Journal article
Phenotype Harmonization in the GLIDE2 Oral Health Genomics Consortium
Journal of dental research, Vol.101(11), pp.1408-1416
08/24/2022
DOI: 10.1177/00220345221109775
PMCID: PMC9516613
PMID: 36000800
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.
Details
- Title: Subtitle
- Phenotype Harmonization in the GLIDE2 Oral Health Genomics Consortium
- Creators
- K. Divaris - University of North Carolina at Chapel HillS. Haworth - University of BristolJ. R. Shaffer - University of PittsburghV Anttonen - University of OuluJ. D. Beck - Univ North Carolina Chapel Hill, Div Comprehens Oral Hlth Periodontol, Adams Sch Dent, Chapel Hill, NC USAY. Furuichi - Health Sciences University of HokkaidoB. Holtfreter - Universitätsmedizin GreifswaldD. Jonsson - Public Dental Service Västra GötalandT. Kocher - Universitätsmedizin GreifswaldS. M. Levy - Univ Iowa, Coll Dent, Dept Prevent & Community Dent, Iowa City, IA 52242 USAP. K. E. Magnusson - Karolinska InstitutetD. W. McNeil - Ctr Oral Hlth Res Appalachia, Appalachia, NY USAK. Michaelsson - Uppsala UniversityK. E. North - Univ North Carolina Chapel Hill, Dept Epidemiol, Gillings Sch Global Publ Hlth, Chapel Hill, NC USAU. Palotie - University of HelsinkiP. N. Papapanou - Columbia UniversityP. J. Pussinen - University of HelsinkiD. Porteous - Edinburgh Cancer ResearchK. Reis - University of TartuA. Salminen - University of HelsinkiA. S. Schaefer - Charite Univ Med Berlin, Inst Dent & Craniofacial Sci, Dept Periodontol Oral Med & Oral Surg, Berlin, GermanyT. Sudo - Tokyo Medical and Dental UniversityY. Q. Sun - Norwegian University of Science and TechnologyA. L. Suominen - University of Eastern FinlandT. Tamahara - Tohoku Medical Megabank OrganizationS. M. Weinberg - University of PittsburghP. Lundberg - Umeå UniversityM. L. Marazita - University of PittsburghI Johansson - Umeå University
- Resource Type
- Journal article
- Publication Details
- Journal of dental research, Vol.101(11), pp.1408-1416
- DOI
- 10.1177/00220345221109775
- PMID
- 36000800
- PMCID
- PMC9516613
- NLM abbreviation
- J Dent Res
- ISSN
- 0022-0345
- eISSN
- 1544-0591
- Publisher
- Sage
- Number of pages
- 9
- Grant note
- Ministry of Cultural Affairs RV-96458; RV-832371 / County Council of Vasterbotten Social Ministry of the Federal State of Mecklenburg-West Pomerania 01ZZ9603; 01ZZ0103; 01ZZ0403 / Federal Ministry of Education and Research; Federal Ministry of Education & Research (BMBF) R01-DE014899; U01-DE018903; X01-HG009878-01 / US National Institutes of Health (NIH); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA 2017-00644; 2017-06100; 2017-00641; 2020-00930; 2015-02597 / Swedish Research Council; European Commission Siemens Healthcare, Erlangen, Germany; Siemens AG R01-DE014899; U01-DE018903; R01-DE09551; X01-HG008978; P30-DE10126; R01-DE016148; X01-HG00784; X01-HG011437; U01-DE025046 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
- Language
- English
- Date published
- 08/24/2022
- Academic Unit
- Preventive and Community Dentistry; Epidemiology
- Record Identifier
- 9984367651902771
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