Association between PAX7 and NTN1 gene polymorphisms and nonsyndromic orofacial clefts in a northern Chinese population

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Nonsyndromic orofacial clefts (NSOC) are the most common orofacial congenital defect with a complex etiology. Genome-wide association studies have identified paired box protein 7 (PAX7) and netrin-1 (NTN1) as candidate susceptibility genes for NSOC in both European and Asian populations. Here, possible associations between single-nucleotide polymorphisms (SNPs) in or near PAX7 and NTN1 were investigated in relation to risk of NSOC in a northern Chinese population.


A total of 602 individuals with NSOC and 510 controls were recruited from northern China. Polymerase chain reaction–ligation detection reactions were used to analyze 4 SNPs (rs742071, rs6659735, rs766325, and rs4920520) of PAX7 and 2 SNPs (rs9904526 and rs9788972) of NTN1. Investigations of polymorphisms and risk of NSOC were conducted by using the PLINK software.


NTN1 rs9788972 AG was found to be associated with an increased risk of NSOC compared to the GG homozygous genotype (OR = 1.43, 95% CI = 1.11–1.86, P = .006). When the multifactor dimensionality reduction method was applied, NTN1 rs9788972 still exhibited an increased risk for NSOC (P = .008). In contrast, SNPs in PAX7 were not associated with any increased risk of NSOC.


NTN1 rs9788972 is identified as a risk locus for NSOC susceptibility in a northern Chinese population.

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