Deliverables Documents, reports (34) Framework implementing methods for integrative multi-omics analysis Framework implementing methods for integrative multiomics analysis Stakeholder Platform meeting and report on a concept for EASI-Genomics Expert Centre Stakeholder Platform meeting and report on a concept for EASIGenomics Expert Centre EASI-Genomics Report on ethical international context and networking outcomes EASIGenomics Report on ethical international context and networking outcomes EASI-Genomics data stewardship sustainability report EASIGenomics data stewardship sustainability report Report on second two years of personnel exchange programme Single-cell multi-omics analysis workflow featuring early integration of data layers Singlecell multiomics analysis workflow featuring early integration of data layers Communication tools in place Pilot study on developed cell free nucleic acid workflow (extraction from different liquid types and different species, library preparation and sequence analysis) Pilot study on developed cell free nucleic acid workflow extraction from different liquid types and different species library preparation and sequence analysis Data brokering service available for use by sequencing centres Report on technologies implemented and improved during the project Report on Technology watch set-up Training programme. Based on evaluation of needed competencies and training gaps, full training plan including online training and advanced courses Report on 3rd-4th call, including feedback from users from selected projects of these calls Report on 3rd4th call including feedback from users from selected projects of these calls Helpdesk, training and data stewardship planning services in place Report on first two years of personnel exchange programme Report on outreach actions for TA calls 1 and 2 Report on good laboratory practices for DNA, RNA and DNA methylation analysis by sequencing Report on good practices for data analysis for DNA, RNA and DNA methylation analysis Report on good practices for data analysis for DNA RNA and DNA methylation analysis Dissemination, Outreach and Exploitation Plan, including indicators Report on implementation and improvement of existing methods Data production from at least 30 Transnational Access Projects finished "EASI-Genomics ""ethical vigilance"" reports and policies: assessment of the TA and data sharing activities" EASIGenomics ethical vigilance reports and policies assessment of the TA and data sharing activities Report on landscape of Genomics RIs according to national and international roadmaps Report on 'tips and tricks jamborees' 1 and 2 Report on tips and tricks jamborees 1 and 2 EASI-Genomics “ethics vigilance” reports and policies: assessment of existing tools used by the partners and recommendations Quality and RRI plan: list of indicators Report on 2nd call, including feedback from users of selected projects Report on 2nd call including feedback from users of selected projects Report on the establishment of an EASI-Genomics Expert Centre Report on the establishment of an EASIGenomics Expert Centre Report on 1st call, including feedback from users of selected projects Report on 1st call including feedback from users of selected projects Completed benchmark for DNA, RNA and DNA methylation sequence analysis Completed benchmark for DNA RNA and DNA methylation sequence analysis EASI-Genomics Internal ethics and legal policies analysis for data deposit and access Report on provided training workshops Interim report on provided training workshops Workflow for single-cell analysis for datasets >1 million cells Workflow for singlecell analysis for datasets 1 million cells Evaluation of Quality and RRI indicators and plan update Websites, patent fillings, videos etc. (3) EASI-Genomics Symposium EASIGenomics Symposium Project website, including TA microsite Online questionnaire ready for assessing user needs Other (3) Data Management Plan Report on finished TA projects Data Management practices (DMP, compliance, deposition) Report on finished TA projects Data Management practices DMP compliance deposition Checklist system to support sequencing experiment descriptions Publications Peer reviewed articles (54) Pre-existing Autoantibodies Neutralizing High Concentrations of Type I Interferons in Almost 10% of COVID-19 Patients Admitted to Intensive Care in Barcelona. Author(s): Xavier Solanich; Raül Rigo-Bonnin; Victor-David Gumucio; Paul Bastard; Paul Bastard; Paul Bastard; Jérémie Rosain; Jérémie Rosain; Quentin Philippot; Quentin Philippot; Xose-Luís Pérez-Fernández; Maria-Paz Fuset-Cabanes; Miguel-Ángel Gordillo-Benitez; Guillermo Suarez-Cuartin; Enric Boza-Hernandez; Antoni Riera-Mestre; Alba Parra-Martínez; Roger Colobran; Arnau Antolí; Sergio Navarro; G Published in: Journal of Clinical Immunology, Issue 6, 2021, Page(s) 1733–1744, ISSN 0021-9738 Publisher: American Society for Clinical Investigation DOI: 10.1007/s10875-021-01136-x Effects of Quantification Methods, Isolation Kits, Plasma Biobanking, and Hemolysis on Cell-Free DNA Analysis in Plasma Author(s): Greta Streleckiene, Michael Forster, Ruta Inciuraite, Rokas Lukosevicius, Jurgita Skieceviciene Published in: Biopreservation and Biobanking, Issue 17/6, 2019, Page(s) 553-561, ISSN 1947-5535 Publisher: Mary Ann Liebert Inc. DOI: 10.1089/bio.2019.0026 Evaluating the Impact of Sex-Biased Genetic Admixture in the Americas through the Analysis of Haplotype Data Author(s): Linda Ongaro; Ludovica Molinaro; Rodrigo Flores; Davide Marnetto; Marco Rosario Capodiferro; Marta E. Alarcón-Riquelme; Andrés Moreno-Estrada; Nédio Mabunda; Mario Ventura; Kristiina Tambets; Alessandro Achilli; Cristian Capelli; Mait Metspalu; Luca Pagani; Francesco Montinaro Published in: Genes, Issue 12 (10), 2021, ISSN 2073-4425 Publisher: Multidisciplinary Digital Publishing Institute (MDPI) DOI: 10.3390/genes12101580 scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation Author(s): Amanda Raine, Anders Lundmark, Alva Annett, Ann-Christin Wiman, Marco Cavalli, Claes Wadelius, Claudia Bergin & Jessica Nordlund Published in: Scientific Reports, Issue 12, 2022, ISSN 0028-0836 Publisher: Nature Publishing Group DOI: 10.1038/s41598-022-09798-2 Genome-wide spatial expression profiling in formalin-fixed tissues Author(s): Eva Gracia Villacampa, Ludvig Larsson, Reza Mirzazadeh, Linda Kvastad, Alma Andersson, Annelie Mollbrink, Georgia Kokaraki, Vanessa Monteil, Niklas Schultz, Karin Sofia Appelberg, Nuria Montserrat, Haibo Zhang, Josef M.Penninger, Wolfgang Miesbach, Ali Mirazimi, Joseph Carlson, Joakim Lundeberg Published in: Cell Genomics, Issue 1, December 8, 2021, ISSN 2666-979X Publisher: ScienceDirect.com by Elsevier DOI: 10.1016/j.xgen.2021.100065 Human genetic and immunological determinants of critical COVID-19 pneumonia Author(s): Zhang, Qian; Bastard, Paul; Karbuz, Adem; Gervais, Adrian; Tayoun, Ahmad Abou; Aiuti, Alessandro; Belot, Alexandre; Bolze, Alexandre; Gaudet, Alexandre; Bondarenko, Anastasiia; Liu, Zhiyong; Spaan, András N.; Guennoun, Andrea; Arias, Andres Augusto; Planas, Anna M.; Sediva, Anna; Shcherbina, Anna; Neehus, Anna-Lena; Puel, Anne; Froidure, Antoine; Novelli, Antonio; Parlakay, Aslınur Özkaya; Pujo Published in: Nature, Issue 603, 2022, Page(s) 587–598, ISSN 0028-0836 Publisher: Nature Publishing Group DOI: 10.1038/s41586-022-04447-0 Autoantibodies against type I IFNs in patients with Ph-negative myeloproliferative neoplasms Author(s): Oscar Borsani; Paul Bastard; Jérémie Rosain; Adrian Gervais; Emanuela Sant’Antonio; Daniele Vanni; Ilaria Carola Casetti; Daniela Pietra; Chiara Trotti; Silvia Catricalà; Virginia Valeria Ferretti; Luca Malcovati; Luca Arcaini; Jean-Laurent Casanova; Alessandro Borghesi; Elisa Rumi Published in: Blood, Issue 6, 2022, ISSN 1528-0020 Publisher: The American Society of Hematology DOI: 10.1182/blood.2021014890 Autoantibodies neutralizing type I IFNs are present in ~ 4% of uninfected individuals over 70 years old and account for ~ 20% of COVID-19 deaths. Author(s): Bastard, Paul; Gervais, Adrian; Le Voyer, Tom; Rosain, Jérémie; Philippot, Quentin; Manry, Jérémy; Michailidis, Eleftherios; Hoffmann, Hans-Heinrich; Eto, Shohei; Garcia-Prat, Marina; Bizien, Lucy; Parra-Martínez, Alba; Yang, Rui; Haljasmägi, Liis; Migaud, Mélanie; Särekannu, Karita; Maslovskaja, Julia; de Prost, Nicolas; Tandjaoui-Lambiotte, Yacine; Luyt, Charles-Edouard; Amador-Borrero, Published in: Science Immunology, Issue 36, 2021, ISSN 2470-9468 Publisher: Science DOI: 10.1126/sciimmunol.abl4340 High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing Author(s): Tim Alexander Steiert, Janina Fuß, Simonas Juzenas, Michael Wittig, Marc Patrick Hoeppner, Melanie Vollstedt, Greta Varkalaite, Hesham ElAbd, Christian Brockmann, Siegfried Görg, Christoph Gassner, Michael Forster, Andre Franke Published in: NAR Genomics and Bioinformatics, Issue 4 (3), 2022, ISSN 2631-9268 Publisher: NAR GENOMICS AND BIOINFORMATICS DOI: 10.1093/nargab/lqac051 SSAM-lite: A Light-Weight Web App for Rapid Analysis of Spatially Resolved Transcriptomics Data Author(s): Sebastian Tiesmeyer; Shashwat Sahay; Niklas Müller-Bötticher; Roland Eils; Sebastian D. Mackowiak; Naveed Ishaque Published in: Crossref, Issue 21, 2022, ISSN 1664-8021 Publisher: Frontiers Media DOI: 10.3389/fgene.2022.785877 A growth factor–expressing macrophage subpopulation orchestrates regenerative inflammation via GDF-15 Author(s): Andreas Patsalos, Laszlo Halasz, Miguel A. Medina-Serpas, Wilhelm K. Berger, Bence Daniel, Petros Tzerpos, Máté Kiss, Gergely Nagy, Cornelius Fischer, Zoltan Simandi, Tamas Varga, Laszlo Nagy Published in: Journal of Experimental Medicine, Issue 219 (1) Nov 30, 2021, ISSN 0022-1007 Publisher: Rockefeller University Press DOI: 10.1084/jem.20210420 Human inherited complete STAT2 deficiency underlies inflammatory viral diseases Author(s): Bucciol, Giorgia; Moens, Leen; Ogishi, Masato; Rinchai, Darawan; Matuozzo, Daniela; Momenilandi, Mana; Kerrouche, Nacim; Cale, Catherine M; Treffeisen, Elsa R; Al Salamah, Mohammad; Al-Saud, Bandar K; Lachaux, Alain; Duclaux-Loras, Remi; Meignien, Marie; Bousfiha, Aziz; Benhsaien, Ibtihal; Shcherbina, Anna; Roppelt, Anna; COVID Human Genetic Effort, COVID Human Genetic Effort; Gothe, Florian; Houh Published in: Crossref, Issue 12, 2023, ISSN 1558-8238 Publisher: American Society for Clinical Investigation DOI: 10.1172/jci168321 Detection of Cancer Mutations by Urine Liquid Biopsy as a Potential Tool in the Clinical Management of Bladder Cancer Patients Author(s): Nurul Khalida Ibrahim, Ahmed Eraky, Jan Eggers, Tim Alexander Steiert, Susanne Sebens, Klaus-Peter Jünemann, Alexander Hendricks, Corinna Bang, Martin Stanulla, Andre Franke, Claudius Hamann, Christoph Röcken, Norbert Arnold, Laura Hinze, Michael Forster Published in: Cancers, Issue 14(4), 2022, Page(s) 969, ISSN 2072-6694 Publisher: Multidisciplinary Digital Publishing Institute (MDPI) DOI: 10.3390/cancers14040969 The European Nucleotide Archive in 2021. Author(s): Carla Cummins; Alisha Ahamed; Raheela Aslam; Josephine Burgin; Rajkumar Devraj; Ossama Edbali; Dipayan Gupta; Peter W. Harrison; Muhammad Haseeb; Sam Holt; Talal Ibrahim; Eugene Ivanov; Suran Jayathilaka; Vishnukumar Balavenkataraman Kadhirvelu; Simon Kay; Manish Kumar; Ankur Lathi; Rasko Leinonen; Fábio Madeira; Nandana Madhusoodanan; Milena Mansurova; Colman O’Cathail; Matt Pearce; Stephane P Published in: Nucleic Acids Research, Issue 35, 2021, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkab1051 Respiratory viral infections in otherwise healthy humans with inherited IRF7 deficiency Author(s): Campbell TM, Liu Z, Zhang Q, et al. Published in: Journal of Experimental Medicine, Issue 219 (7), 2022, ISSN 0021-9525 Publisher: Rockefeller University Press DOI: 10.1084/jem.20220202 X-linked recessive TLR7 deficiency in ~1% of men under 60 years old with life-threatening COVID-19. Author(s): Asano, Takaki; Boisson, Bertrand; Onodi, Fanny; Matuozzo, Daniela; Moncada-Velez, Marcela; Maglorius Renkilaraj, Majistor Raj Luxman; Zhang, Peng; Meertens, Laurent; Bolze, Alexandre; Materna, Marie; Korniotis, Sarantis; Gervais, Adrian; Talouarn, Estelle; Bigio, Benedetta; Seeleuthner, Yoann; Bilguvar, Kaya; Zhang, Yu; Neehus, Anna-Lena; Ogishi, Masato; Pelham, Simon J.; Le Voyer, Tom; Rosain, J Published in: SCIENCE IMMUNOLOGY, Issue 6 (62), 2021, ISSN 2470-9468 Publisher: AAAS DOI: 10.1126/sciimmunol.abl4348 The European Nucleotide Archive in 2020. Author(s): Peter W. Harrison; Alisha Ahamed; Raheela Aslam; Blaise T. F. Alako; Josephine Burgin; Nicola Buso; Mélanie Courtot; Jun Fan; Dipayan Gupta; Muhammad Haseeb; Sam Holt; Talal Ibrahim; Eugene Ivanov; Suran Jayathilaka; Vishnukumar Balavenkataraman Kadhirvelu; Manish Kumar; Rodrigo Lopez; Simon Kay; Rasko Leinonen; Xin Liu; Colman O’Cathail; Amir Pakseresht; Youngmi Park; Stephane Pesant; Nadim Ra Published in: Nucleic Acids Research, Issue 37, 2020, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkaa1028 Inborn errors of OAS–RNase L in SARS-CoV-2–related multisystem inflammatory syndrome in children Author(s): Lee, Danyel; Le Pen, Jérémie; Yatim, Ahmad; Dong, Beihua; Aquino, Yann; Ogishi, Masato; Pescarmona, Rémi; Talouarn, Estelle; Rinchai, Darawan; Zhang, Peng; Perret, Magali; Liu, Zhiyong; Jordan, Iolanda; Elmas Bozdemir, Sefika; Bayhan, Gulsum Iclal; Beaufils, Camille; Bizien, Lucy; Bisiaux, Aurelie; Lei, Weite; Hasan, Milena; Chen, Jie; Gaughan, Christina; Asthana, Abhishek; Libri, Valentina; Lu Published in: Science, Issue 379, 2022, ISSN 0036-8075 Publisher: American Association for the Advancement of Science DOI: 10.1126/science.abo3627 The SEQC2 epigenomics quality control (EpiQC) study Author(s): Jonathan Foox; Jessica Nordlund; Claudia Lalancette; Ting Gong; Michelle Lacey; Samantha Lent; Bradley W. Langhorst; V. K. Chaithanya Ponnaluri; Louise Williams; Karthik Ramaswamy Padmanabhan; Raymond Cavalcante; Anders Lundmark; Daniel Butler; Christopher Mozsary; Justin Gurvitch; John M. Greally; Masako Suzuki; Mark Menor; Masaki Nasu; Alicia Alonso; Caroline Sheridan; Andreas Scherer; Stephen B Published in: Genome Biology, Issue 5, 2021, ISSN 1474-760X Publisher: Springer Nature DOI: 10.1186/s13059-021-02529-2 SARS-CoV-2–related MIS-C: A key to the viral and genetic causes of Kawasaki disease? Author(s): Vanessa Sancho-Shimizu , Petter Brodin, Aurélie Cobat, Catherine M Biggs, Julie Toubiana, Carrie L Lucas, Sarah E Henrickson, Alexandre Belot, MIS-C@CHGE; Stuart G Tangye, Joshua D Milner, Michael Levin, Laurent Abel, Dusan Bogunovic, Jean-Laurent Casanova, Shen-Ying Zhang Published in: Journal of Experimental Medicine, Issue Jun 7; 218(6), 2021, Page(s) e20210446, ISSN 0022-1007 Publisher: Rockefeller University Press DOI: 10.1084/jem.20210446 Seamless integration of image and molecular analysis for spatial transcriptomics workflows Author(s): Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg Published in: BMC Genomics, Issue 21/1, 2020, ISSN 1471-2164 Publisher: BioMed Central DOI: 10.1186/s12864-020-06832-3 Monoclonal antibody-mediated neutralization of SARS-CoV-2 in an IRF9-deficient child. Author(s): Romain Lévy; Peng Zhang; Paul Bastard; Paul Bastard; Karim Dorgham; Isabelle Melki; Alice Hadchouel; George C. Hartoularos; Bénédicte Neven; Martin Castelle; Charlotte Roy; Tom Toin; Laureline Berteloot; Lucy Bizien; Hanène Abid; Marianne Burgard; Nadhira Houhou-Fidouh; Flore Rozenberg; Emmanuelle Jouanguy; Emmanuelle Jouanguy; Chun Jimmie Ye; Guy Gorochov; Qian Zhang; Qian Zhang; Jean-Laurent Published in: https://hal.sorbonne-universite.fr/hal-03408790, Issue 21, 2021, ISSN 1091-6490 Publisher: Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.2114390118 Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp Author(s): Kuhl H, Du K, Schartl M, Kalous L, Stöck M, Lamatsch DK. Published in: Nature Communications, Issue 13, 2022, Page(s) 4092, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-022-31515-w Single-cell RNA-seq analysis and cell-cluster deconvolution of the human preovulatory follicular fluid cells provide insights into the pathophysiology of ovarian hyporesponse Author(s): Kristine Roos; Ilmatar Rooda; Robyn-Stefany Keif; Maria Liivrand; Olli-Pekka Smolander; Andres Salumets; Agne Velthut-Meikas Published in: Frontiers in Endocrinology, Issue 35, 2022, ISSN 1664-2392 Publisher: Frontiers DOI: 10.3389/fendo.2022.945347 Defective type I interferon immunity is associated with increasing COVID-19 severity Author(s): Darragh Duffy; Nikaïa SMITH; Céline Possémé; Vincent Bondet; Jamie Sugrue; Liam Townsend; Bruno Charbit; Vincent Rouilly; Violaine Saint-André; Tom Dott; Andre Rodriguez Pozo; Nader Yatim; Olivier Schwartz; Minerva Cervantes-Gonzales; Jade Ghosn; Paul Bastard; Jean-Laurent Casanova; Tali-Anne Szwebel; Benjamin Terrier; Niall Conlon; Cliona O'Farrelly; Cliona Ni Cheallaigh; Nollaig Bourke Published in: 2022, Issue 20, 2022, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.21203/rs.3.rs-1685544/v1 Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19 Author(s): Matuozzo, Daniela; Gut, Marta; Cobat, Aurélie Published in: Genome Medicine, Issue 15, 2023, ISSN 1756-994X Publisher: BioMed Central DOI: 10.1186/s13073-023-01173-8 Inborn errors of type I IFN immunity in patients with life-threatening COVID-19 Author(s): Qian Zhang, Paul Bastard, Zhiyong Liu, Jérémie Le Pen, Marcela Moncada-Velez, Jie Chen, Masato Ogishi, Ira K. D. Sabli, Stephanie Hodeib, Cecilia Korol, Jérémie Rosain, Kaya Bilguvar, Junqiang Ye, Alexandre Bolze, Benedetta Bigio, Rui Yang, Andrés Augusto Arias, Qinhua Zhou, Yu Zhang, Fanny Onodi, Sarantis Korniotis, Léa Karpf, Quentin Philippot, Marwa Chbihi, Lucie Bonnet-Madin, Karim Dorgh Published in: Science, Issue Science 24 Sep 2020: eabd4570, 2020, Page(s) eabd4570, ISSN 0036-8075 Publisher: American Association for the Advancement of Science DOI: 10.1126/science.abd4570 Long-read genome sequencing identifies cryptic structural variants in congenital aniridia cases Author(s): Damián, A., Núñez-Moreno, G., Jubin, C. et al. Published in: Human Genomics, Issue 17, 2023, ISSN 1479-7364 Publisher: Springer Nature DOI: 10.1186/s40246-023-00490-8 Defective activation and regulation of type I interferon immunity is associated with increasing COVID-19 severity Author(s): Nikaïa Smith; Céline Possémé; Vincent Bondet; Jamie Sugrue; Liam Townsend; Bruno Charbit; Vincent Rouilly; Violaine Saint-André; Tom Dott; Andre Rodriguez Pozo; Nader Yatim; Olivier Schwartz; Minerva Cervantes-Gonzalez; Jade Ghosn; Paul Bastard; Jean Laurent Casanova; Tali-Anne Szwebel; Benjamin Terrier; Niall Conlon; Cliona O’Farrelly; Clíona Ní Cheallaigh; Nollaig M. Bourke; Darragh Duf Published in: Nature Communications, Issue 7, 2022, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-022-34895-1 Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue Author(s): Lee, H., Marco Salas, S., Gyllborg, D. et al. Published in: Scientific Reports, Issue 12, 2022, ISSN 0028-0836 Publisher: Nature Publishing Group DOI: 10.1038/s41598-022-11534-9 Single-nucleus RNA sequencing of plant tissues using a nanowell-based system Author(s): Daniele Y Sunaga-Franze, Jose M Muino, Caroline Braeuning, Xiaocai Xu, Minglei Zong, Cezary Smaczniak, Wenhao Yan, Cornelius Fischer, Ramon Vidal, Magdalena Kliem, Kerstin Kaufmann, Sascha Sauer Published in: The Plant Journal, Issue 108, 2021, Page(s) 859-869, ISSN 0960-7412 Publisher: Blackwell Publishing Inc. DOI: 10.1111/tpj.15458 Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps. Author(s): Sergio Marco Salas; Daniel Gyllborg; Christoffer Mattsson Langseth; Mats Nilsson Published in: BMC Bioinformatics, Issue 3, 2021, ISSN 1471-2105 Publisher: BioMed Central DOI: 10.1186/s12859-021-04302-5 Stage IV Colorectal Cancer Patients with High Risk Mutation Profiles Survived 16 Months Longer with Individualized Therapies Author(s): Alexander Hendricks, Anu Amallraja, Tobias Meißner, Peter Forster, Philip Rosenstiel, Greta Burmeister, Clemens Schafmayer, Andre Franke, Sebastian Hinz, Michael Forster, Casey B. Williams Published in: Cancers, Issue 12/2, 2020, Page(s) 393, ISSN 2072-6694 Publisher: Multidisciplinary Digital Publishing Institute (MDPI) DOI: 10.3390/cancers12020393 Combining Solid and Liquid Biopsy for Therapy Monitoring in Esophageal Cancer Author(s): Richter, F.; Henssen, C.; Steiert, T.A.; Meissner, T.; Mehdorn, A.-S.; Röcken, C.; Franke, A.; Egberts, J.-H.; Becker, T.; Sebens, S.; et al. Published in: International Journal of Molecular Sciences, Issue 24(13), 2023, ISSN 1422-0067 Publisher: Multidisciplinary Digital Publishing Institute (MDPI) DOI: 10.3390/ijms241310673 A loss-of-function <i>IFNAR1</i> allele in Polynesia underlies severe viral diseases in homozygotes Author(s): Paul Bastard; Kuang-Chih Hsiao; Qian Zhang; Jeremy Choin; Emma Best; Jie Chen; Adrian Gervais; Lucy Bizien; Marie Materna; Christine Harmant; Maguelonne Roux; Nicola L. Hawley; Daniel E. Weeks; Stephen T. McGarvey; Karla Sandoval; Carmina Barberena-Jonas; Consuelo D. Quinto-Cortés; Erika Hagelberg; Alexander J. Mentzer; Kathryn Robson; Boubacar Coulibaly; Yoann Seeleuthner; Benedetta Bigio; Zhi L Published in: Journal of Experimental Medicine, Issue 219 (6), 2022, ISSN 0021-9525 Publisher: Rockefeller University Press DOI: 10.1084/jem.20220028 Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue. Author(s): Daniel Gyllborg; Christoffer Mattsson Langseth; Xiaoyan Qian; Eunkyoung Choi; Sergio Marco Salas; Markus M. Hilscher; Ed S. Lein; Mats Nilsson Published in: Nucleic Acids Research, Issue 5, 2020, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkaa792 Autoantibodies against type I IFNs in patients with life-threatening COVID-19 Author(s): Bastard P, Rosen LB, Zhang Q, et al Published in: Science, Issue 370, 2020, ISSN 0036-8075 Publisher: American Association for the Advancement of Science DOI: 10.1126/science.abd4585 Autoantibodies neutralizing type I interferons in 20% of COVID-19 deaths in a French hospital Author(s): Angelique Chauvineau-Grenier; Paul Bastard; Antoine Servajean; Adrian Gervais; Jérémie Rosain; Emmanuelle Jouanguy; Aurélie Cobat; Jean-Laurent Casanova; Benjamin Rossi Published in: Journal of Clinical Immunology, Issue 3, 2021, ISSN 0271-9142 Publisher: Kluwer Academic/Plenum Publishers DOI: 10.21203/rs.3.rs-915062/v1 Human genetic and immunological determinants of SARS-CoV-2 and Epstein-Barr virus diseases in childhood: Insightful contrasts Author(s): Pan-Hammarström Q, Casanova JL Published in: Journal of Internal Medicine, Issue 294 (2), 2023, Page(s) 127-144, ISSN 1613-6810 Publisher: Wiley - V C H Verlag GmbbH & Co. DOI: 10.1111/joim.13628 Case Report: Benign Infantile Seizures Temporally Associated With COVID-19 Author(s): García-Howard M, Herranz-Aguirre M, Moreno-Galarraga L, et al Published in: Frontiers Pediatrics, Issue 8, 2020, ISSN 2296-2360 Publisher: Frontiers DOI: 10.3389/fped.2020.00507 A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome Author(s): Ieva Keraite; Philipp Becker; Davide Canevazzi; Cristina Frias-López; Marc Dabad; Raúl Tonda-Hernandez; Ida Paramonov; Matthew John Ingham; Isabelle Brun-Heath; Jordi Leno; Anna Abulí; Elena Garcia-Arumí; Simon Charles Heath; Marta Gut; Ivo Glynne Gut Published in: Scientia, Issue 21, 2022, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-022-33530-3 A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection. Author(s): Andreakos, Evangelos; Abel, Laurent; Vinh, Donald C.; Kaja, Elżbieta; Drolet, Beth A.; Zhang, Qian; O’Farrelly, Cliona; Novelli, Giuseppe; Rodríguez-Gallego, Carlos; Haerynck, Filomeen; Prando, Carolina; Pujol, Aurora; Bastard, Paul; Biggs, Catherine M.; Bigio, Benedetta; Boisson, Bertrand; Bolze, Alexandre; Bondarenko, Anastasiia; Brodin, Petter; Chakravorty, Samya; Christodoulou, John; Cobat Published in: instacron:USP, Issue 21, 2021, ISSN 1529-2916 Publisher: Nature DOI: 10.1038/s41590-021-01030-z Neutralizing Autoantibodies to Type I IFNs in >10% of Patients with Severe COVID-19 Pneumonia Hospitalized in Madrid, Spain. Author(s): Jesús Troya; Paul Bastard; Paul Bastard; Paul Bastard; Laura Planas-Serra; Pablo Ryan; Montse Ruiz; María de Carranza; Juan Torres; Amalia Martínez; Laurent Abel; Laurent Abel; Laurent Abel; Jean-Laurent Casanova; Aurora Pujol; Aurora Pujol; Aurora Pujol Published in: Journal of Clinical Immunology, Issue 41, 2021, Page(s) 914–922, ISSN 2193-1801 Publisher: Springer Science and Business Media Deutschland GmbH DOI: 10.1007/s10875-021-01036-0 Inherited IFNAR1 Deficiency in a Child with Both Critical COVID-19 Pneumonia and Multisystem Inflammatory Syndrome Author(s): Hassan Abolhassani; Nils Landegren; Paul Bastard; Marie Materna; Mohammadreza Modaresi; Likun Du; Maribel Aranda-Guillén; Fabian Sardh; Fanglei Zuo; Peng Zhang; Harold Marcotte; Nico Marr; Taushif Khan; Manar Ata; Fatima Al-Ali; Remi Pescarmona; Alexandre Belot; Vivien Béziat; Qian Zhang; Jean-Laurent Casanova; Olle Kämpe; Shen-Ying Zhang; Lennart Hammarström; Qiang Pan-Hammarström Published in: https://hal-univ-paris.archives-ouvertes.fr/hal-03691612, Issue 21, 2022, ISSN 2164-7712 Publisher: e-Century Publishing Corporation DOI: 10.1007/s10875-022-01215-7 Framework for quality assessment of whole genome cancer sequences. Author(s): Justin P. Whalley; Ivo Buchhalter; Esther Rheinbay; Esther Rheinbay; Keiran Raine; Miranda D. Stobbe; Kortine Kleinheinz; Johannes Werner; Sergi Beltran; Marta Gut; Daniel Hübschmann; Barbara Hutter; Dimitri Livitz; Marc D. Perry; Mara Rosenberg; Mara Rosenberg; Gordon Saksena; Jean-Rémi Trotta; Roland Eils; Roland Eils; Daniela S. Gerhard; Peter J. Campbell; Matthias Schlesner; Ivo Gut Published in: Nature Communications, Issue 10, 2020, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-020-18688-y Human autoantibodies underlying infectious diseases Author(s): Anne Puel; Paul Bastard; Jacinta Bustamante; Jean-Laurent Casanova Published in: Journal of Experimental Medicine, Issue 219 (4), 2022, ISSN 0021-9525 Publisher: Rockefeller University Press DOI: 10.1084/jem.20211387 Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. Author(s): Butler-Laporte G, Povysil G, Kosmicki JA, et al. Published in: PLoS Genetics, Issue 18(11), 2022, ISSN 1553-7390 Publisher: Public Library of Science DOI: 10.1371/journal.pgen.1010367 A critical spotlight on the paradigms of FFPE-DNA sequencing Author(s): Tim A Steiert, Genís Parra, Marta Gut, Norbert Arnold, Jean-Rémi Trotta, Raúl Tonda, Alice Moussy, Zuzana Gerber, Peter M Abuja, Kurt Zatloukal, Christoph Röcken, Trine Folseraas, Marit M Grimsrud, Arndt Vogel, Benjamin Goeppert, Stephanie Roessler, Sebastian Hinz, Clemens Schafmayer, Philip Rosenstiel, Jean-François Deleuze, Ivo G Gut, Andre Franke, Michael Forster Published in: Nucleic Acids Research, Issue 51 (14), 2023, Page(s) 7143–7162, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkad519 Impaired IL-23-dependent induction of IFN-γ underlies mycobacterial disease in patients with inherited TYK2 deficiency Author(s): Ogishi M, Arias AA, Yang R, et al Published in: Journal of Experimental Medicine, Issue 219 (10), 2022, ISSN 0021-9525 Publisher: Rockefeller University Press DOI: 10.1084/jem.20220094 Autoantibodies against type I IFNs in patients with critical influenza pneumonia Author(s): Zhang, Qian; Pizzorno, Andrés; Miorin, Lisa; Bastard, Paul; Gervais, Adrian; Le Voyer, Tom; Bizien, Lucy; Manry, Jeremy; Rosain, Jérémie; Philippot, Quentin; Goavec, Kelian; Wroblewski, Isabelle; Husebye, Eystein; Fellay, Jacques; Pothier, Pierre; Morand, Patrice; Navarrete, Nicolás; Franco, José Luis; Uddin, Mohammed J.; Carratalà, Jordi; Merino Díaz, Laura; Palomo, Virginia; Seppänen, Mi Published in: Journal of Experimental Medicine, Issue 219 (11), 2022, ISSN 0021-9525 Publisher: Rockefeller University Press DOI: 10.1084/jem.20220514 Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri. Author(s): Julie Thomy; Frederic Sanchez; Marta Gut; Fernando Cruz; Tyler Alioto; Gwenael Piganeau; Nigel Grimsley; Sheree Yau Published in: Cells, Issue 10(3), 2021, Page(s) 664, ISSN 2073-4409 Publisher: MDPI DOI: 10.3390/cells10030664 Human type I IFN deficiency does not impair B cell response to SARS-CoV-2 mRNA vaccination Author(s): Aurélien Sokal; Paul Bastard; Pascal Chappert; Giovanna Barba-Spaeth; Slim Fourati; Alexis Vanderberghe; Pauline Lagouge-Roussey; Isabelle Meyts; Adrian Gervais; Magali Bouvier-Alias; Imane Azzaoui; Ignacio Fernández; Andréa de la Selle; Qian Zhang; Lucy Bizien; Isabelle Pellier; Agnès Linglart; Anya Rothenbuhler; Estelle Marcoux; Raphael Anxionnat; Nathalie Cheikh; Juliane Léger; Blanca Amad Published in: Journal of Experimental Medicine, Issue 220, 2023, ISSN 0021-9525 Publisher: Rockefeller University Press DOI: 10.1084/jem.20220258 The European Genome-phenome Archive in 2021. Author(s): Mallory A. Freeberg; Lauren A Fromont; Teresa D’Altri; Anna Foix Romero; Jorge Izquierdo Ciges; Aina Jene; Giselle Kerry; Mauricio Moldes; Roberto Ariosa; Silvia Bahena; Daniel Barrowdale; Marcos Casado Barbero; Dietmar Fernandez-Orth; Carles Garcia-Linares; Emilio Garcia-Rios; Frédéric Haziza; Bela Juhasz; Oscar Martinez Llobet; Gemma Milla; Anand Mohan; Manuel Rueda; Aravind Sankar; Dona Sha Published in: Nucleic Acids Research, Issue 8, 2021, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkab1059 Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity Author(s): Chiara Fallerini, Nicola Picchiotti, Margherita Baldassarri, Kristina Zguro, Sergio Daga, Francesca Fava, Elisa Benetti, Sara Amitrano, Mirella Bruttini, Maria Palmieri, Susanna Croci, Mirjam Lista, Giada Beligni, Floriana Valentino, Ilaria Meloni, Marco Tanfoni, Francesca Minnai, Francesca Colombo, Enrico Cabri, Maddalena Fratelli, Chiara Gabbi, Stefania Mantovani, Elisa Frullanti, Marco Gori, Fr Published in: Human Genetics, Issue 141, 2022, Page(s) 147–173, ISSN 0340-6717 Publisher: Springer Verlag DOI: 10.1007/s00439-021-02397-7 Conference proceedings (1) Ensuring ethical and legal compliance of cutting-edge DNA sequencing technologies. Practical considerations from H2020 project EASI-Genomics Author(s): Gennet, Éloïse; Chassang, Gauthier; Coulbault-Azzouz, Maxime; Rial-Sebbag, Emmanuelle Published in: Congrès annuel de la Société européenne de génétique humaine (ESHG, Issue 13, 2020 Publisher: HalSHS Non-peer reviewed articles (3) Chromatin insulation orchestrates matrix metalloproteinase gene cluster expression reprogramming in aggressive breast cancer tumors Author(s): Pere Llinàs-Arias, Javier IJ Orozco, Miquel Ensenyat-Mendez et al. Published in: Molecular Cancer., 2023, ISSN 1476-4598 Publisher: BioMed Central DOI: 10.21203/rs.3.rs-2909119/v1 The European Nucleotide Archive in 2019 Author(s): Clara Amid, Blaise T F Alako, Vishnukumar Balavenkataraman Kadhirvelu, Tony Burdett, Josephine Burgin, Jun Fan, Peter W Harrison, Sam Holt, Abdulrahman Hussein, Eugene Ivanov, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu, Josue Martinez-Villacorta, Annalisa Milano, Amir Pakseresht, Nadim Rahman, Jeena Rajan, Kethi Reddy, Edward Richards, Dmitriy Smirnov, Alexey Sokolov, Sen Published in: Nucleic Acids Research, Issue Volume 48, Issue D1, 08 January 2020, 2019, Page(s) D70–D76, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkz1063 A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797) Author(s): Dalila Destanović, Darrin T. Schultz, Ruth Styfhals, Fernando Cruz, Jèssica Gómez-Garrido, Marta Gut, Ivo Gut, Graziano Fiorito, Oleg Simakov, Tyler S. Alioto, Giovanna Ponte, Eve Seuntjens Published in: bioRxiv, 2023, ISSN 1559-6095 Publisher: Cold Spring Harbor Laboratory Press DOI: 10.1101/2023.05.16.540928 Searching for OpenAIRE data... There was an error trying to search data from OpenAIRE No results available
