Evidence map›Paper›PMID 28100911›Full record

ArticleJournal of human genetics2017

Variants on chromosome 4q21 near PKD2 and SIBLINGs are associated with dental caries.

Scott Eckert, Eleanor Feingold, Margaret Cooper, Michael M Vanyukov, Brion S Maher, Rebecca L Slayton, Marcia C Willing, Steven E Reis, Daniel W McNeil, Richard J Crout and 5 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of human genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed, 1 pooled it
1.5field-weighted citation impact, top 19% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed, 1 synthesis or guideline pooled it, 15 citations in OpenAlex.

  1. Pooled it
  2. Trial
  3. Review
  4. Article
  5. Review
  6. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors at 6 institutions in 1 country.

Scott EckertDepartment of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Eleanor FeingoldDepartment of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
Margaret CooperCenter for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Michael M VanyukovDepartment of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
Brion S MaherDepartment of Mental Health, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
Rebecca L SlaytonDepartment of Pediatric Dentistry, School of Dentistry, University of Washington, Seattle, WA, USA.
Marcia C WillingDivision of Genetics and Genomics, Department of Pediatrics, School of Medicine, Washington University at St Louis, St Louis, MO, USA.
Steven E ReisDepartment of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Daniel W McNeilDepartment of Dental Practice and Rural Health, West Virginia University, Morgantown, WV, USA.
Richard J CroutDepartment of Periodontics, School of Dentistry, West Virginia University, Morgantown, WV, USA.
Robert J WeyantDepartment of Dental Public Health and Information Management, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Steven M LevyDepartment of Preventive and Community Dentistry, University of Iowa College of Dentistry, Iowa City, IA, USA.
Alexandre R VieiraCenter for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Mary L MarazitaDepartment of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
John R ShafferDepartment of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.ORCID http://orcid.org/0000-0003-1897-1131
University of Pittsburgh · USWest Virginia University · USJohns Hopkins University · USUniversity of Iowa · USUniversity of Washington · USWashington University in St. Louis · US

Funding

Psychosocial Influences on Rural Children's Oral HealthR01DE014899 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI FOXMAN, BETSY, MARAZITA, MARY L. · 2002 to 2020
$39.9M
TRANSLATION MODULEP50DA005605 · NIDA · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI TARTER, RALPH E · 1989 to 2014
$25.7M
Fluoride & Other Factors in Childhood and Adolescent Bone DevelopmentR01DE012101 · NIDCR · UNIVERSITY OF IOWA · PI LEVY, STEVEN M. · 1998 to 2013
$11.9M
LONGITUDINAL STUDY OF FLUORIDE EXPOSURES &FLUORIDER01DE009551 · NIDCR · UNIVERSITY OF IOWA · PI LEVY, STEVEN M. · 1991 to 2008
$4.7M
Fluoride, Dietary, and Other Factors Related to Young Adult Bone Measures and Dental CariesR56DE012101 · NIDCR · UNIVERSITY OF IOWA · PI LEVY, STEVEN M. · 2015 to 2017
$3.5M
Genetics of CariesR01DE018914 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI VIEIRA, ALEXANDRE REZENDE · 2009 to 2013
$2.2M
Substance Use Disorder Liability: Candidate Gene SystemR01DA019157 · NIDA · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI VANYUKOV, MICHAEL M · 2004 to 2008
$2.2M
Dental Caries: Whole Genome Association and Gene x Environment StudiesU01DE018903 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L. · 2007 to 2010
$1.2M
Modeling childhood dental caries patterns for genomic and epigenetic analysisR03DE024264 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI SHAFFER, JOHN R · 2015 to 2016
$462k
NIDA NIH HHS P50 DA005605NIDA NIH HHS R01 DA019157NIDCR NIH HHS R01 DE009551NIDCR NIH HHS R01 DE012101NIDCR NIH HHS R01 DE014899NIDCR NIH HHS R01 DE018914NIDCR NIH HHS R03 DE024264NIDCR NIH HHS R56 DE012101NIDCR NIH HHS U01 DE018903
6 · The paper itself

Abstract

A recent genome-wide association study (GWAS) for dental caries nominated the chromosomal region 4q21 near ABCG2, PKD2 and the SIBLING (small integrin-binding ligand N-linked glycoprotein) gene family. In this investigation, we followed up and fine-mapped this region using a tag-SNP (single-nucleotide polymorphism) approach in 13 age- and race-stratified samples from 6 independent studies (N=4089). Participants were assessed for dental caries via intraoral examination and 49 tag-SNPs were genotyped capturing much of the variation in the 4q21 locus. Linear models were used to test for genetic association, while adjusting for sex, age and components of ancestry. SNPs in and near PKD2 showed significant evidence of association in individual samples of black adults (rs17013735, P-value=0.0009) and white adults (rs11938025; P-value=0.0005; rs2725270, P-value=0.003). Meta-analyses across black adult samples recapitulated the association with rs17013735 (P-value=0.003), which occurs at low frequency in non-African populations, possibly explaining the race specificity of the effect. In addition to race-specific associations, we also observed evidence of gene-by-fluoride exposure interaction effects in white adults for SNP rs2725233 upstream of PKD2 (P=0.002). Our results show evidence of regional replication, though no single variant clearly accounted for the original GWAS signal. Therefore, while we interpret our results as strengthening the hypothesis that chromosome 4q21 may impact dental caries, additional work is needed.

Indexed as

Genetic Association StudiesAdultATP Binding Cassette Transporter, Subfamily G, Member 2Black or African AmericanChromosome MappingChromosomes, Human, Pair 4Dental CariesFemaleGenetic Predisposition to DiseaseGenotypeHumansMaleMiddle AgedNeoplasm ProteinsPolymorphism, Single NucleotideProtein Kinase D2ABCG2 protein, humanATP Binding Cassette Transporter, Subfamily G, Member 2Neoplasm ProteinsProtein Kinase D2Protein Kinases

Identifiers

PMID28100911
PMCPMC5367940
OpenAlexW2574116657

What OpenQuestion holds

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Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.