Chronic periodontitis genome-wide association studies: gene-centric and gene set enrichment analyses. |
| Authors: |
Rhodin, K Divaris, K North, K E Barros, S P Moss, K Beck, J D Offenbacher, S
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| Citation: |
Rhodin K, etal., J Dent Res. 2014 Sep;93(9):882-90. doi: 10.1177/0022034514544506. Epub 2014 Jul 23. |
| RGD ID: |
401938645 |
| Pubmed: |
PMID:25056994 (View Abstract at PubMed) |
| PMCID: |
PMC4213253 (View Article at PubMed Central) |
| DOI: |
DOI:10.1177/0022034514544506 (Journal Full-text) |
Recent genome-wide association studies (GWAS) of chronic periodontitis (CP) offer rich data sources for the investigation of candidate genes, functional elements, and pathways. We used GWAS data of CP (n = 4,504) and periodontal pathogen colonization (n = 1,020) from a cohort of adult Americans of European descent participating in the Atherosclerosis Risk in Communities study and employed a MAGENTA approach (i.e., meta-analysis gene set enrichment of variant associations) to obtain gene-centric and gene set association results corrected for gene size, number of single-nucleotide polymorphisms, and local linkage disequilibrium characteristics based on the human genome build 18 (National Center for Biotechnology Information build 36). We used the Gene Ontology, Ingenuity, KEGG, Panther, Reactome, and Biocarta databases for gene set enrichment analyses. Six genes showed evidence of statistically significant association: 4 with severe CP (NIN, p = 1.6 × 10(-7); ABHD12B, p = 3.6 × 10(-7); WHAMM, p = 1.7 × 10(-6); AP3B2, p = 2.2 × 10(-6)) and 2 with high periodontal pathogen colonization (red complex-KCNK1, p = 3.4 × 10(-7); Porphyromonas gingivalis-DAB2IP, p = 1.0 × 10(-6)). Top-ranked genes for moderate CP were HGD (p = 1.4 × 10(-5)), ZNF675 (p = 1.5 × 10(-5)), TNFRSF10C (p = 2.0 × 10(-5)), and EMR1 (p = 2.0 × 10(-5)). Loci containing NIN, EMR1, KCNK1, and DAB2IP had showed suggestive evidence of association in the earlier single-nucleotide polymorphism-based analyses, whereas WHAMM and AP2B2 emerged as novel candidates. The top gene sets included severe CP ("endoplasmic reticulum membrane," "cytochrome P450," "microsome," and "oxidation reduction") and moderate CP ("regulation of gene expression," "zinc ion binding," "BMP signaling pathway," and "ruffle"). Gene-centric analyses offer a promising avenue for efficient interrogation of large-scale GWAS data. These results highlight genes in previously identified loci and new candidate genes and pathways possibly associated with CP, which will need to be validated via replication and mechanistic studies.
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| Genes (Rattus norvegicus) |
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| Dab2ip (DAB2 interacting protein) | Kcnk1 (potassium two pore domain channel subfamily K member 1) |
| Genes (Mus musculus) |
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| Dab2ip (disabled 2 interacting protein) | Kcnk1 (potassium channel, subfamily K, member 1) |
| Genes (Homo sapiens) |
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| DAB2IP (DAB2 interacting protein) | KCNK1 (potassium two pore domain channel subfamily K member 1) |
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