Genome-wide association study of chronic periodontitis in a general German population
Aim To identify loci associated with chronic periodontitis through a genome‐wide association study (GWAS). Materials and Methods A GWAS was performed in 4032 individuals of two independent cross‐sectional studies of West Pomerania (SHIP n = 3365 and SHIP‐TREND n = 667) with different periodontal cas...
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| Vydané v: | Journal of clinical periodontology Ročník 40; číslo 11; s. 977 - 985 |
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| Hlavní autori: | , , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
United States
Blackwell Publishing Ltd
01.11.2013
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| Predmet: | |
| ISSN: | 0303-6979, 1600-051X, 1600-051X |
| On-line prístup: | Získať plný text |
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| Shrnutí: | Aim
To identify loci associated with chronic periodontitis through a genome‐wide association study (GWAS).
Materials and Methods
A GWAS was performed in 4032 individuals of two independent cross‐sectional studies of West Pomerania (SHIP n = 3365 and SHIP‐TREND n = 667) with different periodontal case definitions. Samples were genotyped with the Affymetrix Genome‐Wide Human SNP Array 6.0 or the Illumina Human Omni 2.5 array. Imputation of the HapMap as well as the 1000 Genome‐based autosomal and X‐chromosomal genotypes and short insertions and deletions (INDELs) was performed in both cohorts. Finally, more than 17 million SNPs and short INDELs were analysed.
Results
No genome‐wide significant associations were found for any periodontitis case definition, regardless of whether individuals aged >60 years where excluded or not. Despite no single SNP association reached genome‐wide significance, the proportion of variance explained by additive effects of all common SNPs was around 23% for mean proximal attachment loss. Excluding subjects aged >60 years increased the explained variance to 34%.
Conclusions
No single SNPs were found to be genome‐wide significantly associated with chronic periodontitis in this study. |
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| Bibliografia: | Ministry of Cultural Affairs Siemens Healthcare istex:86D83FDE9BABF430CA4475903E71C429C2BB21A8 ArticleID:JCPE12154 GABA Social Ministry of the Federal State of Mecklenburg-West Pomerania Figure S1. GWAS results quantile-quantile plots of all analyzed traits. (a) mean PAL (all individuals); (b) mean PAL (age ≤60 years); (c) PAL4Q3 (all individuals); (d) PAL4Q3 (age ≤60 years); (e) CDC/AAP (all individuals); (f) CDC/AAP (age ≤60 years); (g) DPAL (all individuals); (h) DPAL (age ≤60 years); (i) mean PAL (1000G); (j) CDC/AAP (1000G). Figure S2. GWAS results quantile-quantile plots of SHIP used for meta-analysis. (a) mean PAL (all individuals); (b) mean PAL (age ≤60 years); (c) PAL4Q3 (all individuals); (d) PAL4Q3 (age ≤60 years); (e) CDC/AAP (all individuals); (f) CDC/AAP (age ≤60 years); (g) mean PAL (1000G); (h) CDC/AAP (1000G).Figure S3. GWAS results quantile-quantile plots of SHIP-TREND used for meta-analysis. (a) mean PAL (all individuals); (b) mean PAL (age ≤60 years); (c) PAL4Q3 (all individuals); (d) PAL4Q3 (age ≤60 years); (e) CDC/AAP (all individuals); (f) CDC/AAP (age ≤60 years); (g) mean PAL (1000G); (h) CDC/AAP (1000G). Figure S4. Comparison of the effect sizes of the top SNPs reported in Divaris et al. (ARIC) with the CDC/AAP (all individuals) results. The effects directions are set to have higher odds of chronic periodontitis in the ARIC sample. The SNP identifier and the name of the closest gene are shown. Table S1. Information on genotyping and imputation. Table S2. GWAS results on mean proximal attachment loss related phenotypes with GC corrected p-value < 1E-5 after quality control filters. All individuals were included (meta-analysis of SHIP and SHIP-TREND cohorts, N = 4032). Table S3. GWAS results on periodontitis with GC corrected p-value < 1E-5 after quality control filters. Subjects within the first versus the third tertile of proportion of proximal sites with AL ≥4 mm were opposed. All individuals were included (meta-analysis of SHIP and SHIP-TREND cohorts, N = 2969). Table S4. GWAS results on the CDC/AAP case definition for periodontitis (Page & Eke ) with GC corrected p-value < 1E-5 after quality control filters. All individuals were included (meta-analysis of SHIP and SHIP-TREND cohorts, N = 3915). Table S5. GWAS results on 5-year change in mean proximal attachment loss related phenotypes with GC corrected p-value < 1E-5 after quality control filters. All individuals were included (SHIP cohort, N=2501). Table S6 GWAS results on mean proximal attachment loss with GC corrected p-value < 1E-5 after quality control filters. Individuals aged >60 years were excluded (meta-analysis of SHIP and SHIP-TREND cohorts, N=3189). Table S7. GWAS results on periodontitis with GC corrected p-value < 1E-5 after quality control filters. Subjects within the first versus the third tertile of proportion of proximal sites with AL ≥4 mm were opposed. Individuals aged >60 years were excluded (meta-analysis of SHIP and SHIP-TREND cohorts, N = 2412). Table S8. GWAS results on the CDC/AAP case definition for periodontitis (Page & Eke ) with GC corrected p-value < 1E-5 after quality control filters. Individuals aged >60 years were excluded (meta-analysis of SHIP and SHIP-TREND cohorts, N = 3151). Table S9. GWAS results on 5-year change in mean proximal attachment loss related phenotypes with GC corrected p-value < 1E-5 after quality control filters. Individuals aged >60 years were excluded (SHIP cohort, N = 2098). Table S10. GWAS results on proximal attachment loss related phenotypes with GC corrected p-value < 1E-5 after quality control filters using the 1000 Genomes imputation. Individuals aged >60 years were excluded (meta-analysis of SHIP and SHIP-TREND cohorts, N = 3189). Table S11. GWAS results on the CDC/AAP case definition for periodontitis (Page & Eke ) with GC corrected p-value < 1E-5 after quality control filters using the 1000 Genomes imputation. Individuals aged >60 years excluded (meta-analysis of SHIP and SHIP-TREND cohorts, N = 3151). ark:/67375/WNG-ZNGPC76D-V Federal Ministry of Education and Research - No. 01ZZ9603; No. 01ZZ0103; No. 01ZZ0403; No. 03IS2061A; No. 03ZIK012 http://www.community-medicine.de There are no conflicts of interest associated with this study. SHIP is part of the Community Medicine Research net (CMR Conflict of interest and source of funding statement of the University of Greifswald, Germany, which is funded by the Federal Ministry of Education and Research (grants no. 01ZZ9603, 01ZZ0103, and 01ZZ0403), the Ministry of Cultural Affairs as well as the Social Ministry of the Federal State of Mecklenburg‐West Pomerania, and the network “Greifswald Approach to Individualized Medicine (GANI_MED)” funded by the Federal Ministry of Education and Research (grant 03IS2061A). This study was granted by BMBF‐01‐ZZ‐9603/0 and BH was supported by GABA, Switzerland. Generation of genome‐wide SNP data has been supported by the Federal Ministry of Education and Research (grant no. 03ZIK012) and a joint grant from Siemens Healthcare, Erlangen, Germany and the Federal State of Mecklenburg, West Pomerania. The University of Greifswald is a member of the “Center of Knowledge Interchange” programme of the Siemens AG and the Caché Campus programme of the InterSystems GmbH. ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 |
| ISSN: | 0303-6979 1600-051X 1600-051X |
| DOI: | 10.1111/jcpe.12154 |