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Integrating GWAS and eQTL to predict genes and pathways for non-syndromic cleft lip with or without palate.
- Source :
-
Oral diseases [Oral Dis] 2021 Oct; Vol. 27 (7), pp. 1747-1754. Date of Electronic Publication: 2020 Dec 14. - Publication Year :
- 2021
-
Abstract
- Objective: To explore susceptibility genes and pathways for non-syndromic cleft lip with or without cleft palate (NSCL/P).<br />Materials and Methods: Two genome-wide association studies (GWAS) datasets, including 858 NSCL/P cases and 1,248 controls, were integrated with expression quantitative trait loci (eQTL) dataset identified by Genotype-Tissue Expression (GTEx) project in whole-blood samples. The expression of the candidate genes in mouse orofacial development was inquired from FaceBase. Protein-protein interaction (PPI) network was visualized to identify protein functions. Go and KEGG pathway analyses were performed to explore the underlying risk pathways.<br />Results: A total of 233 eQTL single-nucleotide polymorphisms (SNPs) in 432 candidate genes were identified to be associated with the risk of NSCL/P. One hundred and eighty-three susceptible genes were expressed in mouse orofacial development according to FaceBase. PPI network analysis highlighted that these genes involved in ubiquitin-mediated proteolysis (KCTD7, ASB1, UBOX5, ANAPC4) and DNA synthesis (XRCC3, RFC3, KAT5, RHNO1) were associated with the risk of NSCL/P. GO and KEGG pathway analyses revealed that the fatty acid metabolism pathway (ACADL, HSD17B12, ACSL5, PPT1, MCAT) played an important role in the development of NSCL/P.<br />Conclusions: Our results identified novel susceptibility genes and pathways associated with the development of NSCL/P.<br /> (© 2020 Wiley Periodicals LLC.)
- Subjects :
- 17-Hydroxysteroid Dehydrogenases
Animals
Case-Control Studies
Genetic Predisposition to Disease
Genome-Wide Association Study
Genotype
Mice
Polymorphism, Single Nucleotide
Potassium Channels
Quantitative Trait Loci genetics
Suppressor of Cytokine Signaling Proteins
Cleft Lip genetics
Cleft Palate genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1601-0825
- Volume :
- 27
- Issue :
- 7
- Database :
- MEDLINE
- Journal :
- Oral diseases
- Publication Type :
- Academic Journal
- Accession number :
- 33128317
- Full Text :
- https://doi.org/10.1111/odi.13699