Evidence map›Paper›PMID 25663376›Full record

ArticleGenetic epidemiology2015

Gene-Gene Interaction Among WNT Genes for Oral Cleft in Trios.

Qing Li, Yoonhee Kim, Bhoom Suktitipat, Jacqueline B Hetmanski, Mary L Marazita, Priya Duggal, Terri H Beaty, Joan E Bailey-Wilson

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genetic epidemiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
21citing papers in PubMed, 1 pooled it
3.0field-weighted citation impact, top 9% 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

21 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.

  1. Pooled it
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  9. Brief Survey on Machine Learning in Epistasis.Methods in molecular biology (Clifton, N.J.) · 2021
    Review
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  18. Exon sequencing reveals that missense mutation ofInternational journal of clinical and experimental pathology · 2019
    Article
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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

8 authors at 4 institutions in 2 countries.

Qing LiComputational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America.
Yoonhee KimComputational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America.
Bhoom SuktitipatComputational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America.
Jacqueline B HetmanskiDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America.
Mary L MarazitaDepartment of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
Priya DuggalDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America.
Terri H BeatyDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America.
Joan E Bailey-WilsonComputational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America.
Johns Hopkins University · USNational Human Genome Research Institute · USNational Institutes of Health · USUniversity of Pittsburgh · US

Funding

Extending the Phenotype of Nonsyndromic Orofacial CleftsR01DE016148 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L., WEINBERG, SETH M · 2004 to 2018
$19.7M
Genetic Epidemiology of Complex TraitsZIAHG200327 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI BAILEY-WILSON, JOAN ELLEN · 2009 to 2022
$10.5M
PHENOTYPE AND GENETICS IN OROFACIAL CLEFT FAMILIESP50DE016215 · NIDCR · UNIVERSITY OF IOWA · PI LOVETT, MICHAEL · 2004 to 2008
$10.1M
Molecular Genetic Epidemiology of Cleft Lip and PalateR37DE008559 · NIDCR · UNIVERSITY OF IOWA · PI MURRAY, JEFFREY C · 2004 to 2013
$6.8M
International Genetic Epidemiology of Oral CleftsR01DE014581 · NIDCR · JOHNS HOPKINS UNIVERSITY · PI BEATY, TERRI H · 2004 to 2013
$6.6M
Development of statistical genetics methodologyZIAHG000153 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI BAILEY-WILSON, JOAN ELLEN · 2009 to 2022
$5.0M
International Consortium to Identify Genes and Interactions Controlling Oral ClefU01DE018993 · NIDCR · JOHNS HOPKINS UNIVERSITY · PI BEATY, TERRI H · 2007 to 2008
$1.6M
GENETIC MAPPING STUDIES OF ORAL-FACIAL CLEFTS IN CHINAR01DE009886 · NIDCR · VIRGINIA COMMONWEALTH UNIVERSITY · PI MARAZITA, MARY L · 1992 to 2002
$1.0M
Nutrition and Oral Clefts in Asia: Planning GrantR21DE016877 · NIDCR · UTAH STATE UNIVERSITY · PI MUNGER, RONALD G · 2009 to 2010
$381k
Planning International Orofacial Cleft Genetic StudiesR21DE016930 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L · 2006 to 2007
$293k
HOMOZYGOSITY MAPPING OF ORAL-FACIAL CLEFTS IN TURKEYR01DE012472 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L · 1998 to 2000
$241k
Intramural NIH HHS Z99 DE999999Intramural NIH HHS Z99 HG999999Intramural NIH HHS ZIA HG200327NHGRI NIH HHS HHSN268200782096CNICHD NIH HHS R01-HD390661NIDCR NIH HHS P50 DE016215NIDCR NIH HHS P50-DE016215NIDCR NIH HHS R01 DE009886NIDCR NIH HHS R01-DE012472NIDCR NIH HHS R01 DE014581NIDCR NIH HHS R01-DE-014581NIDCR NIH HHS R01-DE014677NIDCR NIH HHS R01 DE016148NIDCR NIH HHS R01-DE016148NIDCR NIH HHS R01-DE016877NIDCR NIH HHS R01-DE09886NIDCR NIH HHS R21 DE016877NIDCR NIH HHS R21 DE016930NIDCR NIH HHS R21-DE016930NIDCR NIH HHS R37 DE008559NIDCR NIH HHS R37-DE08559NIDCR NIH HHS U01 DE018993NIDCR NIH HHS U01-DE-018993
6 · The paper itself

Abstract

Genome-wide association studies (GWAS) for nonsyndromic cleft lip with or without cleft palate (CL/P) have identified multiple genes as important in the etiology of this common birth defect. We performed a candidate gene/pathway analysis explicitly considering gene-gene (G × G) interaction to further explore the etiology of CL/P. Animal models have shown the WNT signaling pathway plays an important role in mid-facial development, and various genes in this pathway have been associated with nonsyndromic CL/P in previous studies. We propose a combined approach to search for possible G × G interactions using machine learning and regression-based methods to test for interactions between genes in the WNT family, and between these genes and other genes identified by GWAS in case-parent trios. Using this combined approach of regression-based and machine learning methods in CL/P case-parent trios, we found robust evidence of G × G interaction between markers in WNT5B and MAFB (empiric P-values = 0.0076 among Asian trios and P-values = 0.018 among European trios). Additional evidence for epistatic interaction between markers in WNT5A, IRF6, and C1orf107 was seen among Asian trios, and markers in the 8q24 region and WNT5B among European trios.

Indexed as

Artificial IntelligenceAsian PeopleCleft LipCleft PalateEpistasis, GeneticEthnicityGenome-Wide Association StudyHumansInterferon Regulatory FactorsModels, GeneticParentsPolymorphism, Single NucleotideProto-Oncogene ProteinsWhite PeopleWnt-5a ProteinWnt ProteinsInterferon Regulatory FactorsIRF6 protein, humanProto-Oncogene ProteinsWnt-5a ProteinWNT5A protein, humanWNT5B protein, humanWnt Proteinscomplex diseasefamily-based studymachine learning

Identifiers

PMID25663376
PMCPMC4469492
OpenAlexW1516844016

What OpenQuestion holds

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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.