European Advanced infraStructure for Innovative Genomics

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

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

EASI-Genomics Symposium

EASIGenomics Symposium

Project website, including TA microsite
Online questionnaire ready for assessing user needs

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

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

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

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

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

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

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

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