Identification of the Single Nucleotide Polymorphisms Affecting Normal Phenotypic Variability in Human Craniofacial Morphology Using Candidate Gene Approach

There is a remarkable variety of human facial appearances, almost exclusively the result of genetic differences, as exemplified by the striking resemblance of identical twins. Despite intensive research on the genetics of craniofacial morphology using animal models and human craniofacial syndromes, the genetic variation that underpins normal human facial appearance is still largely elusive. As a part of efforts on detecting genomic variants affecting normal craniofacial appearance, we have implemented a targeted candidate gene approach by selecting 1,319 single nucleotide polymorphisms (SNPs) in over 170 candidate genes and intergenic regions. This list has been further expanded with additional 4,732 tag polymorphisms, representing extended haplotype. All the markers were genotyped in 587 DNA samples using a massively parallel sequencing approach. We used 3-dimentional (3D) facial scans and direct cranial measurements to calculate 104 craniofacial anthropometric distances, which were analysed for associations with 2,332 polymorphisms. An application of a Bonferroni corrected genome wide significance threshold produced associations between six SNPs and five craniofacial traits. Specifically, significant associations of nasal width with rs8035124 (15q26.1), cephalic index with rs16830498 (2q23.3), nasal index with rs37369 (5q13.2), transverse nasal prominence angle with rs59037879 (10p11.23) and rs10512572 (17q24.3), and a composite trait represented by a principal component with rs37369 (5p13.2) and rs390345 (14q31.3) were observed. Due to over-conservative nature of the Bonferroni correction, we also report the associations that reached the traditional genome-wide p-value threshold (< 5.00E-08) as suggestive. Based on the genome-wide significance threshold, 8 craniofacial phenotypes demonstrated significant and mostly novel associations with 33 intergenic and extragenic SNPs, potentially involved in gene regulation. This study identified a large number of genetic variants associated with normal craniofacial morphology variation, including confirmation of the two previously reported genes. These results enhance our understanding of the craniofacial genetics affecting normal craniofacial appearance and will be of particular value for clinical diagnostics and forensic molecular phenotyping.