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A first update on mapping the human genetic architecture of COVID-19
Gita A. Pathak, Juha Karjalainen, Christine Stevens, Mark J. Daly, Andrea Ganna, Shea J. Andrews, Masahiro Kanai, Renato Polimanti, Nadia V. Harerimana, Matti Pirinen, Rachel G. Liao, Karolina Chwiałkowska, Amy Trankiem, Mary K. Balaconis, Huy Nguyen, Matthew Solomonson, Kumar Veerapen, Genevieve Roberts, Catherine A. Ball, Marie V. Coignet, Shannon McCurdy, Spencer C. Knight, Raghavendran Partha, Brooke Rhead, Miao Zhang, Nathan Berkowitz, Michael Gaddis, Keith Noto, Luong Ruiz, Miloš Pavlović, Eurie L. Hong, Kristin A. Rand, Ahna R. Girshick, Harendra Guturu, Asher Haug Baltzell, Mari Niemi, Souad Rahmouni, Julien Guntz, Y Beguin, Sara Pigazzini, Lindokuhle Nkambule, Michel Georges, Michel Moutschen, Benoît Misset, Gilles Darcis, Julien Guiot, Samira Azarzar, Stéphanie Gofflot, Sabine Claassen, Olivier Malaise, Pascale Huynen, Christelle Meuris, Marie Thys, Jessica Jacques, Philippe Léonard, Frédéric Frippiat, Jean‐Baptiste Giot, Anne-Sophie Sauvage, Christian Von Frenckell, Yasmine Belhaj, Bernard Lambermont, Tomoko Nakanishi, David Morrison, Vincent Mooser, J. 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J. Timmers, James F. Wilson, Albert Tenesa, Shona M. Kerr, Kenton D’Mellow, Doaa Shahin, Yasser M. El‐Sherbiny, Kathrin Aprile von Hohenstaufen, Ali Sobh, Madonna M. Eltoukhy, Lindokuhle Nkambul, Tamer Elhadidy, Mohamed S. Abd Elghafar, Jehan J. El‐Jawhari, Attia A. S. Mohamed, Marwa H. Elnagdy, Amr Samir, Mahmoud Abdel-Aziz, Walid T. Khafaga, Walaa M. El-Lawaty, Mohamed Torky, Mohamed El‐Shanshory, Amr M. Yassen, M. Hegazy, Kamal Okasha, Mohammed Eid, Hanteera S. Moahmed, Carolina Medina‐Gómez, M. Arfan Ikram, André G. Uitterlinden, Reedik Mägi, Lili Milani, Andres Metspalu, Triin Laisk, Kristi Läll, Maarja Lepamets, Tõnu Esko, Ene Reimann, Paul Naaber, Edward Laane, Jaana Pesukova, Pärt Peterson, Kai Kisand, Jekaterina Tabri, Raili Allos, Kati Hensen, Joel Starkopf, Inge Ringmets, Anu Tamm, Anne Kallaste, Helene Alavere, Kristjan Metsalu, Mairo Puusepp, Chiara Batini, Martin D. Tobin, Laura D. Venn, Paul H. Lee, Nick Shrine, Alexander T. Williams, Anna L. 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Pantet, Pierre–Yves Bochud, Valérie D’Acremont, S. Estoppey Younes, A. Cerny, L. O’Mahony, C. von Mering, Mirjam Frischknecht, G-R. Kleger, M. Filipovic, C. R. Kahlert, Hannah Wozniak, Tommaso Rochat Negro, J. Pugin, Konstantinos Bouras, C. Knapp, Thomas Egger, A. Perret, P. Montillier, C. di Bartolomeo, Beatrice Barda, Rafael de Cid, Anna Carreras, Vı́ctor Moreno, Manolis Kogevinas, Iván Galván‐Femenía, Natàlia Blay, Xavier Farré, Lauro Sumoy, Beatriz Cortés, Josep M. Mercader, Marta Guindo-Martínez, David Torrents, Judith García‐Aymerich, Gemma Castaño‐Vinyals, Carlota Dobaño, Marco Gori, Alessandra Renieri, Francesca Mari, Mario U. 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MacArthur, Bev MacLaughlin, Shefa Miah, Nishat Safa, Farah Tahmasebi, Albert V. Smith, Andrew P. Boughton, Kevin Li, Jonathon LeFaive, Aubrey Annis, Ahmadreza Niavarani, Rasoul Aliannejad, Bahareh Sharififard, Ali Amirsavadkouhi, Zeinab Naderpour, Hengameh Ansari Tadi, Afshar Etemadi-Aleagha, Saeideh Ahmadi, Seyed Behrooz Mohseni Moghaddam, Alireza Adamsara, Morteza Saeedi, Hamed Abdollahi, Abdolmajid Hosseini, Pajaree Chariyavilaskul, Watsamon Jantarabenjakul, Nattiya Hirankarn, Monpat Chamnanphon, Thitima B. Suttichet, Vorasuk Shotelersuk, Monnat Pongpanich, Chureerat Phokaew, Wanna Chetruengchai, Opass Putchareon, Pattama Torvorapanit, Thanyawee Puthanakit, Pintip Suchartlikitwong, Voraphoj Nilaratanakul, Pimpayao Sodsai, Ben Brumpton, Kristian Hveem, Cristen J. Willer, Wei Zhou, Tormod Rogne, Erik Solligård, Bjørn Olav Åsvold, Lude Franke, Marike Boezen, Patrick Deelen, Annique Claringbould, Robert Warmerdam, Judith M. Vonk, Irene V. van Blokland, Pauline Lanting, Anil P. S. Ori, Yen‐Chen Anne Feng, Scott T. Weiss, Elizabeth W. Karlson, Jordan W. Smoller, Shawn N. Murphy, James B. Meigs, Ann E. Woolley, Emma Perez, Brooke N. Wolford, Sebastian Zöllner, Jiongming Wang, Andrew F. Beck, Laura Sloofman, Steven Ascolillo, Robert Sebra, Brett Collins, Tess Levy, Joseph D. Buxbaum, Stuart C. Sealfon, Daniel M. Jordan, Ryan C. Thompson, Kyle Gettler, Kumardeep Chaudhary, Gillian M. Belbin, Michael Preuß, Clive Hoggart, Sam Choi, Slayton J. Underwood, Irene Salib, Bari Britvan, Katherine Keller, Lara Tang, Michael Peruggia, Liam L. Hiester, Kristi Niblo, Alexandra Aksentijevich, Alexander Labkowsky, Avrohom Karp, Menachem Zlatopolsky, Marissa Zyndorf, Alexander W. Charney, Noam D. Beckmann, Eric E. Schadt, Noura S. Abul‐Husn, Judy H. Cho, Yuval Itan, Eimear E. Kenny, Ruth J. F. Loos, Girish N. Nadkarni, Ron Do, Paul F. O’Reilly, Laura M. Huckins, Manuel A. R. Ferreira, Gonçalo R. Abecasis, Joseph B. Leader, Michael Cantor, Anne E. Justice, Dave J. Carey, Geetha Chittoor, Navya Shilpa Josyula, Jack A. Kosmicki, Julie Horowitz, Aris Baras, Matthew C. Gass, Ashish Yadav, Tooraj Mirshahi, Meike Bartels, Eco J. C. de Geus, Michel G. Nivard, Anurag Verma, Marylyn D. Ritchie, Daniel J. Rader, Binglan Li, Shefali S. Verma, Anastasia Lucas, Yuki Bradford, Malak Abedalthagafi, Manal Alaamery, Abdulraheem Alshareef, Mona Sawaji, Salam Massadeh, Abdulaziz Almalik, Saleh A. Alqahtani, Dona Baraka, Fawz Al Harthi, Ebtehal Alsolm, Leen Abu Safieh, Albandary M. Alowayn, Fatimah Alqubaishi, Amal Al Mutairi, Serghei Mangul, Mansour Almutairi, Nora Aljawini, Nour Albesher, Yaseen M. Arabi, Ebrahim Mahmoud, Amin Khattab, Roaa T. Halawani, Ziab Z. Alahmadey, Jehad K. Albakri, Walaa A. Felemban, Bandar A. Suliman, Rana Hasanato, Laila Alawdah, Jahad Alghamdi, Deema AlZahrani, Sameera Aljohani, Hani Al-Afghani, Nouf AlDhawi, Hadeel AlBardis, Sarah Alkwai, Moneera Alswailm, Faisal A. 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Bibliographic record
VenueNature · 2022
Typeletter
Languageen
FieldMedicine
TopicSARS-CoV-2 and COVID-19 Research
Canadian institutionsMcGill University Health CentreUniversité de MontréalMcGill Genome CentreJewish General HospitalCentre Hospitalier de l’Université de MontréalMcGill University
FundersMedical Research CouncilNational Institutes of HealthWellcome TrustNational Institute of Environmental Health SciencesEuropean Hematology Association
KeywordsCoronavirus disease 2019 (COVID-19)2019-20 coronavirus outbreakSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)ArchitectureComputational biologyBiologyEvolutionary biologyComputer scienceVirologyGeographyMedicineDiseaseOutbreakInfectious disease (medical specialty)
Abstract
The COVID-19 pandemic continues to pose a major public health threat,\nespecially in countries with low vaccination rates. To better understand\nthe biological underpinnings of SARS-CoV-2 infection and COVID-19\nseverity, we formed the COVID-19 Host Genetics Initiative1\n. Here we\npresent a genome-wide association study meta-analysis of up to 125,584\ncases and over 2.5 million control individuals across 60 studies from\n25 countries, adding 11 genome-wide significant loci compared with\nthose previously identified2\n. Genes at new loci, including SFTPD, MUC5B\nand ACE2, reveal compelling insights regarding disease susceptibility\nand severity
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMeta-epidemiology (narrow), Research integrity
Consensus categoriesResearch integrity
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Commentary · Consensus signal: Commentary
Teacher disagreement score0.021
Threshold uncertainty score1.000
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.003 | 0.024 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
Opus teacher head0.040
GPT teacher head0.340
Teacher spread0.300 · how far apart the two teachers sit on this one work
Validation status
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; both teacher heads agree on what is shown here.
Study designNot applicable
Domainnot available
GenreCommentary
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".
Quick stats
Citations174
Published2022
Admission routes1
Has abstractyes