Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19
A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF-7 dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 wi...
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| Vydáno v: | The Journal of clinical investigation Ročník 131; číslo 14 |
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| Médium: | Journal Article |
| Jazyk: | angličtina |
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American Society for Clinical Investigation
15.07.2021
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| ISSN: | 1558-8238, 0021-9738, 1558-8238 |
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| Abstract | A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF-7 dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 with mild disease) and 15,033 ancestry- matched population controls across 4 independent COVID-19 biobanks. We tested whether rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only 1 rare pLOF mutation across these genes among 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We found no evidence of association of rare LOF variants in the 13 candidate genes with severe COVID-19 outcomes. |
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| AbstractList | A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 with mild disease) and 15,033 ancestry-matched population controls across 4 independent COVID-19 biobanks. We tested whether rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only 1 rare pLOF mutation across these genes among 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We found no evidence of association of rare LOF variants in the 13 candidate genes with severe COVID-19 outcomes. A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF-7 dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 with mild disease) and 15,033 ancestry- matched population controls across 4 independent COVID-19 biobanks. We tested whether rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only 1 rare pLOF mutation across these genes among 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We found no evidence of association of rare LOF variants in the 13 candidate genes with severe COVID-19 outcomes. A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 with mild disease) and 15,033 ancestry-matched population controls across 4 independent COVID-19 biobanks. We tested whether rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only 1 rare pLOF mutation across these genes among 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We found no evidence of association of rare LOF variants in the 13 candidate genes with severe COVID-19 outcomes.A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 with mild disease) and 15,033 ancestry-matched population controls across 4 independent COVID-19 biobanks. We tested whether rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only 1 rare pLOF mutation across these genes among 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We found no evidence of association of rare LOF variants in the 13 candidate genes with severe COVID-19 outcomes. |
| Audience | Academic |
| Author | Shang, Ning Alghamdi, Bader Mbarek, Hamdi Abedalthagafi, Malak S. Scherer, Stephen W. Ragoussis, Jiannis Harthi, Fawz S. Al Alqahtani, Saleh A. Bourque, Guillaume Badji, Radja Suliman, Bandar Ali Knoppers, Bartha Almalik, Abdulaziz Strug, Lisa J. El Bardisy, Hadeel Bourgey, Mathieu Khan, Atlas Alaamery, Manal Lathrop, Mark Saad, Chadi Alghamdi, Jahad Ismail, Said I. Arabi, Yaseen M. Lepage, Pierre Abu-Safieh, Leen Jung, Junghyun Alrashed, May M. Al-Muftah, Wadha Alshareef, Abdulraheem Jones, Steven J.M. Almutairi, Mansour S. Nakanishi, Tomoko Albes, Nour Eveleigh, Robert J.M. Kiryluk, Krzysztof Al-Afghani, Hani M. Povysil, Gundula Goldstein, David B. Mooser, Vincent Mangul, Serghei Richards, J. Brent Butler-Laporte, Guillaume Aziz, Naveed Fawzy, Mohamed Zhou, Sirui Massadeh, Salam Gharavi, Ali G. Forgetta, Vincenzo Thani, Asma Al Wang, Chen Aljawini, Nora Mahmoud, Ebrahim Sabri |
| AuthorAffiliation | 15 Laboratory Department, Security Forces Hospital, General Directorate of Medical Services, Ministry of Interior, Makkah, Saudi Arabia 27 Department of Twin Research, King’s College London, London, United Kingdom 20 Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, USA 22 Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia 10 McGill Genome Center, McGill University, Montréal, Québec, Canada 19 Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia 4 Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA 9 Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada 7 Department of Human Genetics, McGill University, Montréal, Québec, Canada 13 Saudi Biobank, King Abdullah International Medical Research Center, King Saud bin Abdulaziz Un |
| AuthorAffiliation_xml | – name: 8 Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan – name: 17 Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia – name: 15 Laboratory Department, Security Forces Hospital, General Directorate of Medical Services, Ministry of Interior, Makkah, Saudi Arabia – name: 18 College of Applied Medical Sciences, Taibah University, Madina, Saudi Arabia – name: 27 Department of Twin Research, King’s College London, London, United Kingdom – name: 14 KACST-BWH Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia – name: 3 Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada – name: 16 Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia – name: 25 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA – name: 2 Lady Davis Institute for Medical Research, Montréal, Québec, Canada – name: 11 Canadian COVID Genomics Network, HostSeq Project, Canada – name: 7 Department of Human Genetics, McGill University, Montréal, Québec, Canada – name: 12 Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada – name: 13 Saudi Biobank, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia – name: 10 McGill Genome Center, McGill University, Montréal, Québec, Canada – name: 1 Institute for Genomic Medicine, Columbia University, New York, New York, USA – name: 9 Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada – name: 4 Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA – name: 19 Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia – name: 21 Life Science and Environmental Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia – name: 6 Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia – name: 24 Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA – name: 22 Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia – name: 28 Department of Genetics & Development, Columbia University, New York, New York, USA – name: 23 Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar – name: 26 Center for Precision Medicine and Genomics, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA – name: 20 Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, USA – name: 5 Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia |
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| Cites_doi | 10.1038/s41576-019-0177-4 10.1101/2021.03.10.21252820 10.1101/2020.10.28.20221804 10.1001/jamacardio.2020.6500 10.7326/0003-4819-150-3-200902030-00011 10.1126/science.abd4570 |
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| Snippet | A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF-7 dependent type I IFN pathways explain... A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up... |
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| Title | Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19 |
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