University of Oulu

Divaris K, Haworth S, Shaffer JR, et al. Phenotype Harmonization in the GLIDE2 Oral Health Genomics Consortium. Journal of Dental Research. 2022;101(11):1408-1416. doi:10.1177/00220345221109775

Phenotype harmonization in the GLIDE2 oral health genomics consortium

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Author: Divaris, K.1,2; Haworth, S.3,4; Shaffer, J.R.5,6;
Organizations: 1Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
3Medical Research Council Integrative Epidemiology United, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
4Bristol Dental School, University of Bristol, Bristol, UK
5Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
6Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
7Research Unit of Oral Health Sciences, Faculty of Medicine, University of Oulu, Oulu, Finland
8Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
9Division of Comprehensive Oral Health–Periodontology, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
10Division of Endodontology and Periodontology, Department of Oral Rehabilitation, Graduate School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, Japan
11Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
12Public Dental Service of Skåne, Lund, Sweden
13Hypertension and Cardiovascular Disease, Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
14Faculty of Odontology, Malmö University, Malmö, Sweden
15Department of Preventive and Community Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
16Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
17Center for Oral Health Research in Appalachia, Appalachia, NY, USA
18Department of Psychology, West Virginia University, Morgantown, WV, USA
19Department of Dental Public Health & Professional Practice, West Virginia University, Morgantown, WV, USA
20Department of Surgical Sciences, Unit of Medical Epidemiology, Uppsala University, Uppsala, Sweden
21Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
22Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
23Division of Periodontics, Section of Oral, Diagnostic and Rehabilitation Sciences, Columbia University, College of Dental Medicine, New York, NY, USA
24Institute of Dentistry, School on Medicine, University of Eastern Finland, Kuopio, Finland
25Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
26Institute of Genomics, University of Tartu, Tartu, Estonia
27Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité–Universitätsmedizin Berlin, Berlin, Germany
28Institute of Education, Tokyo Medical and Dental University, Tokyo, Japan
29Center for Oral Health Services and Research Mid-Norway (TkMidt), Trondheim, Norway
30Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
31Department of Oral and Maxillofacial Diseases, Kuopio University Hospital, Kuopio, Finland
32Public Health Evaluation and Projection Unit, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
33Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
34Department of Odontology, Section of Molecular Periodontology, Umeå University, Umeå, Sweden
35Department of Odontology, Section of Cariology, Umeå University, Umeå, Sweden
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.5 MB)
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Language: English
Published: SAGE Publications, 2022
Publish Date: 2023-05-26


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.

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Series: Journal of dental research
ISSN: 0022-0345
ISSN-E: 1544-0591
ISSN-L: 0022-0345
Volume: 101
Issue: 11
Pages: 1408 - 1416
DOI: 10.1177/00220345221109775
Type of Publication: A1 Journal article – refereed
Field of Science: 3111 Biomedicine
313 Dentistry
Funding: The authors disclosed receipt of th following financial support for the research, authorship, and/or publication of this article: Funding support for participating studies and investigators is also acknowledged: CCDG: COHRA1/Dental SCORE and CCDG: COHRA2/COHRA Smile were supported by US National Institutes of Health (NIH) grants R01-DE014899, U01-DE018903, and X01-HG009878-01. IFS was supported by NIH grants R01-DE09551, U01-DE018903, X01-HG008978, R01-DE014899, and P30-DE10126. CCDG: OFC1 and CCDG: OFC2 were sup-ported by NIH grants R01-DE016148, X01-HG00784, and X01-HG011437. HIP is funded by the Federal Ministry of Education and Research (grants 01ZZ9603, 01ZZ0103, and 01ZZ0403), the Ministry of Cultural Affairs, and the Social Ministry of theFederal State of Mecklenburg–West Pomerania and Siemens Healthcare, Erlangen, Germany. SIMPLER receives funding through the Swedish Research Council under grants 2017-00644 and 2017-06100. The Swedish Twin Registry is managed by Karolinska Institutet and receives funding through the Swedish Research Council under grant 2017-00641. Periogene North was funded by the County Council of Västerbotten under grants RV-96458 and RV-832371. The Swedish GLIDE receives fund-ing through the Swedish Research Council under grants 2020-00930 and 2015-02597. K. Divaris acknowledges support by NIH grant U01-DE025046.
Copyright information: © International Association for Dental Research and American Association for Dental, Oral, and Craniofacial Research 2022. This article is distributed under the terms of the Creative Commons Attribution 4.0 License ( which permits any use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (