X-linked genes and risk of orofacial clefts: evidence from two population-based studies in Scandinavia

Abstract

Background: Orofacial clefts are common birth defects of complex etiology, with an excess of males among babies with cleft lip and palate, and an excess of females among those with cleft palate only. Although genes on the X chromosome have been implicated in clefting, there has been no association analysis of X-linked markers.

Methodology/principal findings: We added new functionalities in the HAPLIN statistical software to enable association analysis of X-linked markers and an exploration of various causal scenarios relevant to orofacial clefts. Genotypes for 48 SNPs in 18 candidate genes on the X chromosome were analyzed in two population-based samples from Scandinavia (562 Norwegian and 235 Danish case-parent triads). For haplotype analysis, we used a sliding-window approach and assessed isolated cleft lip with or without cleft palate (iCL/P) separately from isolated cleft palate only (iCPO). We tested three statistical models in HAPLIN, allowing for: i) the same relative risk in males and females, ii) sex-specific relative risks, and iii) X-inactivation in females. We found weak but consistent associations with the oral-facial-digital syndrome 1 (OFD1) gene (formerly known as CXORF5) in the Danish iCL/P samples across all models, but not in the Norwegian iCL/P samples. In sex-specific analyses, the association with OFD1 was in male cases only. No analyses showed associations with iCPO in either the Norwegian or the Danish sample.

Conclusions: The association of OFD1 with iCL/P is plausible given the biological relevance of this gene. However, the lack of replication in the Norwegian samples highlights the need to verify these preliminary findings in other large datasets. More generally, the novel analytic methods presented here are widely applicable to investigations of the role of X-linked genes in complex traits.

Figure 1. Single-marker analyses of 48 SNPs in 18 X-linked cleft candidate genes.

These analyses are based on Model 2 in which we assume different baseline risks for males and females, a shared relative risk for males and females, and no X-inactivation. Quantile-quantile (QQ) plots of p-values for iCL/P (left-hand side) and iCPO (right-hand side). Top panels: Norwegian and Danish samples, respectively. Bottommost panels: Fisher combined p-values. Shaded areas represent 95% confidence interval bands and dotted lines indicate the expected ranked p-value of 0.05. Note that the oral-facial-digital syndrome 1 gene (OFD1) was formerly known as CXORF5.

Figure 2. Haplotype analyses using up to 4 SNPs per sliding-window, Model 2.

Figure 3. Haplotype analyses of female cases only using up to 4 SNPs per sliding-window.

These sex-specific analyses are based on Model 3 in which we assume different baseline risks for males and females, different relative risks for males and females, and no X-inactivation.

Figure 4. Haplotype analyses of male cases only using up to 4 SNPs per sliding-window, Model 3.

Figure 5. Haplotype analyses using up to 4 SNPs per sliding-window and taking X-inactivation into account.

These analyses are based on Model 4 in which we assume different baseline risks for males and females, a shared relative risk for males and females, and X-inactivation.