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Table 5 Suggestive loci observed for dfs

From: Pilot GWAS of caries in African-Americans shows genetic heterogeneity

Lead SNP

CHR

BP

African-American cohort

Caucasian cohort

Q Statistic P-value

Nearby Gene(s) and Corroborating Evidence

Effect Size

SE

P-value

Effect Size

 

rs11240576

1

205,816,923

6.548

1.338

4.36E-06

    

rs74574927

3

24,768,865

16.13

2.251

2.44E-06

−0.6646

0.6546

7.83E-13

RARB Likely targeted by miRNAs involved in tooth morphogenesis and differentiation of dental cells [96]. Upregulated in ameloblastoma [53]. Has increased methylation in context of/is associated with head and neck squamous cell carcinoma, which, in turn, is associated with dental hygiene and inflammation due to microbial factors [97].

rs7630386

3

29,024,237

22.38

2.805

9.51E-07

   

RBMS3 Candidate gene for a complex chronic periodontitis trait involving a periodontal pathogen load [107].

rs1505809

3

131,901,392

5.215

1.089

9,301,573

    

rs552922

3

150,281,061

6.1

1.074

4.19E-06

0.08645

0.2895

6.44E-08

 

rs11932181

4

17,279,517

−5.766

1.66

4.94E-06

    

rs1602815

4

131,105,072

7.756

1.35

2.47E-06

0.1524

0.3582

5.21E-08

 

rs36162355

5

2,246,469

11.62

1.926

4.38E-06

   

IRX4 Differentially expressed in incisors versus molars [108].

IRX2 Localizes to cervical loop during replacement tooth morphogenesis in fish model [133].

rs17606253

6

111,526,445

12.19

1.928

1.85E-06

0.2342

0.4277

1.41E-09

TRAF3IP2 Involved in mucosal immunity and IL-17 signaling, and associated with a complex chronic periodontitis trait involving high levels of A. actinomycetemcomitans and a profile of aggressive periodontal disease [107].

rs10815750

9

8,087,319

5.522

1.05

1.55E-06

0.1317

0.3258

9.44E-07

 

rs1434274

9

8,817,244

6.899

1.306

4.53E-06

−0.08817

0.3447

2.30E-07

 

rs11008779

10

32,413,987

9.853

1.725

3.22E-06

−0.4776

0.3681

4.72E-09

 

rs6585998

10

87,943,609

−5.642

1.184

4.45E-06

−0.5171

0.3351

3.12E-05

MIR346 Predicted to regulate a gene related to calcium binding during amelogenesis [119].

rs6483205

11

92,669,908

−7.844

1.396

1.24E-06

0.4095

0.3187

8.22E-09

FAT3 Gene enriched in the GO category “calcium ion binding” and are differentially expressed throughout different stages of tooth development [119].

MTNR1B Polymorphisms associated with fasting glucose [134] and type 2 diabetes [135].

rs61950818

13

63,216,679

15.35

2.346

2.70E-06

− 0.01181

0.4964

1.49E-10

 

rs9915753

17

73,011,448

12.24

1.905

3.60E-07

−0.1695

0.348

1.47E-10

CD300E Significantly upregulated in healing gingiva [136].

SLC9A3R1 Heterozygous mutations cause hypophosphatemic nephrolithiasis/osteoporosis which causes decreased bone mineral density [128].

rs2012033

19

34,163,298

5.763

1.136

1.40E-06

0.6308

0.3967

2.00E-05

CHST8 Candidate gene for hypodontia [129].

KCTD15 Associated with obesity and preference for carbohydrates [130].

  1. Loci associated with caries, and genes within +/− 500 kb of the GWAS signal that have supporting evidence for a putative role in dental caries. Shown are lead SNPs of all loci meeting suggestive significance (p-value < 5 × 10− 6), their effect size in the Caucasian cohort and heterogeneity test p-value. Loci associated in the African-American cohort, but not found in the Caucasian GWAS don’t have values in the Caucasian cohort columns. Note: not all genes near GWAS signal are listed. CHR Chromosome, BP Basepair position. Bolded p-values are statistically significant (p ≤ 5 × 10− 8).
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BMC Oral Health

ISSN: 1472-6831

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