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International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium

Gabriel A. Brat ¹ Griffin M. Weber ¹ Nils Gehlenborg ¹ Paul Avillach ¹ Nathan P. Palmer ¹ Luca Chiovato ² James Cimino ³ Brett K. Beaulieu-Jones ¹ Sehi L'Yi ¹ Mark S. Keller ¹ Douglas S. Bell ⁴ Robert W. Follett ⁴ Lav P. Patel ⁵ Anne Sophie Jannot ⁶ Lemuel R. Waitman ⁵ Gilbert Omenn ⁷ Alberto Malovini ⁸ Jason H. Moore ⁹ Valentina Tibollo ⁸ Shawn N Murphy ¹⁰ Riccardo Bellazzi ¹¹ David A Hanauer ¹² Arnaud Serret-Larmande ¹³ Alba Gutierrez-Sacristan ¹ John J Holmes ⁹ Douglas Bell ⁴ Kenneth D. Mandl ¹⁴ Jeffrey G Klann ¹⁰ Douglas A Murad ⁴ Luigia Scudeller ¹⁵ Mauro Bucalo ¹⁶ Katie Kirchoff ¹⁷ Jean Craig ¹⁷ Jihad Obeid ¹⁷ Vianney Jouhet ^{18, 19} Romain Griffier ²⁰ Sébastien Cossin ^{21, 19} Bertrand Moal ²² Antonio Bellasi ²³ Hans U Prokosch ²⁴ Detlef Kraska ²⁵ Piotr Sliz ¹⁴ Amelia L.M. Tan ¹ Kee Yuan Ngiam ²⁶ Alberto Zambelli ²³ Danielle L Mowery ⁹ Emily Schiver ⁹ Batsal Devkota ²⁷ Robert Bradford ²⁸ Mohamad Daniar ¹⁴ Christel Daniel ²⁹ Vincent Benoit ²⁹ Romain Bey ²⁹ Nicolas Paris ²⁹ Patricia Serre ²⁹ Nina Orlova ²⁹ Julien Dubiel ²⁹ Martin Hilka ²⁹ Stephane Breant ²⁹ Judith Leblanc ³⁰ Nicolas Griffon ³¹ Anita Burgun ³² Melodie Bernaux ²⁹ Arnaud Sandrin ²⁹ Elisa Salamanca ²⁹ Sylvie Cormont ²⁹ Thomas Ganslandt ³³ Tobias Gradinger ³³ Julien Champ ³⁴ Martin Boeker ³⁵ Patricia Martel ²⁹ Loïc Estève ³⁶ Alexandre Gramfort ³⁶ Olivier Grisel ³⁶ Damien Leprovost ³⁷ Thomas Moreau ³⁶ Gael Varoquaux ^{36, 38, 39} Jill-Jênn Vie ^{40, 41} Demian Wassermann ³⁶ Arthur Mensch ³⁶ Charlotte Caucheteux ⁴² Christian Haverkamp ³⁵ Guillaume Lemaître ³⁶ Silvano Bosari ⁴³ Andrew South ⁴⁴ Tianxi Cai ⁴⁵ Isaac Kohane ¹

1 HMS - Harvard Medical School [Boston]

2 University of Pavia

3 UAB - University of Alabama at Birmingham [ Birmingham]

4 David Geffen School of Medicine [Los Angeles]

5 University of Kansas [Kansas City]

6 HEGP - Hôpital Européen Georges Pompidou [APHP]

7 University of Michigan [Ann Arbor]

8 IRCCS Pavia - ICS Maugeri - Istituti Clinici Scientifici Maugeri [Pavia]

9 Perelman School of Medicine

10 Massachusetts General Hospital [Boston]

11 BMI - Laboratory for BioMedical Informatics

12 University of Michigan Medical School [Ann Arbor]

13 AP-HP - Hôpital Bichat - Claude Bernard [Paris]

14 Boston Children's Hospital

15 IRCCS Ospedale San Raffaele [Milan, Italy]

16 BIOMERIS [Pavia]

17 MUSC - Medical University of South Carolina [Charleston]

18 Unité d'épidémiologie, biostatistique et registre des cancers [Poitou-Charentes]

19 BPH - Bordeaux population health

20 CHU Bordeaux [Bordeaux]

21 UB - Université de Bordeaux

22 LBM - Laboratoire de biomécanique

23 Azienda Ospedaliera Ospedale Papa Giovanni XXIII [Bergamo, Italy]

24 FAU - Friedrich-Alexander Universität Erlangen-Nürnberg

25 Universitätsklinikum Erlangen [Erlangen]

26 NUHS - National University Health System [Singapore]

27 CHOP - Children’s Hospital of Philadelphia

28 NC TraCS - North Carolina Translational and Clinical Sciences [Chapel Hill]

29 AP-HP - Assistance publique - Hôpitaux de Paris (AP-HP)

30 2I - Infection et inflammation

31 LITIS - Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes

32 Modélisation Conceptuelle des Connaissances Biomédicales

33 Universität Heidelberg [Heidelberg]

34 ZENITH - Scientific Data Management

LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier, CRISAM - Inria Sophia Antipolis - Méditerranée

35 University of Freiburg [Freiburg]

36 PARIETAL - Modelling brain structure, function and variability based on high-field MRI data

NEUROSPIN - Service NEUROSPIN, Inria Saclay - Ile de France

37 clevy.io - Clevy.io - Agents conversationnels à destination des grandes entreprises et du secteur public [Paris]

38 MILA - Montreal Institute for Learning Algorithms [Montréal]

39 MNI - McConnell Brain Imaging Centre

40 Scool - Scool

Inria Lille - Nord Europe, CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189

41 CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189

42 X - École polytechnique

43 UNIMI - Università degli Studi di Milano [Milano]

44 Jefferson (Philadelphia University + Thomas Jefferson University)

45 Harvard T.H. Chan School of Public Health

Abstract : We leveraged the largely untapped resource of electronic health record data to address critical clinical and epidemiological questions about Coronavirus Disease 2019 (COVID-19). To do this, we formed an international consortium (4CE) of 96 hospitals across 5 countries (www.covidclinical.net). Contributors utilized the Informatics for Integrating Biology and the Bedside (i2b2) or Observational Medical Outcomes Partnership (OMOP) platforms to map to a common data model. The group focused on comorbidities and temporal changes in key laboratory test values. Harmonized data were analyzed locally and converted to a shared aggregate form for rapid analysis and visualization of regional differences and global commonalities. Data covered 27,584 COVID-19 cases with 187,802 laboratory tests. Case counts and laboratory trajectories were concordant with existing literature. Laboratory tests at the time of diagnosis showed hospital-level differences equivalent to country-level variation across the consortium partners. Despite the limitations of decentralized data generation, we established a framework to capture the trajectory of COVID-19 disease in patients and their response to interventions.

Keywords : Databases Outcomes research Viral infection

Document type :

Journal articles

Domain :

Physics [physics] / Physics [physics] / Atomic Physics [physics.atom-ph]

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https://hal.archives-ouvertes.fr/hal-02918344
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Submitted on : Friday, August 21, 2020 - 10:32:49 PM
Last modification on : Friday, August 5, 2022 - 3:03:28 PM
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