Investigating genetic influences of facial morphology

Rationale
Craniofacial morphology is highly heritable, but little is known about which genetic variants influence normal facial variation in the general population. A previous genome-wide association study in ALSPAC analysed 54 distances and 14 principal components and identified a genetic variant in the gene PAX3 that influences the position of the nasion (bridge of the nose) (Paternoster et al., 2012). Since this paper was published, more participants are available with genetic data, the genome-wide has been imputed to a new reference panel (using the 1000 genomes reference) and new facial parameters have been generated. This project will analyse this new data in an attempt to identify additional genetic variants for facial morphology.

Aims & Objectives
Aim: Identify genetic variants associated with facial morphology
Objectives:
1.Investigate the distributions & correlations of facial parameters
2.Explore techniques to deal with the phenotype complexity
3.Review heritability estimates & carry out genome-wide complex trait analysis to identify the most heritable parameters
4.Use genome-wide association analysis to identify associated genetic variants
5.Replicate in additional cohorts
6.Explore the functional basis of any genetic associations

Methods
4747 children from the Avon Longitudinal Study of Parents & Children (ALSPAC) have 3D high-resolution face scans, with a number of facial traits extracted.

Genome-wide complex trait analysis (Yang et al, 2010) and genome-wide association studies (GWAS) will be used to explore the genetic influences on facial morphology. Additional analysis methods will be explored to make the most of the multi-dimensionality of the data. Significant findings will be replicated in independent cohorts through existing collaborations.

Any genetic associations found may represent broader growth or developmental signals and so it will be interesting to compare the findings with those from other developmental phenotypes (e.g. head circumference, tooth eruption, cleft lip/palate).

ENCODE and RoadMap functional data will be used to explore the functional underpinnings of any associated loci. Methylation data (available for 1000 ALSPAC children) allows the opportunity to explore mediation by methylation.