Genomic Risk Variants in Orofacial Clefting: Discovery and Functional Validation

ABSTRACT Orofacial clefts (OFCs, comprising cleft lip-CL, cleft palate-CP, or both-CLP) are the most common craniofacial anomalies in humans, affecting approximately 1 in 700 newborns worldwide, and are thus one of the most common structural birth defects. There are substantial public health impacts of OFCs, due to associated morbidity and mortality. An average child with an OFC initially faces feeding difficulties, undergoes 6 surgeries, spends 30 days in hospital, receives 5 years of orthodontic treatment, and participates in ongoing speech therapy, leading to an estimated total lifetime treatment cost of about $200,000. Further, individuals born with an OFC have an increased incidence of mental health problems, higher mortality rates at all stages of life and higher risk for other disorders (notably including breast, brain, and colon cancers), and higher infant mortality (particularly in developing countries where access to medical care may be limited). OFCs are etiologically complex, resulting from genetic variants, environmental exposures, and their interactions. Genome wide association studies coupled with sequencing results have identified at least 35 genes/regions achieving genome-wide significance from multiple independent studies but these results only account for a fraction of heritability. Rare variant studies are emerging with the availability of whole genome sequencing (WGS) datasets, but functional validation of rare variants is essential to generate the support necessary to link these genes/variants to OFCs, to understand the biology behind OFCs, to translate association signals into accurate risk predictions, and ultimately to develop and/or improve therapies. The overall goal of this new collaborative project is to identify the functional significance of rare risk variants identified in our large resource of OFC families and controls. The proposed aims of this new project will help achieve our overall goal. We will utilize our OFC WGS resources (2,078 OFC case/parent trios) to discover new genomic risk variants with innovative analyses emphasizing single nucleotide variants (SNVs), structural variants (SVs), and indels. For functional validation, this new project will take advantage of the high-efficiency and flexibility of CRISPR/Cas9 technology: research team members at the Jackson Laboratory have developed a novel approach to rapidly validate putative causative variants in the mouse, thus enabling the use of a mammalian system for both variant validation and for more detailed investigation of the resulting cleft phenotypes.