Phenotype Harmonization in the GLIDE2 Oral Health Genomics Consortium

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Creator
  • Divaris, K.
    • Affiliation: Gillings School of Global Public Health, Department of Epidemiology
  • Haworth, S.
    • Other Affiliation: University of Bristol
  • Shaffer, J.R.
    • Other Affiliation: University of Pittsburgh
  • Anttonen, V.
    • Other Affiliation: University of Oulu
  • Beck, J.D.
    • Affiliation: School of Dentistry
  • Furuichi, Y.
    • Other Affiliation: Health Sciences University of Hokkaido
  • Holtfreter, B.
    • Other Affiliation: University Medicine Greifswald
  • Jönsson, D.
    • Other Affiliation: Malmö University
  • Kocher, T.
    • Other Affiliation: University Medicine Greifswald
  • Levy, S.M.
    • Other Affiliation: University of Iowa
  • Magnusson, P.K.E.
    • Other Affiliation: Karolinska Institutet
  • McNeil, D.W.
    • Other Affiliation: West Virginia University
  • Michaëlsson, K.
    • Other Affiliation: Uppsala University
  • North, K.E.
    • Affiliation: Gillings School of Global Public Health, Department of Epidemiology
  • Palotie, U.
    • Other Affiliation: University of Helsinki
  • Papapanou, P.N.
    • Other Affiliation: Columbia University
  • Pussinen, P.J.
    • Other Affiliation: University of Eastern Finland
  • Porteous, D.
    • Other Affiliation: University of Edinburgh
  • Reis, K.
    • Other Affiliation: University of Tartu
  • Salminen, A.
    • Other Affiliation: University of Helsinki
  • Schaefer, A.S.
    • Other Affiliation: Charité–Universitätsmedizin Berlin
  • Sudo, T.
    • Other Affiliation: Tokyo Medical and Dental University
  • Sun, Y.Q.
    • Other Affiliation: Norwegian University of Science and Technology
  • Suominen, A.L.
    • Other Affiliation: Kuopio University Hospital
  • Tamahara, T.
    • Other Affiliation: Tohoku University
  • Weinberg, S.M.
    • Other Affiliation: University of Pittsburgh
  • Lundberg, P.
    • Other Affiliation: Umeå University
  • Marazita, M.L.
    • Other Affiliation: University of Pittsburgh
  • Johansson, I.
    • Other Affiliation: Umeå University
Abstract
  • Genetic risk factors play important roles in the etiology of oral, dental, and craniofacial diseases. Identifying the relevant risk loci and understanding their molecular biology could highlight new prevention and management avenues. Our current understanding of oral health genomics suggests that dental caries and periodontitis are polygenic diseases, and very large sample sizes and informative phenotypic measures are required to discover signals and adequately map associations across the human genome. In this article, we introduce the second wave of the Gene-Lifestyle Interactions and Dental Endpoints consortium (GLIDE2) and discuss relevant data analytics challenges, opportunities, and applications. In this phase, the consortium comprises a diverse, multiethnic sample of over 700,000 participants from 21 studies contributing clinical data on dental caries experience and periodontitis. We outline the methodological challenges of combining data from heterogeneous populations, as well as the data reduction problem in resolving detailed clinical examination records into tractable phenotypes, and describe a strategy that addresses this. Specifically, we propose a 3-tiered phenotyping approach aimed at leveraging both the large sample size in the consortium and the detailed clinical information available in some studies, wherein binary, severity-encompassing, and ?precision,? data-driven clinical traits are employed. As an illustration of the use of data-driven traits across multiple cohorts, we present an application of dental caries experience data harmonization in 8 participating studies (N = 55,143) using previously developed permanent dentition tooth surface?level dental caries pattern traits. We demonstrate that these clinical patterns are transferable across multiple cohorts, have similar relative contributions within each study, and thus are prime targets for genetic interrogation in the expanded and diverse multiethnic sample of GLIDE2. We anticipate that results from GLIDE2 will decisively advance the knowledge base of mechanisms at play in oral, dental, and craniofacial health and disease and further catalyze international collaboration and data and resource sharing in genomics research.
Date of publication
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DOI
Identifier
Resource type
  • Article
Rights statement
  • In Copyright
License
  • Attribution 4.0 International
Journal title
  • Journal of Dental Research
Journal volume
  • 101
Journal issue
  • 11
Page start
  • 1408
Page end
  • 1416
Language
  • English
Version
  • Publisher
Funder
  • National Institutes of Health, NIH: P30-DE10126, R01-DE014899, R01-DE016148, R01-DE09551, U01-DE018903, X01-HG00784, X01-HG008978, X01-HG009878-01, X01-HG011437; Bundesministerium für Bildung und Forschung, BMBF: 01ZZ0103, 01ZZ0403, 01ZZ9603; Västerbotten Läns Landsting: 2015-02597, 2020-00930, RV-832371, RV-96458, U01-DE025046; Karolinska Institutet, KI: 2017-00641; Vetenskapsrådet, VR: 2017-00644, 2017-06100; Ministry of Cultural Affairs
ISSN
  • 0022-0345
Publisher
  • SAGE Publications Ltd

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