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Francesc Rudilla
- Histocompatibility and Immunogenetics Laboratory, Blood and Tissue Bank, Barcelona, Spain
- Transfusional Medicine Group, Vall d'Hebron Research Institute, Autonomous University of Barcelona, Barcelona, Spain
| | - Jordi Yagüe
- Department of Immunology-CDB (esc 4-pl 0), Hospital Clínic, Villarroel, 170, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Xavier Estivill
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Barcelona, Catalonia, Spain
| | - Vicente García-Patos
- Department of Pediatric Dermatology, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Ramon M Pujol
- Department of Dermatology, Hospital del Mar, Institut Mar d'Investigacions Mèdiques, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Institut de Recerca, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
- Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Matilda Katan
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Pablo Pelegrín
- Instituto Murciano de Investigación Biosanitaria IMIB-Arrixaca, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
- Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona, Barcelona, Spain
| | - Asun Vicente
- Department of Pediatric Dermatology, Hospital Sant Joan de Deu, Esplugues, Spain
| | - Juan I Arostegui
- Department of Immunology-CDB (esc 4-pl 0), Hospital Clínic, Villarroel, 170, 08036, Barcelona, Spain.
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.
- School of Medicine, Universitat de Barcelona, Barcelona, Spain.
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18
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Barrio PA, García Ó, Phillips C, Prieto L, Gusmão L, Fernández C, Casals F, Freitas JM, González-Albo MDC, Martín P, Mosquera A, Navarro-Vera I, Paredes M, Pérez JA, Pinzón A, Rasal R, Ruiz-Ramírez J, Trindade BR, Alonso A. The first GHEP-ISFG collaborative exercise on forensic applications of massively parallel sequencing. Forensic Sci Int Genet 2020; 49:102391. [PMID: 32957016 DOI: 10.1016/j.fsigen.2020.102391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 01/17/2023]
Abstract
One of the main goals of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the field of forensic genetics. The GHEP-ISFG supports several Working Commissions which develop different scientific activities. One of them, the Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications", organized its first collaborative exercise on forensic applications of MPS technology in 2019. The aim of this exercise was to assess the concordance between the MPS results and those obtained with conventional technologies (capillary electrophoresis and Sanger sequencing), as well as to compare the results obtained within the different MPS platforms and/or the different kits/panels and analysis software packages (commercial and open-access) available on the market. The seven participating laboratories analyzed some samples of the annual GHEP-ISFG proficiency test (EIADN No. 27 (2019)), using Ion Torrent™ or MiSeq FGx® platforms. Six of them sent autosomal STR sequence data, five laboratories performed MPS analysis of individual identification SNPs, four laboratories reported MPS data of Y-chromosomal STRs, and X-chromosomal STRs, three laboratories performed MPS analysis of ancestry informative SNPs and phenotype informative SNPs, two labs performed MPS analysis of the mitochondrial DNA control region, and only one lab produced MPS data of lineage informative SNPs. Autosomal STR sequencing results were highly concordant to the consensus obtained by capillary electrophoresis in the EIADN No. 27 (2019) exercise. Furthermore, in general, a high level of concordance was observed between the results of the participating laboratories, regardless of the platform used. The main discordances were due to errors during the analysis process or from sequence data obtained with low depth of coverage. In this paper we highlight some issues that still arise, such as standardization of the nomenclature for STRs analyzed by sequencing with MPS, the universal uptake of a nomenclature framework by the analysis software, and well established validation and accreditation of the new MPS platforms for use in routine forensic case-work.
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Affiliation(s)
- Pedro A Barrio
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Biology Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain.
| | - Óscar García
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio, Bizkaia, Spain
| | - Christopher Phillips
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - Lourdes Prieto
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Forensic Genetics Unit, University of Santiago de Compostela, Spain; Comisaría General de Policía Científica, Madrid, Spain
| | - Leonor Gusmão
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; DNA Diagnostics Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Coro Fernández
- Quality Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jorge M Freitas
- Instituto Nacional de Criminalística, Polícia Federal, Brazil
| | | | - Pablo Martín
- Biology Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain
| | - Ana Mosquera
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | | | - Manuel Paredes
- Subdirección de Investigación Científica, Instituto Nacional de Medicina Legal y Ciencias Forenses, Colombia
| | - Juan Antonio Pérez
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio, Bizkaia, Spain
| | - Andrea Pinzón
- Grupo Nacional de Ciencias Forenses, Instituto Nacional de Medicina Legal y Ciencias Forenses, Colombia
| | - Raquel Rasal
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | - Antonio Alonso
- Working Commission on "Massively Parallel Sequencing (MPS): Forensic Applications" of the GHEP-ISFG (The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics), Spain; Biology Service, National Institute of Toxicology and Forensic Sciences, Department of Madrid, Spain
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19
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Harding T, Milot E, Moreau C, Lefebvre JF, Bournival JS, Vézina H, Laprise C, Lalueza-Fox C, Anglada R, Loewen B, Casals F, Ribot I, Labuda D. Historical human remains identification through maternal and paternal genetic signatures in a founder population with extensive genealogical record. Am J Phys Anthropol 2020; 171:645-658. [PMID: 32064591 DOI: 10.1002/ajpa.24024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/13/2020] [Accepted: 02/04/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES We describe a method to identify human remains excavated from unmarked graves in historical Québec cemeteries by combining parental-lineage genetic markers with the whole-population genealogy of Québec contained in the BALSAC database. MATERIALS AND METHODS The remains of six men were exhumed from four historical cemeteries in the province of Québec, Canada. DNA was extracted from the remains and genotyped to reveal their mitochondrial and Y-chromosome haplotypes, which were compared to a collection of haplotypes of genealogically-anchored modern volunteers. Maternal and paternal genealogies were searched in the BALSAC genealogical record for parental couples matching the mitochondrial and the Y-chromosome haplotypic signatures, to identify candidate sons from whom the remains could have originated. RESULTS Analysis of the matching genealogies identified the parents of one man inhumed in the cemetery of the investigated parish during its operating time. The candidate individual died in 1833 at the age of 58, a plausible age at death in light of osteological analysis of the remains. DISCUSSION This study demonstrates the promising potential of coupling genetic information from living individuals to genealogical data in BALSAC to identify historical human remains. If genetic coverage is increased, the genealogical information in BALSAC could enable the identification of 87% of the men (n = 178,435) married in Québec before 1850, with high discriminatory power in most cases since >75% of the parental couples have unique biparental signatures in most regions. Genotyping and identifying Québec's historical human remains are a key to reconstructing the genomes of the founders of Québec and reinhuming archeological remains with a marked grave.
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Affiliation(s)
- Tommy Harding
- Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada.,Laboratoire de recherche en criminalistique, Département de chimie, biochimie et sciences de l'énergie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - Emmanuel Milot
- Laboratoire de recherche en criminalistique, Département de chimie, biochimie et sciences de l'énergie, Université du Québec à Trois-Rivières, Trois-Rivières, Canada.,Centre international de criminologie comparée and Centre interuniversitaire d'études québécoises, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - Claudia Moreau
- Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada.,Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Canada
| | | | | | - Hélène Vézina
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Canada.,Projet BALSAC, Université du Québec à Chicoutimi, Chicoutimi, Canada.,Département des sciences humaines et sociales, Université du Québec à Chicoutimi, Chicoutimi, Canada
| | - Catherine Laprise
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Canada.,Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Canada
| | - Carles Lalueza-Fox
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Roger Anglada
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona, Spain
| | - Brad Loewen
- Département d'anthropologie, Université de Montréal, Montréal, Canada
| | - Ferran Casals
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona, Spain
| | - Isabelle Ribot
- Département d'anthropologie, Université de Montréal, Montréal, Canada
| | - Damian Labuda
- Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Canada.,Département de pédiatrie, Université de Montréal, Montréal, Canada
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20
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Viñas-Giménez L, Padilla N, Batlle-Masó L, Casals F, Rivière JG, Martínez-Gallo M, de la Cruz X, Colobran R. FHLdb: A Comprehensive Database on the Molecular Basis of Familial Hemophagocytic Lymphohistiocytosis. Front Immunol 2020; 11:107. [PMID: 32076423 PMCID: PMC7006814 DOI: 10.3389/fimmu.2020.00107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/15/2020] [Indexed: 12/26/2022] Open
Abstract
Background: Primary immunodeficiencies (PIDs) are a heterogeneous group of disorders. The lack of comprehensive disease-specific mutation databases may hinder or delay classification of the genetic variants found in samples from these patients. This is especially true for familial hemophagocytic lymphohistiocytosis (FHL), a life-threatening PID classically considered an autosomal recessive condition, but with increasingly demonstrated genetic heterogeneity. Objective: The aim of this study was to build an open-access repository to collect detailed information on the known genetic variants reported in FHL. Methods: We manually reviewed more than 120 articles to identify all reported variants related to FHL. We retrieved relevant information about the allelic status, the number of patients with the same variant, and whether functional assays were done. We stored all the data retrieved in a PostgreSQL database and then built a website on top of it, using the Django framework. Results: The database designed (FHLdb) (https://www.biotoclin.org/FHLdb) contains comprehensive information on reported variants in the 4 genes related to FHL (PRF1, UNC13D, STXBP2, STX11). It comprises 240 missense, 69 frameshift, 51 nonsense, 51 splicing, 10 in-frame indel, 7 deep intronic, and 5 large rearrangement variants together with their allelic status, carrier(s) information, and functional evidence. All genetic variants have been classified as pathogenic, likely pathogenic, uncertain significance, likely benign or benign, according to the American College of Medical Genetics guidelines. Additionally, it integrates information from other relevant databases: clinical evidence from ClinVar and UniProt, population allele frequency from ExAC and gnomAD, and pathogenicity predictions from well-recognized tools (e.g., PolyPhen-2, SIFT). Finally, a diagram depicts the location of the variant relative to the gene exon and protein domain structures. Conclusion: FHLdb includes a broad range of data on the reported genetic variants in familial HLH genes. It is a free-access and easy-to-use resource that will facilitate the interpretation of molecular results of FHL patients, and it illustrates the potential value of disease-specific databases for other PIDs.
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Affiliation(s)
- Laura Viñas-Giménez
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Natàlia Padilla
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Laura Batlle-Masó
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Jacques G Rivière
- Pediatric Infectious Diseases and Immunodeficiencies Unit (UPIIP), Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Xavier de la Cruz
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Institut Catala per la Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Roger Colobran
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Genetics Department, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
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21
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Kuderna LFK, Solís-Moruno M, Batlle-Masó L, Julià E, Lizano E, Anglada R, Ramírez E, Bote A, Tormo M, Marquès-Bonet T, Fornas Ò, Casals F. Flow Sorting Enrichment and Nanopore Sequencing of Chromosome 1 From a Chinese Individual. Front Genet 2020; 10:1315. [PMID: 31998370 PMCID: PMC6962354 DOI: 10.3389/fgene.2019.01315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/02/2019] [Indexed: 11/23/2022] Open
Abstract
Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome. We have recently developed a workflow to sequence native, unamplified DNA and applied it to the smallest human chromosome, the Y chromosome. Here, we modify improve upon that workflow to increase DNA recovery from chromosome sorting as well as sequencing yield. We apply it to sequence and assemble the largest human chromosome - chromosome 1 - of a Chinese individual using a single Oxford Nanopore MinION flow cell. We generate a selective and highly continuous assembly whose continuity reaches into the order of magnitude of the human reference GRCh38. We then use this assembly to call candidate structural variants against the reference and find 685 putative novel SV candidates. We propose this workflow as a potential solution to assemble structurally complex chromosomes, or the study of very large plant or animal genomes that might challenge traditional assembly strategies.
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Affiliation(s)
- Lukas F K Kuderna
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB)", Barcelona, Spain
| | - Manuel Solís-Moruno
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB)", Barcelona, Spain.,Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Laura Batlle-Masó
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB)", Barcelona, Spain.,Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Eva Julià
- Serveis Científico-Tècnics, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.,Flow Cytometry Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB)", Barcelona, Spain
| | - Roger Anglada
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Erika Ramírez
- Flow Cytometry Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Alex Bote
- Flow Cytometry Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Marc Tormo
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain.,Scientific IT Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB)", Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Òscar Fornas
- Flow Cytometry Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
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22
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Palomo-Díez S, Gomes C, López-Parra A, Baeza-Richer C, Cuscó I, Raffone C, García-Arumí E, Vinueza-Espinosa D, Santos C, Montes N, Rasal R, Escala O, Cuellar J, Subirá E, Casals F, Malgosa A, Tizzano E, Tartera E, Domenech G, Arroyo-Pardo E. Genetic identification of Spanish civil war victims. The state of the art in Catalonia (Northeastern Spain). Forensic Science International: Genetics Supplement Series 2019. [DOI: 10.1016/j.fsigss.2019.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Gea J, Pascual S, Castro-Acosta A, Hernández-Carcereny C, Castelo R, Márquez-Martín E, Montón C, Palou A, Faner R, Furlong LI, Seijo L, Sanz F, Torà M, Vilaplana C, Casadevall C, López-Campos JL, Monsó E, Peces-Barba G, Cosío BG, Agustí A, Admetlló M, Agustí A, Alvarez-Martínez C, Barreiro E, Casadevall C, Casals F, Castelo R, Castro-Acosta A, Córdova R, Cosío BG, Faner R, Furlong LI, García M, Gea J, González-García JG, Hernández-Carcereny C, López-Campos JL, Márquez E, Monsó E, Montón C, Ormaza MJ, Palou A, Pascual S, Peces-Barba G, Puigdevall P, Sanz F, Seijó L, Torà M, Torralba Y, Vilaplana C. The BIOMEPOC Project: Personalized Biomarkers and Clinical Profiles in Chronic Obstructive Pulmonary Disease. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.arbr.2018.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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24
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Gea J, Pascual S, Castro-Acosta A, Hernández-Carcereny C, Castelo R, Márquez-Martín E, Montón C, Palou A, Faner R, Furlong LI, Seijo L, Sanz F, Torà M, Vilaplana C, Casadevall C, López-Campos JL, Monsó E, Peces-Barba G, Cosío BG, Agustí A, Admetlló M, Agustí A, Alvarez-Martínez C, Barreiro E, Casadevall C, Casals F, Castelo R, Castro-Acosta A, Córdova R, Cosío BG, Faner R, Furlong LI, García M, Gea J, González-García JG, Hernández-Carcereny C, López-Campos JL, Márquez E, Monsó E, Montón C, Ormaza MJ, Palou A, Pascual S, Peces-Barba G, Puigdevall P, Sanz F, Seijó L, Torà M, Torralba Y, Vilaplana C. Proyecto de biomarcadores y perfiles clínicos personalizados en la enfermedad pulmonar obstructiva crónica (proyecto BIOMEPOC). Arch Bronconeumol 2019; 55:93-99. [DOI: 10.1016/j.arbres.2018.07.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/16/2018] [Accepted: 07/31/2018] [Indexed: 02/01/2023]
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25
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Schwab C, Gabrysch A, Olbrich P, Patiño V, Warnatz K, Wolff D, Hoshino A, Kobayashi M, Imai K, Takagi M, Dybedal I, Haddock JA, Sansom DM, Lucena JM, Seidl M, Schmitt-Graeff A, Reiser V, Emmerich F, Frede N, Bulashevska A, Salzer U, Schubert D, Hayakawa S, Okada S, Kanariou M, Kucuk ZY, Chapdelaine H, Petruzelkova L, Sumnik Z, Sediva A, Slatter M, Arkwright PD, Cant A, Lorenz HM, Giese T, Lougaris V, Plebani A, Price C, Sullivan KE, Moutschen M, Litzman J, Freiberger T, van de Veerdonk FL, Recher M, Albert MH, Hauck F, Seneviratne S, Pachlopnik Schmid J, Kolios A, Unglik G, Klemann C, Speckmann C, Ehl S, Leichtner A, Blumberg R, Franke A, Snapper S, Zeissig S, Cunningham-Rundles C, Giulino-Roth L, Elemento O, Dückers G, Niehues T, Fronkova E, Kanderová V, Platt CD, Chou J, Chatila TA, Geha R, McDermott E, Bunn S, Kurzai M, Schulz A, Alsina L, Casals F, Deyà-Martinez A, Hambleton S, Kanegane H, Taskén K, Neth O, Grimbacher B. Phenotype, penetrance, and treatment of 133 cytotoxic T-lymphocyte antigen 4-insufficient subjects. J Allergy Clin Immunol 2018; 142:1932-1946. [PMID: 29729943 PMCID: PMC6215742 DOI: 10.1016/j.jaci.2018.02.055] [Citation(s) in RCA: 281] [Impact Index Per Article: 46.8] [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: 09/06/2017] [Revised: 02/16/2018] [Accepted: 02/25/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Cytotoxic T-lymphocyte antigen 4 (CTLA-4) is a negative immune regulator. Heterozygous CTLA4 germline mutations can cause a complex immune dysregulation syndrome in human subjects. OBJECTIVE We sought to characterize the penetrance, clinical features, and best treatment options in 133 CTLA4 mutation carriers. METHODS Genetics, clinical features, laboratory values, and outcomes of treatment options were assessed in a worldwide cohort of CTLA4 mutation carriers. RESULTS We identified 133 subjects from 54 unrelated families carrying 45 different heterozygous CTLA4 mutations, including 28 previously undescribed mutations. Ninety mutation carriers were considered affected, suggesting a clinical penetrance of at least 67%; median age of onset was 11 years, and the mortality rate within affected mutation carriers was 16% (n = 15). Main clinical manifestations included hypogammaglobulinemia (84%), lymphoproliferation (73%), autoimmune cytopenia (62%), and respiratory (68%), gastrointestinal (59%), or neurological features (29%). Eight affected mutation carriers had lymphoma, and 3 had gastric cancer. An EBV association was found in 6 patients with malignancies. CTLA4 mutations were associated with lymphopenia and decreased T-, B-, and natural killer (NK) cell counts. Successful targeted therapies included application of CTLA-4 fusion proteins, mechanistic target of rapamycin inhibitors, and hematopoietic stem cell transplantation. EBV reactivation occurred in 2 affected mutation carriers after immunosuppression. CONCLUSIONS Affected mutation carriers with CTLA-4 insufficiency can present in any medical specialty. Family members should be counseled because disease manifestation can occur as late as 50 years of age. EBV- and cytomegalovirus-associated complications must be closely monitored. Treatment interventions should be coordinated in clinical trials.
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Affiliation(s)
- Charlotte Schwab
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annemarie Gabrysch
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Olbrich
- Sección de Infectología e Inmunopatología, Unidad de Pediatría, Hospital Virgen del Rocío/Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
| | | | - Klaus Warnatz
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniel Wolff
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Akihiro Hoshino
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Kohsuke Imai
- Department of Community Pediatrics, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masatoshi Takagi
- Department of Community Pediatrics, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ingunn Dybedal
- Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Jamanda A Haddock
- Department of Radiology, Royal Free Hospital, University College London, London, United Kingdom
| | - David M Sansom
- UCL Institute of Immunity and Transplantation, Royal Free Hospital, London, United Kingdom
| | - Jose M Lucena
- Unidad de Inmunología, Hospital Universitario Virgen del Rocío/Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
| | - Maximilian Seidl
- Center for Chronic Immunodeficiency and Molecular Pathology, Department of Pathology, University Medical Center, University of Freiburg, Freiburg, Germany
| | - Annette Schmitt-Graeff
- Department of Pathology, University Medical Center, University of Freiburg, Freiburg, Germany
| | - Veronika Reiser
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Florian Emmerich
- Institute for Transfusion Medicine and Gene Therapy, University Medical Center Freiburg, Freiburg, Germany
| | - Natalie Frede
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alla Bulashevska
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ulrich Salzer
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Desirée Schubert
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine, Freiburg University, Freiburg, Germany
| | - Seiichi Hayakawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Maria Kanariou
- Department of Immunology and Histocompatibility, Centre for Primary Immunodeficiencies, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Zeynep Yesim Kucuk
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati, Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hugo Chapdelaine
- Department of Medicine, Clinical Immunology and Allergy Division, Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal, Montreal, Quebec, Canada
| | - Lenka Petruzelkova
- Department of Pediatrics, University Hospital Motol and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Zdenek Sumnik
- Department of Pediatrics, University Hospital Motol and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anna Sediva
- Department of Immunology, University Hospital Motol and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Mary Slatter
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, and Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Peter D Arkwright
- University of Manchester, Royal Manchester Children's Hospital, Manchester, United Kingdom
| | - Andrew Cant
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, and Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Hanns-Martin Lorenz
- Division of Rheumatology, Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Thomas Giese
- Institute of Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vassilios Lougaris
- Pediatrics Clinic and Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Alessandro Plebani
- Pediatrics Clinic and Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Christina Price
- Section of Allergy and Clinical Immunology, Yale University School of Medicine, New Haven, Conn
| | - Kathleen E Sullivan
- Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Michel Moutschen
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, Liege, Belgium
| | - Jiri Litzman
- Department of Clinical Immunology and Allergology, Medical Faculty, Masaryk University, Brno, Czech Republic; Department of Clinical Immunology and Allergology, St Anne's University Hospital, Brno, Czech Republic
| | - Tomas Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Medical Genomics RG, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Frank L van de Veerdonk
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases (RCI), Nijmegen, The Netherlands
| | - Mike Recher
- Immunodeficiency Clinic, Medical Outpatient Unit and Immunodeficiency Lab, Department Biomedicine, University Hospital, Basel, Switzerland
| | - Michael H Albert
- Department of Pediatric Immunology and Stem Cell Transplantation, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Fabian Hauck
- Department of Pediatric Immunology and Stem Cell Transplantation, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Suranjith Seneviratne
- Institute of Immunology and Transplantation, Royal Free Hospital, University College London, London, United Kingdom
| | - Jana Pachlopnik Schmid
- Division of Immunology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Antonios Kolios
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Gary Unglik
- Department of Clinical Immunology and Allergy, Royal Melbourne Hospital, Melbourne, Australia
| | - Christian Klemann
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Pediatric Pneumology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany; Center of Pediatric Surgery, Hannover Medical School, Hannover, Germany
| | - Carsten Speckmann
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Pediatrics, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Ehl
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alan Leichtner
- Division of Gastroenterology and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Richard Blumberg
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Scott Snapper
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Children's Hospital Boston, Mass
| | - Sebastian Zeissig
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Medicine I, University Medical Center Dresden, Technical University Dresden, Dresden, Germany; Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Charlotte Cunningham-Rundles
- Mount Sinai Hospital, Mount Sinai St Luke's and Mount Sinai West, Department of Medicine-Allergy & Immunology, New York, NY
| | - Lisa Giulino-Roth
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Weill Cornell Medicine, New York, NY
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY
| | | | - Tim Niehues
- HELIOS Children's Hospital, Krefeld, Germany
| | - Eva Fronkova
- CLIP, Department of Paediatric Haematology/Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Veronika Kanderová
- CLIP, Department of Paediatric Haematology/Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Craig D Platt
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Raif Geha
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Elizabeth McDermott
- Clinical Immunology and Allergy Unit, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Su Bunn
- Department of Paediatric Gastroenterology, Great North Children's Hospital, Newcastle, United Kingdom
| | - Monika Kurzai
- Department of Pediatrics, University Hospital Jena, Jena, Germany
| | - Ansgar Schulz
- Department of Pediatrics, University Medical Center Ulm, Ulm, Germany
| | - Laia Alsina
- Allergy and Clinical Immunology Department, Functional Unit of Immunology SJD-Clinic, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Angela Deyà-Martinez
- Allergy and Clinical Immunology Department, Functional Unit of Immunology SJD-Clinic, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Sophie Hambleton
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, and Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Hirokazu Kanegane
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kjetil Taskén
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Institute for Cancer Research, University Hospital Oslo, Oslo, Norway
| | - Olaf Neth
- Sección de Infectología e Inmunopatología, Unidad de Pediatría, Hospital Virgen del Rocío/Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Institute of Immunology and Transplantation, Royal Free Hospital, University College London, London, United Kingdom.
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26
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Mattle-Greminger MP, Bilgin Sonay T, Nater A, Pybus M, Desai T, de Valles G, Casals F, Scally A, Bertranpetit J, Marques-Bonet T, van Schaik CP, Anisimova M, Krützen M. Genomes reveal marked differences in the adaptive evolution between orangutan species. Genome Biol 2018; 19:193. [PMID: 30428903 PMCID: PMC6237011 DOI: 10.1186/s13059-018-1562-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. Here, we used whole-genome sequencing data from critically endangered orangutans from North Sumatra (Pongo abelii) and Borneo (P. pygmaeus) to investigate adaptive responses of each species to environmental differences during the Pleistocene. RESULTS Taking into account the markedly disparate demographic histories of each species after their split ~ 1 Ma ago, we show that persistent environmental differences on each island had a strong impact on the adaptive evolution of the genus Pongo. Across a range of tests for positive selection, we find a consistent pattern of between-island and species differences. In the more productive Sumatran environment, the most notable signals of positive selection involve genes linked to brain and neuronal development, learning, and glucose metabolism. On Borneo, however, positive selection comprised genes involved in lipid metabolism, as well as cardiac and muscle activities. CONCLUSIONS We find strikingly different sets of genes appearing to have evolved under strong positive selection in each species. In Sumatran orangutans, selection patterns were congruent with well-documented cognitive and behavioral differences between the species, such as a larger and more complex cultural repertoire and higher degrees of sociality. However, in Bornean orangutans, selective responses to fluctuating environmental conditions appear to have produced physiological adaptations to generally lower and temporally more unpredictable food supplies.
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Affiliation(s)
- Maja P. Mattle-Greminger
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Tugce Bilgin Sonay
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne, Switzerland
| | - Alexander Nater
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Marc Pybus
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Tariq Desai
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
| | - Guillem de Valles
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Ferran Casals
- Servei de Genòmica, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyola del Vallès, Barcelona, Spain
| | - Carel P. van Schaik
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Maria Anisimova
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne, Switzerland
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences ZHAW, Einsiedlerstrasse 31a, 8820 Wädenswil, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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27
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Mensa-Vilaró A, Bravo García-Morato M, de la Calle-Martin O, Franco-Jarava C, Martínez-Saavedra MT, González-Granado LI, González-Roca E, Fuster JL, Alsina L, Mutchinick OM, Balderrama-Rodríguez A, Ramos E, Modesto C, Mesa-Del-Castillo P, Ortego-Centeno N, Clemente D, Souto A, Palmou N, Remesal A, Leslie KS, Gómez de la Fuente E, Yadira Bravo Gallego L, Campistol JM, Dhouib NG, Bejaoui M, Dutra LA, Terreri MT, Mosquera C, González T, Cañellas J, García-Ruiz de Morales JM, Wouters CH, Bosque MT, Cham WT, Jiménez-Treviño S, de Inocencio J, Bloomfield M, Pérez de Diego R, Martínez-Pomar N, Rodríguez-Pena R, González-Santesteban C, Soler-Palacín P, Casals F, Yagüe J, Allende LM, Rodríguez-Gallego JC, Colobran R, Martínez-Martínez L, López-Granados E, Aróstegui JI. Unexpected relevant role of gene mosaicism in patients with primary immunodeficiency diseases. J Allergy Clin Immunol 2018; 143:359-368. [PMID: 30273710 DOI: 10.1016/j.jaci.2018.09.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 08/21/2018] [Accepted: 09/08/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Postzygotic de novo mutations lead to the phenomenon of gene mosaicism. The 3 main types are called somatic, gonadal, and gonosomal mosaicism, which differ in terms of the body distribution of postzygotic mutations. Mosaicism has been reported occasionally in patients with primary immunodeficiency diseases (PIDs) since the early 1990s, but its real involvement has not been systematically addressed. OBJECTIVE We sought to investigate the incidence of gene mosaicism in patients with PIDs. METHODS The amplicon-based deep sequencing method was used in the 3 parts of the study that establish (1) the allele frequency of germline variants (n = 100), (2) the incidence of parental gonosomal mosaicism in families with PIDs with de novo mutations (n = 92), and (3) the incidence of mosaicism in families with PIDs with moderate-to-high suspicion of gene mosaicism (n = 36). Additional investigations evaluated body distribution of postzygotic mutations, their stability over time, and their characteristics. RESULTS The range of allele frequency (44.1% to 55.6%) was established for germline variants. Those with minor allele frequencies of less than 44.1% were assumed to be postzygotic. Mosaicism was detected in 30 (23.4%) of 128 families with PIDs, with a variable minor allele frequency (0.8% to 40.5%). Parental gonosomal mosaicism was detected in 6 (6.5%) of 92 families with de novo mutations, and a high incidence of mosaicism (63.9%) was detected among families with moderate-to-high suspicion of gene mosaicism. In most analyzed cases mosaicism was found to be both uniformly distributed and stable over time. CONCLUSION This study represents the largest performed to date to investigate mosaicism in patients with PIDs, revealing that it affects approximately 25% of enrolled families. Our results might have serious consequences regarding treatment and genetic counseling and reinforce the use of next-generation sequencing-based methods in the routine analyses of PIDs.
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Affiliation(s)
- Anna Mensa-Vilaró
- Department of Immunology-CDB, Hospital Clínic-IDIBAPS, Barcelona, Spain.
| | | | | | - Clara Franco-Jarava
- Department of Immunology, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Barcelona, Spain; Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | | | - Luis I González-Granado
- Primary Immunodeficiencies Unit, Department of Pediatrics, Hospital Universitario 12 de Octubre, Madrid, Spain; Instituto de Investigación i+12, Hospital Universitario 12 de Octubre, Madrid, Spain; Universidad Complutense, Madrid, Spain
| | - Eva González-Roca
- Department of Immunology-CDB, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Jose Luis Fuster
- Department of Hematology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Laia Alsina
- Department of Allergy and Clinical Immunology, Hospital Sant Joan de Deu, Esplugues, Spain; Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues, Spain
| | - Osvaldo M Mutchinick
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Eduardo Ramos
- Department of Pediatrics, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Consuelo Modesto
- Department of Pediatric Rheumatology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Pablo Mesa-Del-Castillo
- Department of Pediatric Rheumatology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | | | - Daniel Clemente
- Department of Pediatric Rheumatology, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Alejandro Souto
- Department of Rheumatology, Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Natalia Palmou
- Department of Rheumatology, Hospital Universitario Marques de Valdecilla, Santander, Spain
| | - Agustín Remesal
- Department of Pediatric Rheumatology, Hospital Universitario La Paz, Madrid, Spain
| | - Kieron S Leslie
- Department of Dermatology, University of California San Francisco, San Francisco, Calif
| | | | | | | | - Naouel Guirat Dhouib
- Pediatric Immuno-Hematology Unit, Bone Marrow Transplantation Center, Tunis, Tunisia
| | - Mohamed Bejaoui
- Pediatric Immuno-Hematology Unit, Bone Marrow Transplantation Center, Tunis, Tunisia
| | - Lívia Almeida Dutra
- Division of General Neurology, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Maria Teresa Terreri
- Department of Pediatrics, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Catalina Mosquera
- Department of Pediatric Rheumatology, Universidad El Bosque, Bogota, Colombia
| | - Tatiana González
- Department of Pediatric Rheumatology, Universidad de Cartagena, Cartagena, Colombia
| | - Jerónima Cañellas
- Department of Rheumatology, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | - Carine H Wouters
- Departments of Pediatric Rheumatology, Microbiology and Immunology, University Hospitals Leuven, KU University of Leuven, Leuven, Belgium
| | - María Teresa Bosque
- Department of Rheumatology, Hospital Clinico Universitario Lozano Blesa, Zaragoza, Spain
| | - Weng Tarng Cham
- Department of Pediatric Rheumatology, Sunway Medical Centre, Kuala Lumpur, Malaysia
| | | | - Jaime de Inocencio
- Instituto de Investigación i+12, Hospital Universitario 12 de Octubre, Madrid, Spain; Department of Pediatric Rheumatology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Markéta Bloomfield
- Department of Immunology, 2(nd) Faculty of Medicine, Charles University and University Hospital in Motol, Prague, Czech Republic
| | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Diseases, IdiPAZ Institute for Health Research, Hospital Universitario La Paz, Madrid, Spain; Innate Immunity Group, IdiPAZ Institute for Health Research, Hospital Universitario La Paz, Madrid, Spain
| | | | | | | | - Pere Soler-Palacín
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain; Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Ferran Casals
- Department of Genomics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Yagüe
- Department of Immunology-CDB, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Luis M Allende
- Instituto de Investigación i+12, Hospital Universitario 12 de Octubre, Madrid, Spain; Universidad Complutense, Madrid, Spain; Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain; Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain; Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona, Barcelona, Spain
| | | | | | - Juan I Aróstegui
- Department of Immunology-CDB, Hospital Clínic-IDIBAPS, Barcelona, Spain.
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28
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de Valles-Ibáñez G, Esteve-Solé A, Piquer M, González-Navarro EA, Hernandez-Rodriguez J, Laayouni H, González-Roca E, Plaza-Martin AM, Deyà-Martínez Á, Martín-Nalda A, Martínez-Gallo M, García-Prat M, Del Pino-Molina L, Cuscó I, Codina-Solà M, Batlle-Masó L, Solís-Moruno M, Marquès-Bonet T, Bosch E, López-Granados E, Aróstegui JI, Soler-Palacín P, Colobran R, Yagüe J, Alsina L, Juan M, Casals F. Evaluating the Genetics of Common Variable Immunodeficiency: Monogenetic Model and Beyond. Front Immunol 2018; 9:636. [PMID: 29867916 PMCID: PMC5960686 DOI: 10.3389/fimmu.2018.00636] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/14/2018] [Indexed: 12/16/2022] Open
Abstract
Common variable immunodeficiency (CVID) is the most frequent symptomatic primary immunodeficiency characterized by recurrent infections, hypogammaglobulinemia and poor response to vaccines. Its diagnosis is made based on clinical and immunological criteria, after exclusion of other diseases that can cause similar phenotypes. Currently, less than 20% of cases of CVID have a known underlying genetic cause. We have analyzed whole-exome sequencing and copy number variants data of 36 children and adolescents diagnosed with CVID and healthy relatives to estimate the proportion of monogenic cases. We have replicated an association of CVID to p.C104R in TNFRSF13B and reported the second case of homozygous patient to date. Our results also identify five causative genetic variants in LRBA, CTLA4, NFKB1, and PIK3R1, as well as other very likely causative variants in PRKCD, MAPK8, or DOCK8 among others. We experimentally validate the effect of the LRBA stop-gain mutation which abolishes protein production and downregulates the expression of CTLA4, and of the frameshift indel in CTLA4 producing expression downregulation of the protein. Our results indicate a monogenic origin of at least 15–24% of the CVID cases included in the study. The proportion of monogenic patients seems to be lower in CVID than in other PID that have also been analyzed by whole exome or targeted gene panels sequencing. Regardless of the exact proportion of CVID monogenic cases, other genetic models have to be considered for CVID. We propose that because of its prevalence and other features as intermediate penetrancies and phenotypic variation within families, CVID could fit with other more complex genetic scenarios. In particular, in this work, we explore the possibility of CVID being originated by an oligogenic model with the presence of heterozygous mutations in interacting proteins or by the accumulation of detrimental variants in particular immunological pathways, as well as perform association tests to detect association with rare genetic functional variation in the CVID cohort compared to healthy controls.
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Affiliation(s)
- Guillem de Valles-Ibáñez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ana Esteve-Solé
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Mònica Piquer
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - E Azucena González-Navarro
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Bioinformatics Studies, ESCI-UPF, Barcelona, Spain
| | - Eva González-Roca
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ana María Plaza-Martin
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Ángela Deyà-Martínez
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina García-Prat
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Lucía Del Pino-Molina
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Ivón Cuscó
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Marta Codina-Solà
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Laura Batlle-Masó
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Manuel Solís-Moruno
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Juan Ignacio Aróstegui
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Yagüe
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Laia Alsina
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Manel Juan
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
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29
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Hernandez-Rodriguez J, Arandjelovic M, Lester J, de Filippo C, Weihmann A, Meyer M, Angedakin S, Casals F, Navarro A, Vigilant L, Kühl HS, Langergraber K, Boesch C, Hughes D, Marques-Bonet T. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Mol Ecol Resour 2017; 18:319-333. [PMID: 29058768 PMCID: PMC5900898 DOI: 10.1111/1755-0998.12728] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/06/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
Abstract
Target-capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off-target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.
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Affiliation(s)
- Jessica Hernandez-Rodriguez
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Arcadi Navarro
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hjalmar S Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution & Social Change, Arizona State University, Tempe, AZ, USA
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David Hughes
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tomas Marques-Bonet
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, Groves C, Pybus M, Sonay TB, Roos C, Lameira AR, Wich SA, Askew J, Davila-Ross M, Fredriksson G, de Valles G, Casals F, Prado-Martinez J, Goossens B, Verschoor EJ, Warren KS, Singleton I, Marques DA, Pamungkas J, Perwitasari-Farajallah D, Rianti P, Tuuga A, Gut IG, Gut M, Orozco-terWengel P, van Schaik CP, Bertranpetit J, Anisimova M, Scally A, Marques-Bonet T, Meijaard E, Krützen M. Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species. Curr Biol 2017; 27:3487-3498.e10. [PMID: 29103940 DOI: 10.1016/j.cub.2017.09.047] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/17/2017] [Accepted: 09/20/2017] [Indexed: 12/30/2022]
Abstract
Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.
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Affiliation(s)
- Alexander Nater
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
| | - Maja P Mattle-Greminger
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Anton Nurcahyo
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - Matthew G Nowak
- Sumatran Orangutan Conservation Programme (PanEco-YEL), Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia; Department of Anthropology, Southern Illinois University, 1000 Faner Drive, Carbondale, IL 62901, USA
| | - Marc de Manuel
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Tariq Desai
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Colin Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - Marc Pybus
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Tugce Bilgin Sonay
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Adriano R Lameira
- Department of Anthropology, Durham University, Dawson Building, South Road, Durham DH1 3LE, UK; School of Psychology & Neuroscience, St. Andrews University, St. Mary's Quad, South Street, St. Andrews, Fife KY16 9JP, Scotland, UK
| | - Serge A Wich
- School of Natural Sciences and Psychology, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, UK; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam 1098, the Netherlands
| | - James Askew
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
| | - Marina Davila-Ross
- Department of Psychology, University of Portsmouth, King Henry Building, King Henry 1(st) Street, Portsmouth PO1 2DY, UK
| | - Gabriella Fredriksson
- Sumatran Orangutan Conservation Programme (PanEco-YEL), Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam 1098, the Netherlands
| | - Guillem de Valles
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Ferran Casals
- Servei de Genòmica, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain
| | | | - Benoit Goossens
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, 88100 Kota Kinabalu, Sabah, Malaysia; Sabah Wildlife Department, Wisma Muis, 88100 Kota Kinabalu, Sabah, Malaysia; Sustainable Places Research Institute, Cardiff University, 33 Park Place, Cardiff CF10 3BA, UK
| | - Ernst J Verschoor
- Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288GJ Rijswijk, the Netherlands
| | - Kristin S Warren
- Conservation Medicine Program, College of Veterinary Medicine, Murdoch University, South Street, Murdoch, WA 6150, Australia
| | - Ian Singleton
- Sumatran Orangutan Conservation Programme (PanEco-YEL), Jalan Wahid Hasyim 51/74, Medan 20154, Indonesia; Foundation for a Sustainable Ecosystem (YEL), Medan, Indonesia
| | - David A Marques
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Joko Pamungkas
- Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia; Faculty of Veterinary Medicine, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia
| | - Dyah Perwitasari-Farajallah
- Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia; Animal Biosystematics and Ecology Division, Department of Biology, Bogor Agricultural University, Jalan Agatis, Dramaga Campus, Bogor 16680, Indonesia
| | - Puji Rianti
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia; Animal Biosystematics and Ecology Division, Department of Biology, Bogor Agricultural University, Jalan Agatis, Dramaga Campus, Bogor 16680, Indonesia
| | - Augustine Tuuga
- Sabah Wildlife Department, Wisma Muis, 88100 Kota Kinabalu, Sabah, Malaysia
| | - Ivo G Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
| | - Carel P van Schaik
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain; Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31a, 8820 Wädenswil, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015 Lausanne, Switzerland
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona 08003, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Erik Meijaard
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia; Borneo Futures, Bandar Seri Begawan, Brunei Darussalam.
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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Mondal M, Bergström A, Xue Y, Calafell F, Laayouni H, Casals F, Majumder PP, Tyler-Smith C, Bertranpetit J. Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Hum Genet 2017; 136:499-510. [PMID: 28444560 DOI: 10.1007/s00439-017-1800-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/10/2017] [Indexed: 01/25/2023]
Abstract
We present 42 new Y-chromosomal sequences from diverse Indian tribal and non-tribal populations, including the Jarawa and Onge from the Andaman Islands, which are analysed within a calibrated Y-chromosomal phylogeny incorporating South Asian (in total 305 individuals) and worldwide (in total 1286 individuals) data from the 1000 Genomes Project. In contrast to the more ancient ancestry in the South than in the North that has been claimed, we detected very similar coalescence times within Northern and Southern non-tribal Indian populations. A closest neighbour analysis in the phylogeny showed that Indian populations have an affinity towards Southern European populations and that the time of divergence from these populations substantially predated the Indo-European migration into India, probably reflecting ancient shared ancestry rather than the Indo-European migration, which had little effect on Indian male lineages. Among the tribal populations, the Birhor (Austro-Asiatic-speaking) and Irula (Dravidian-speaking) are the nearest neighbours of South Asian non-tribal populations, with a common origin in the last few millennia. In contrast, the Riang (Tibeto-Burman-speaking) and Andamanese have their nearest neighbour lineages in East Asia. The Jarawa and Onge shared haplogroup D lineages with each other within the last ~7000 years, but had diverged from Japanese haplogroup D Y-chromosomes ~53000 years ago, most likely by a split from a shared ancestral population. This analysis suggests that Indian populations have complex ancestry which cannot be explained by a single expansion model.
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Affiliation(s)
- Mayukh Mondal
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
| | - Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | | | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK.
| | - Jaume Bertranpetit
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain.
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Cagan A, Theunert C, Laayouni H, Santpere G, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J, Andrés AM. Natural Selection in the Great Apes. Mol Biol Evol 2016; 33:3268-3283. [PMID: 27795229 PMCID: PMC5100057 DOI: 10.1093/molbev/msw215] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Natural selection is crucial for the adaptation of populations to their environments. Here, we present the first global study of natural selection in the Hominidae (humans and great apes) based on genome-wide information from population samples representing all extant species (including most subspecies). Combining several neutrality tests we create a multi-species map of signatures of natural selection covering all major types of natural selection. We find that the estimated efficiency of both purifying and positive selection varies between species and is significantly correlated with their long-term effective population size. Thus, even the modest differences in population size among the closely related Hominidae lineages have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments. Most signatures of balancing and positive selection are species-specific, with signatures of balancing selection more often being shared among species. We also identify loci with evidence of positive selection across several lineages. Notably, we detect signatures of positive selection in several genes related to brain function, anatomy, diet and immune processes. Our results contribute to a better understanding of human evolution by putting the evidence of natural selection in humans within its larger evolutionary context. The global map of natural selection in our closest living relatives is available as an interactive browser at http://tinyurl.com/nf8qmzh.
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Affiliation(s)
- Alexander Cagan
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christoph Theunert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA
| | - Hafid Laayouni
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Catalonia, Spain
| | - Gabriel Santpere
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
| | - Marc Pybus
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Arcadi Navarro
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Tomas Marques-Bonet
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Jaume Bertranpetit
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Department of Archaeology and Anthropology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Spataro N, Roca-Umbert A, Cervera-Carles L, Vallès M, Anglada R, Pagonabarraga J, Pascual-Sedano B, Campolongo A, Kulisevsky J, Casals F, Clarimón J, Bosch E. Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients. Mov Disord 2016; 32:165-169. [PMID: 28124432 PMCID: PMC5297984 DOI: 10.1002/mds.26845] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/12/2016] [Accepted: 09/27/2016] [Indexed: 12/18/2022] Open
Abstract
Background The analysis of coverage depth in next‐generation sequencing data allows the detection of gene dose alterations. We explore the frequency of such structural events in a Spanish cohort of sporadic PD cases. Methods Gene dose alterations were detected with the eXome‐Hidden Markov Model (XHMM) software from depth of coverage in resequencing data available for 38 Mendelian and other risk PD loci in 394 individuals (249 cases and 145 controls) and subsequently validated by quantitative PCR. Results We identified 10 PD patients with exon dosage alterations in PARK2, GBA‐GBAP1, and DJ1. Additional functional variants, including 2 novel nonsense mutations (p.Arg1552Ter in LRRK2 and p.Trp90Ter in PINK1), were confirmed by Sanger sequencing. This combined approach disclosed the genetic cause of 12 PD cases. Conclusions Gene dose alterations related to PD can be correctly identified from targeting resequencing data. This approach substantially improves the detection rate of cases with causal genetic alterations. © 2016 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Nino Spataro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ana Roca-Umbert
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura Cervera-Carles
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Mònica Vallès
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Roger Anglada
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
| | - Javier Pagonabarraga
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Berta Pascual-Sedano
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Health Sciences Department, Universitat Oberta de Catalunya, Catalonia, Spain
| | - Antònia Campolongo
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Health Sciences Department, Universitat Oberta de Catalunya, Catalonia, Spain
| | - Jaime Kulisevsky
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Health Sciences Department, Universitat Oberta de Catalunya, Catalonia, Spain
| | - Ferran Casals
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
| | - Jordi Clarimón
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T, Prado-Martinez J, Hernandez-Rodriguez J, Dupanloup I, Lao O, Hallast P, Schmidt JM, Heredia-Genestar JM, Benazzo A, Barbujani G, Peter BM, Kuderna LFK, Casals F, Angedakin S, Arandjelovic M, Boesch C, Kühl H, Vigilant L, Langergraber K, Novembre J, Gut M, Gut I, Navarro A, Carlsen F, Andrés AM, Siegismund HR, Scally A, Excoffier L, Tyler-Smith C, Castellano S, Xue Y, Hvilsom C, Marques-Bonet T. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 2016; 354:477-481. [PMID: 27789843 DOI: 10.1126/science.aag2602] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 12/13/2022]
Abstract
Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.
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Affiliation(s)
- Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Peter Frandsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tariq Desai
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Javier Prado-Martinez
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Isabelle Dupanloup
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Oscar Lao
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Pille Hallast
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Joshua M Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - José María Heredia-Genestar
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Benjamin M Peter
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Ferran Casals
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Hjalmar Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution and Social Change and Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Marta Gut
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ivo Gut
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain
| | - Frands Carlsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Hans R Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Sergi Castellano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Christina Hvilsom
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.
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Calafell F, Anglada R, Bonet N, González-Ruiz M, Prats-Muñoz G, Rasal R, Lalueza-Fox C, Bertranpetit J, Malgosa A, Casals F. An assessment of a massively parallel sequencing approach for the identification of individuals from mass graves of the Spanish Civil War (1936-1939). Electrophoresis 2016; 37:2841-2847. [DOI: 10.1002/elps.201600180] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/21/2016] [Accepted: 07/30/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Francesc Calafell
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut; Universitat Pompeu Fabra; 08003 Barcelona Catalonia Spain
| | - Roger Anglada
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra; Parc de Recerca Biomèdica de Barcelona; Barcelona Catalonia Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra; Parc de Recerca Biomèdica de Barcelona; Barcelona Catalonia Spain
| | - Mercedes González-Ruiz
- Unitat d'Antropologia Biològica, Departament de Biologia Animal, Biologia Vegetal i Ecologia; Universitat Autònoma de Barcelona, 08193 Bellaterra; Barcelona Catalonia Spain
| | - Gemma Prats-Muñoz
- Unitat d'Antropologia Biològica, Departament de Biologia Animal, Biologia Vegetal i Ecologia; Universitat Autònoma de Barcelona, 08193 Bellaterra; Barcelona Catalonia Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra; Parc de Recerca Biomèdica de Barcelona; Barcelona Catalonia Spain
| | - Carles Lalueza-Fox
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut; Universitat Pompeu Fabra; 08003 Barcelona Catalonia Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut; Universitat Pompeu Fabra; 08003 Barcelona Catalonia Spain
| | - Assumpció Malgosa
- Unitat d'Antropologia Biològica, Departament de Biologia Animal, Biologia Vegetal i Ecologia; Universitat Autònoma de Barcelona, 08193 Bellaterra; Barcelona Catalonia Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra; Parc de Recerca Biomèdica de Barcelona; Barcelona Catalonia Spain
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36
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Mondal M, Casals F, Xu T, Dall'Olio GM, Pybus M, Netea MG, Comas D, Laayouni H, Li Q, Majumder PP, Bertranpetit J. Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat Genet 2016; 48:1066-70. [DOI: 10.1038/ng.3621] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 06/17/2016] [Indexed: 12/19/2022]
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de Valles-Ibáñez G, Hernandez-Rodriguez J, Prado-Martinez J, Luisi P, Marquès-Bonet T, Casals F. Genetic Load of Loss-of-Function Polymorphic Variants in Great Apes. Genome Biol Evol 2016; 8:871-7. [PMID: 26912403 PMCID: PMC4824148 DOI: 10.1093/gbe/evw040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Loss of function (LoF) genetic variants are predicted to disrupt gene function, and are therefore expected to substantially reduce individual's viability. Knowing the genetic burden of LoF variants in endangered species is of interest for a better understanding of the effects of declining population sizes on species viability. In this study, we have estimated the number of LoF polymorphic variants in six great ape populations, based on whole-genome sequencing data in 79 individuals. Our results show that although the number of functional variants per individual is conditioned by the effective population size, the number of variants with a drastic phenotypic effect is very similar across species. We hypothesize that for those variants with high selection coefficients, differences in effective population size are not important enough to affect the efficiency of natural selection to remove them. We also describe that mostly CpG LoF mutations are shared across species, and an accumulation of LoF variants at olfactory receptor genes in agreement with its pseudogenization in humans and other primate species.
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Affiliation(s)
- Guillem de Valles-Ibáñez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Javier Prado-Martinez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain Present address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Pierre Luisi
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain Centre Nacional d'Análisi Genómica (CNAG), Parc Científic de Barcelona, Barcelona, Catalonia, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
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Spataro N, Calafell F, Cervera-Carles L, Casals F, Pagonabarraga J, Pascual-Sedano B, Campolongo A, Kulisevsky J, Lleó A, Navarro A, Clarimón J, Bosch E. Mendelian genes for Parkinson's disease contribute to the sporadic forms of the disease†. Hum Mol Genet 2014; 24:2023-34. [PMID: 25504046 DOI: 10.1093/hmg/ddu616] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nino Spataro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Laura Cervera-Carles
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Ferran Casals
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain
| | - Javier Pagonabarraga
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Berta Pascual-Sedano
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Antònia Campolongo
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Jaime Kulisevsky
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain, Health Sciences Department, Universitat Oberta de Catalunya, Catalonia, Spain
| | - Alberto Lleó
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain, National Institute for Bioinformatics (INB), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain and Center for Genomic Regulation (CRG), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain
| | - Jordi Clarimón
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain,
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Juyal G, Mondal M, Luisi P, Laayouni H, Sood A, Midha V, Heutink P, Bertranpetit J, Thelma BK, Casals F. Population and genomic lessons from genetic analysis of two Indian populations. Hum Genet 2014; 133:1273-87. [PMID: 24980708 DOI: 10.1007/s00439-014-1462-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/05/2014] [Indexed: 12/25/2022]
Abstract
Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.
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Affiliation(s)
- Garima Juyal
- Department of Genetics, University of Delhi South Campus, New Delhi, 110 021, India
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Casals F, Hodgkinson A, Hussin J, Idaghdour Y, Bruat V, de Maillard T, Grenier JC, Gbeha E, Hamdan FF, Girard S, Spinella JF, Larivière M, Saillour V, Healy J, Fernández I, Sinnett D, Michaud JL, Rouleau GA, Haddad E, Le Deist F, Awadalla P. Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. PLoS Genet 2013; 9:e1003815. [PMID: 24086152 PMCID: PMC3784517 DOI: 10.1371/journal.pgen.1003815] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 08/08/2013] [Indexed: 11/18/2022] Open
Abstract
Whole-exome or gene targeted resequencing in hundreds to thousands of individuals has shown that the majority of genetic variants are at low frequency in human populations. Rare variants are enriched for functional mutations and are expected to explain an important fraction of the genetic etiology of human disease, therefore having a potential medical interest. In this work, we analyze the whole-exome sequences of French-Canadian individuals, a founder population with a unique demographic history that includes an original population bottleneck less than 20 generations ago, followed by a demographic explosion, and the whole exomes of French individuals sampled from France. We show that in less than 20 generations of genetic isolation from the French population, the genetic pool of French-Canadians shows reduced levels of diversity, higher homozygosity, and an excess of rare variants with low variant sharing with Europeans. Furthermore, the French-Canadian population contains a larger proportion of putatively damaging functional variants, which could partially explain the increased incidence of genetic disease in the province. Our results highlight the impact of population demography on genetic fitness and the contribution of rare variants to the human genetic variation landscape, emphasizing the need for deep cataloguing of genetic variants by resequencing worldwide human populations in order to truly assess disease risk.
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Affiliation(s)
- Ferran Casals
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Alan Hodgkinson
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Julie Hussin
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Youssef Idaghdour
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Vanessa Bruat
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Thibault de Maillard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Jean-Cristophe Grenier
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Elias Gbeha
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Fadi F. Hamdan
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Simon Girard
- Centre d'Excellence en Neuromique de l'Université de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Jean-François Spinella
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Mathieu Larivière
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Virginie Saillour
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Jasmine Healy
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Isabel Fernández
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Microbiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Daniel Sinnett
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Jacques L. Michaud
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Guy A. Rouleau
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada
| | - Elie Haddad
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Microbiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
- Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Françoise Le Deist
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Microbiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Philip Awadalla
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- * E-mail:
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Samuels ME, Majewski J, Alirezaie N, Fernandez I, Casals F, Patey N, Decaluwe H, Gosselin I, Haddad E, Hodgkinson A, Idaghdour Y, Marchand V, Michaud JL, Rodrigue MA, Desjardins S, Dubois S, Le Deist F, Awadalla P, Raymond V, Maranda B. Exome sequencing identifies mutations in the gene TTC7A in French-Canadian cases with hereditary multiple intestinal atresia. J Med Genet 2013; 50:324-9. [PMID: 23423984 PMCID: PMC3625823 DOI: 10.1136/jmedgenet-2012-101483] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/22/2013] [Indexed: 12/23/2022]
Abstract
BACKGROUND Congenital multiple intestinal atresia (MIA) is a severe, fatal neonatal disorder, involving the occurrence of obstructions in the small and large intestines ultimately leading to organ failure. Surgical interventions are palliative but do not provide long-term survival. Severe immunodeficiency may be associated with the phenotype. A genetic basis for MIA is likely. We had previously ascertained a cohort of patients of French-Canadian origin, most of whom were deceased as infants or in utero. The goal of the study was to identify the molecular basis for the disease in the patients of this cohort. METHODS We performed whole exome sequencing on samples from five patients of four families. Validation of mutations and familial segregation was performed using standard Sanger sequencing in these and three additional families with deceased cases. Exon skipping was assessed by reverse transcription-PCR and Sanger sequencing. RESULTS Five patients from four different families were each homozygous for a four base intronic deletion in the gene TTC7A, immediately adjacent to a consensus GT splice donor site. The deletion was demonstrated to have deleterious effects on splicing causing the skipping of the attendant upstream coding exon, thereby leading to a predicted severe protein truncation. Parents were heterozygous carriers of the deletion in these families and in two additional families segregating affected cases. In a seventh family, an affected case was compound heterozygous for the same 4bp deletion and a second missense mutation p.L823P, also predicted as pathogenic. No other sequenced genes possessed deleterious variants explanatory for all patients in the cohort. Neither mutation was seen in a large set of control chromosomes. CONCLUSIONS Based on our genetic results, TTC7A is the likely causal gene for MIA.
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Affiliation(s)
- Mark E Samuels
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Najmeh Alirezaie
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Isabel Fernandez
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of Montreal, Montreal, Quebec, Canada
| | - Ferran Casals
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Natalie Patey
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
- Department of Pathology, University of Montreal, Montreal, Quebec, Canada
| | - Hélène Decaluwe
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Isabelle Gosselin
- Department of Neurosciences, Centre de recherche du CHU de Québec, Université Laval, Québec City, Quebec, Canada
| | - Elie Haddad
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of Montreal, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Alan Hodgkinson
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Youssef Idaghdour
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Valerie Marchand
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Jacques L Michaud
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Marc-André Rodrigue
- Department of Neurosciences, Centre de recherche du CHU de Québec, Université Laval, Québec City, Quebec, Canada
- Département de Médecine Moléculaire, Université Laval, Québec City, Quebec, Canada
| | - Sylvie Desjardins
- Department of Neurosciences, Centre de recherche du CHU de Québec, Université Laval, Québec City, Quebec, Canada
| | - Stéphane Dubois
- Department of Neurosciences, Centre de recherche du CHU de Québec, Université Laval, Québec City, Quebec, Canada
| | - Francoise Le Deist
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of Montreal, Montreal, Quebec, Canada
| | - Philip Awadalla
- Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Vincent Raymond
- Department of Neurosciences, Centre de recherche du CHU de Québec, Université Laval, Québec City, Quebec, Canada
- Département de Médecine Moléculaire, Université Laval, Québec City, Quebec, Canada
| | - Bruno Maranda
- Medical Genetics Service, University of Sherbrooke, Sherbrooke, Quebec, Canada
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Cagliani R, Guerini FR, Rubio-Acero R, Baglio F, Forni D, Agliardi C, Griffanti L, Fumagalli M, Pozzoli U, Riva S, Calabrese E, Sikora M, Casals F, Comi GP, Bresolin N, Cáceres M, Clerici M, Sironi M. Long-standing balancing selection in the THBS4 gene: influence on sex-specific brain expression and gray matter volumes in Alzheimer disease. Hum Mutat 2013; 34:743-53. [PMID: 23420636 DOI: 10.1002/humu.22301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/01/2013] [Indexed: 01/08/2023]
Abstract
The THBS4 gene encodes a glycoprotein involved in inflammatory responses and synaptogenesis. THBS4 is expressed at higher levels in the brain of humans compared with nonhuman primates, and the protein accumulates in β-amyloid plaques. We analyzed THBS4 genetic variability in humans and show that two haplotypes (hap1 and hap2) are maintained by balancing selection and modulate THBS4 expression in lymphocytes. Indeed, the balancing selection region covers a predicted transcriptional enhancer. In humans, but not in macaques and chimpanzees, THBS4 brain expression increases with age, and variants in the balancing selection region interact with sex in influencing THBS4 expression (pinteraction = 0.038), with hap1 homozygous females showing lowest expression. In Alzheimer disease (AD) patients, significant interactions between sex and THBS4 genotype were detected for peripheral gray matter (pinteraction = 0.014) and total gray matter (pinteraction = 0.012) volumes. Similarly to the gene expression results, the interaction is mainly mediated by hap1 homozygous AD females, who show reduced volumes. Thus, the balancing selection target in THBS4 is likely represented by one or more variants that regulate tissue-specific and sex-specific gene expression. The selection signature associated with THBS4 might not be related to AD pathogenesis, but rather to inflammatory responses.
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Hussin J, Sinnett D, Casals F, Idaghdour Y, Bruat V, Saillour V, Healy J, Grenier JC, de Malliard T, Busche S, Spinella JF, Larivière M, Gibson G, Andersson A, Holmfeldt L, Ma J, Wei L, Zhang J, Andelfinger G, Downing JR, Mullighan CG, Awadalla P. Rare allelic forms of PRDM9 associated with childhood leukemogenesis. Genome Res 2012; 23:419-30. [PMID: 23222848 PMCID: PMC3589531 DOI: 10.1101/gr.144188.112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
One of the most rapidly evolving genes in humans, PRDM9, is a key determinant of the distribution of meiotic recombination events. Mutations in this meiotic-specific gene have previously been associated with male infertility in humans and recent studies suggest that PRDM9 may be involved in pathological genomic rearrangements. In studying genomes from families with children affected by B-cell precursor acute lymphoblastic leukemia (B-ALL), we characterized meiotic recombination patterns within a family with two siblings having hyperdiploid childhood B-ALL and observed unusual localization of maternal recombination events. The mother of the family carries a rare PRDM9 allele, potentially explaining the unusual patterns found. From exomes sequenced in 44 additional parents of children affected with B-ALL, we discovered a substantial and significant excess of rare allelic forms of PRDM9. The rare PRDM9 alleles are transmitted to the affected children in half the cases; nonetheless there remains a significant excess of rare alleles among patients relative to controls. We successfully replicated this latter observation in an independent cohort of 50 children with B-ALL, where we found an excess of rare PRDM9 alleles in aneuploid and infant B-ALL patients. PRDM9 variability in humans is thought to influence genomic instability, and these data support a potential role for PRDM9 variation in risk of acquiring aneuploidies or genomic rearrangements associated with childhood leukemogenesis.
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Affiliation(s)
- Julie Hussin
- Department of Biochemistry, Faculty of Medicine, University of Montreal, Montreal H3C 3J7, Canada
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Casals F, Idaghdour Y, Hussin J, Awadalla P. Next-generation sequencing approaches for genetic mapping of complex diseases. J Neuroimmunol 2012; 248:10-22. [PMID: 22285396 DOI: 10.1016/j.jneuroim.2011.12.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/30/2011] [Accepted: 12/15/2011] [Indexed: 01/12/2023]
Abstract
The advent of next generation sequencing technologies has opened new possibilities in the analysis of human disease. In this review we present the main next-generation sequencing technologies, with their major contributions and possible applications to the study of the genetic etiology of complex diseases.
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Affiliation(s)
- Ferran Casals
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.
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Casals F, Sikora M, Laayouni H, Montanucci L, Muntasell A, Lazarus R, Calafell F, Awadalla P, Netea MG, Bertranpetit J. Genetic adaptation of the antibacterial human innate immunity network. BMC Evol Biol 2011; 11:202. [PMID: 21745391 PMCID: PMC3155920 DOI: 10.1186/1471-2148-11-202] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 07/11/2011] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Pathogens have represented an important selective force during the adaptation of modern human populations to changing social and other environmental conditions. The evolution of the immune system has therefore been influenced by these pressures. Genomic scans have revealed that immune system is one of the functions enriched with genes under adaptive selection. RESULTS Here, we describe how the innate immune system has responded to these challenges, through the analysis of resequencing data for 132 innate immunity genes in two human populations. Results are interpreted in the context of the functional and interaction networks defined by these genes. Nucleotide diversity is lower in the adaptors and modulators functional classes, and is negatively correlated with the centrality of the proteins within the interaction network. We also produced a list of candidate genes under positive or balancing selection in each population detected by neutrality tests and showed that some functional classes are preferential targets for selection. CONCLUSIONS We found evidence that the role of each gene in the network conditions the capacity to evolve or their evolvability: genes at the core of the network are more constrained, while adaptation mostly occurred at particular positions at the network edges. Interestingly, the functional classes containing most of the genes with signatures of balancing selection are involved in autoinflammatory and autoimmune diseases, suggesting a counterbalance between the beneficial and deleterious effects of the immune response.
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Affiliation(s)
- Ferran Casals
- Institute of Evolutionary Biology (UPF-CSIC), CEXS - UPF - PRBB, Barcelona, Catalonia, Spain.
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Laayouni H, Montanucci L, Sikora M, Melé M, Dall'Olio GM, Lorente-Galdos B, McGee KM, Graffelman J, Awadalla P, Bosch E, Comas D, Navarro A, Calafell F, Casals F, Bertranpetit J. Similarity in recombination rate estimates highly correlates with genetic differentiation in humans. PLoS One 2011; 6:e17913. [PMID: 21464928 PMCID: PMC3065460 DOI: 10.1371/journal.pone.0017913] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 02/14/2011] [Indexed: 11/18/2022] Open
Abstract
Recombination varies greatly among species, as illustrated by the poor conservation of the recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand the evolution of recombination. Here, we analyze its recent evolution in humans. We calculated the recombination rates between adjacent pairs of 636,933 common single-nucleotide polymorphism loci in 28 worldwide human populations and analyzed them in relation to genetic distances between populations. We found a strong and highly significant correlation between similarity in the recombination rates corrected for effective population size and genetic differentiation between populations. This correlation is observed at the genome-wide level, but also for each chromosome and when genetic distances and recombination similarities are calculated independently from different parts of the genome. Moreover, and more relevant, this relationship is robustly maintained when considering presence/absence of recombination hotspots. Simulations show that this correlation cannot be explained by biases in the inference of recombination rates caused by haplotype sharing among similar populations. This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans.
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Affiliation(s)
- Hafid Laayouni
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Ludovica Montanucci
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Martin Sikora
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Marta Melé
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | | | - Belén Lorente-Galdos
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Kate M. McGee
- National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
| | - Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Philip Awadalla
- Faculty of Medicine, Ste-Justine Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Elena Bosch
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - David Comas
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
- National Institute for Bioinformatics (INB), Barcelona, Spain
| | - Francesc Calafell
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Ferran Casals
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
- Faculty of Medicine, Ste-Justine Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Jaume Bertranpetit
- IBE, Institute of Evolutionary Biology (UPF-CSIC), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
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Myers RA, Casals F, Gauthier J, Hamdan FF, Keebler J, Boyko AR, Bustamante CD, Piton AM, Spiegelman D, Henrion E, Zilversmit M, Hussin J, Quinlan J, Yang Y, Lafrenière RG, Griffing AR, Stone EA, Rouleau GA, Awadalla P. A population genetic approach to mapping neurological disorder genes using deep resequencing. PLoS Genet 2011; 7:e1001318. [PMID: 21383861 PMCID: PMC3044677 DOI: 10.1371/journal.pgen.1001318] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 01/24/2011] [Indexed: 01/15/2023] Open
Abstract
Deep resequencing of functional regions in human genomes is key to identifying potentially causal rare variants for complex disorders. Here, we present the results from a large-sample resequencing (n = 285 patients) study of candidate genes coupled with population genetics and statistical methods to identify rare variants associated with Autism Spectrum Disorder and Schizophrenia. Three genes, MAP1A, GRIN2B, and CACNA1F, were consistently identified by different methods as having significant excess of rare missense mutations in either one or both disease cohorts. In a broader context, we also found that the overall site frequency spectrum of variation in these cases is best explained by population models of both selection and complex demography rather than neutral models or models accounting for complex demography alone. Mutations in the three disease-associated genes explained much of the difference in the overall site frequency spectrum among the cases versus controls. This study demonstrates that genes associated with complex disorders can be mapped using resequencing and analytical methods with sample sizes far smaller than those required by genome-wide association studies. Additionally, our findings support the hypothesis that rare mutations account for a proportion of the phenotypic variance of these complex disorders. It is widely accepted that genetic factors play important roles in the etiology of neurological diseases. However, the nature of the underlying genetic variation remains unclear. Critical questions in the field of human genetics relate to the frequency and size effects of genetic variants associated with disease. For instance, the common disease–common variant model is based on the idea that sets of common variants explain a significant fraction of the variance found in common disease phenotypes. On the other hand, rare variants may have strong effects and therefore largely contribute to disease phenotypes. Due to their high penetrance and reduced fitness, such variants are maintained in the population at low frequencies, thus limiting their detection in genome-wide association studies. Here, we use a resequencing approach on a cohort of 285 Autism Spectrum Disorder and Schizophrenia patients and preformed several analyses, enhanced with population genetic approaches, to identify variants associated with both diseases. Our results demonstrate an excess of rare variants in these disease cohorts and identify genes with negative (deleterious) selection coefficients, suggesting an accumulation of variants of detrimental effects. Our results present further evidence for rare variants explaining a component of the genetic etiology of autism and schizophrenia.
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Affiliation(s)
- Rachel A. Myers
- Department of Pediatrics, University of Montreal, Montreal, Canada
- CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Canada
- Bioinformatics Research Centre, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Ferran Casals
- Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Julie Gauthier
- Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
- Department of Medicine, Université of Montréal, Montreal, Canada
| | - Fadi F. Hamdan
- Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
- Department of Medicine, Université of Montréal, Montreal, Canada
| | - Jon Keebler
- Department of Pediatrics, University of Montreal, Montreal, Canada
- CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Canada
- Bioinformatics Research Centre, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Adam R. Boyko
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Amelie M. Piton
- Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
- Department of Medicine, Université of Montréal, Montreal, Canada
| | - Dan Spiegelman
- Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
- Department of Medicine, Université of Montréal, Montreal, Canada
| | - Edouard Henrion
- Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
- Department of Medicine, Université of Montréal, Montreal, Canada
| | | | - Julie Hussin
- Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Jacklyn Quinlan
- Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Yan Yang
- Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
- Department of Medicine, Université of Montréal, Montreal, Canada
| | - Ronald G. Lafrenière
- Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
- Department of Medicine, Université of Montréal, Montreal, Canada
| | - Alexander R. Griffing
- Bioinformatics Research Centre, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Eric A. Stone
- Bioinformatics Research Centre, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Guy A. Rouleau
- CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Canada
- Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
- Department of Medicine, Université of Montréal, Montreal, Canada
- * E-mail: (PA); (GAR)
| | - Philip Awadalla
- Department of Pediatrics, University of Montreal, Montreal, Canada
- CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Canada
- Bioinformatics Research Centre, North Carolina State University, Raleigh, North Carolina, United States of America
- Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
- Department of Medicine, Université of Montréal, Montreal, Canada
- * E-mail: (PA); (GAR)
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Marigorta UM, Lao O, Casals F, Calafell F, Morcillo-Suárez C, Faria R, Bosch E, Serra F, Bertranpetit J, Dopazo H, Navarro A. Recent human evolution has shaped geographical differences in susceptibility to disease. BMC Genomics 2011; 12:55. [PMID: 21261943 PMCID: PMC3039608 DOI: 10.1186/1471-2164-12-55] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 01/24/2011] [Indexed: 01/01/2023] Open
Abstract
Background Searching for associations between genetic variants and complex diseases has been a very active area of research for over two decades. More than 51,000 potential associations have been studied and published, a figure that keeps increasing, especially with the recent explosion of array-based Genome-Wide Association Studies. Even if the number of true associations described so far is high, many of the putative risk variants detected so far have failed to be consistently replicated and are widely considered false positives. Here, we focus on the world-wide patterns of replicability of published association studies. Results We report three main findings. First, contrary to previous results, genes associated to complex diseases present lower degrees of genetic differentiation among human populations than average genome-wide levels. Second, also contrary to previous results, the differences in replicability of disease associated-loci between Europeans and East Asians are highly correlated with genetic differentiation between these populations. Finally, highly replicated genes present increased levels of high-frequency derived alleles in European and Asian populations when compared to African populations. Conclusions Our findings highlight the heterogeneous nature of the genetic etiology of complex disease, confirm the importance of the recent evolutionary history of our species in current patterns of disease susceptibility and could cast doubts on the status as false positives of some associations that have failed to replicate across populations.
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Affiliation(s)
- Urko M Marigorta
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
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Abstract
The life-history tactics of the stone loach Barbatula barbatula were studied in a Mediterranean-type climate stream (Matarranya River) located in the Ebro River basin (north-east Spain). Maximum observed ages were 2+ years in both sexes (1% of individuals), although only 0+ and 1+ year age groups were well represented. It is the lowest longevity reported for this species in its entire distribution. The seasonal growth period started in June and continued until November, but the pattern observed was different to northern populations. Barbatula barbatula in the Matarranya River was a multiple spawner, releasing small batches of oocytes between April and June. The fecundity of females was higher and the size of oocytes smaller in 1984 than in 1985. The relative fecundity (number of ripening and ripe oocytes g(-1) of fish) was lower than in northern European populations. The role of the particular environmental conditions of a Mediterranean stream was discussed in relation to the life-history tactics of B. barbatula.
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Affiliation(s)
- D Vinyoles
- Department of Animal Biology, Faculty of Biology, University of Barcelona, Avda Diagonal 645, 08028 Barcelona, Spain.
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