Genome-Wide Association Study (GWAS) of dental caries in diverse populations

Alotaibi, Rasha N.; Howe, Brian J.; Chernus, Jonathan M.; Mukhopadhyay, Nandita; Sanchez, Carla; Deleyiannis, Frederic W. B.; Neiswanger, Katherine; Padilla, Carmencita; Poletta, Fernando A.; Orioli, Ieda M.; Buxó, Carmen J.; Hecht, Jacqueline T.; Wehby, George L.; Long, Ross E.; Vieira, Alexandre R.; Weinberg, Seth M.; Shaffer, John R.; Moreno Uribe, Lina M.; Marazita, Mary L.

doi:10.1186/s12903-021-01670-5

BMC Oral Health

Table 5 Significant and suggestive SNPs across the analyses

From: Genome-Wide Association Study (GWAS) of dental caries in diverse populations

Lead SNP	Chr band	BP	Beta	P	Nearby Gene(s)	dbSNP Annotation	Biological Role*
Primary analysis
rs80177293	5q14.3	88,865,345	− 2.91	8.23e−10	MIR3660	Non-coding	Essential for post- transcriptional regulation of gene expression in different organism [Hansen, et al. 2010]
rs113021760	9p23	114,805,385	− 2.67	3.36e−09	SUSD1 UGCG	Intronic	A protein coding gene that has been associated with Venous thromboembolism (VTE), a cardiovascular disease [Tang et al. 2013] Involved in the biosynthesis of glycosphingolipid (Ichikawa, et al. 1996)
rs75833698	6p22.3	19,866,520	− 2.17	4.93e−08	ID4	Non-coding	Inhibitor of DNA binding 4 has been, regulate different cellular processes [Benezra, et al. 2001]
rs16948495	17q21.33	48,005,748	− 2.15	5.16e−08	DLX3 DLX4	Non-coding	Mutations in this gene have been associated with tricho-dento-osseous syndrome (TDO), which cause enamel hypoplasia [Y.li et al. 2015] Play a role in forebrain and craniofacial development. Mutations cause non-syndromic orofacial cleft [Wu et al. 2015]
rs75459295	14q13.1	34,767,100	− 2.26	6.08e−08	SPTSSA	Non-coding	Involved in sphingolipid biosynthesis (Han, et al. 2009)
chr9:35,753,170	9p13.3	35,753,170	− 2.27	1.89e−07	CA9 TLN1	Non-coding	Participates in a variety of biological processes, including regulation of pH, and can be found in gastrointestinal mucosa [Yang et al. 2017] Plays a role migration of various cell types, including fibroblasts and osteoclasts [Monkley et al. 2001, Zou et al. 2013]
Permanent analysis
rs17226825	9p21.1	33,010,337	− 1.42	7.47e−08	APTAX NFX1	Non-coding	Repair of DNA damage in cells [Sano et al. 2004] Regulating the duration of an inflammatory response [Yamashita et al. 2016]
rs6708025	2p24.2	178,577,642	− 3.00	1.36e−07	PDE11A	Intronic	Messenger in different signal transduction pathways [Fawcett et al. 2000]
rs11686767	2p16.1	60,990,128	− 0.63	3.09e−07	PAPOLG REL	Intronic	Catalyzing template-independent extension of a DNA/RNA strand [Topalian et al. 2001] Regulate inflammation, immune response & apoptosis [Shono et al. 2014]
rs288547958	7q35	145,203,344	− 176	6.93e−07	CNTNAP2	Non-coding	Role in neuronal migration, dendritic arborisation and synaptic transmission [Anderson et al. 2012]
rs73753796	6q15	92,190,076	− 2.91	1.079e−06	MIR4643	Non-coding	Involved in post-transcriptional regulation of gene expression [Ghanbari et al. 2015]
rs111979811	7q34	141,658,200	− 2.07	1.11e−06	TAS2R38, TAS2R3, TAS2R4, TASR25 OR9A4	Non-coding	Linked to loci influence bitter perception. Significant association for caries risk [Wendell et al. 2010] Activate the neural response that initiate the perception of smell [Niimura, 2012]

^*Although no known role of some of the presented genes in cariogenesis and/or odontogenesis, further investigations is needed to discover if some of these genes could have possible role in dental caries and/or odontogenesis

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ISSN: 1472-6831

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