MultiProng Screening Strategy for Gene Discovery in Nonsyndromic Cleft Lip Palate

Project: Research project

Project Details


Nonsyndromic Cleft Lip/Palate (NSCLP) is a complex genetic disorder caused by both genetic and
environmental factors. While traditional approaches have achieved some success in uncovering NSCLP's
genetic etiology, the majority of NSCLP genetic risk remains unknown. The nature of complex genetic
architectures, wherein many loci contribute modest effects at the population level, entails that genome-wide
association studies are often underpowered for detecting most risk loci, particularly after correction for multiple
testing. Hence, researchers in NSCLP frequently rely on candidate gene approaches to increase statistical
power. Candidate gene strategies, however, are limited by our prior knowledge of the relevant biological
pathways. In effect, we often end up looking under the proverbial lamp post for mutations in genes that are
related to those already identified. Here, we propose a fundamentally different approach. By intelligently
leveraging the detection of spontaneously arising mutations, via three independent strategies, we can extend
our candidate gene search outside known and/or suspected genetic pathways. We propose to conduct a multi-
pronged genome-wide screening strategy to detect disruptive mutations in NSCLP cases. The first component
of our screen targets a rarely studied subtype of structural variation. While the involvement of CNVs in the
etiology of several Mendelian and complex genetic disorders is now widely acknowledged, the contribution of
transposable element (TE) insertions to genetic disease has received scarce attention. Although much of the
TE content in the genome consists of dormant copies that are incapable of further proliferation, several
lineages of type I retrotransposons (Alu, L1, SVA, and ERVs) remain active within humans. Thus far, over 20
distinct genetic disorders have been identified in which TE insertions have resulted in disease alleles. In
laboratory settings, artificially induced TE insertions have routinely been employed in model organisms to
generate knock-out mutations for the purpose of establishing gene-phenotype relationships. The advent of
highly parallel 2nd Generation Sequencing allows this same conceptual strategy to be implemented in humans.
By screening for potentially disruptive TE insertions in individuals with known disease phenotypes, it is possible
to generate an unbiased set of candidate regions for further genetic interrogation. We will combine this novel
TE screening approach with a triad aCGH screening strategy, wherein we cross-hybridize NSCLP cases to
each of their parents, allowing for the immediate identification of de novo copy number events in sporadic
NSCLP cases. Finally, to round out our screening strategy with a methodology targeting inherited NSCLP risk
factors, we will conduct exome sequencing within multiplex NSCLP families. Together, these complementary
approaches can greatly enhance our ability to rapidly identify candidate genes/region for further scrutiny. We
will evaluate these genes/regions via a targeted genotyping approach and conduct further molecular
characterization, including zebrafish modeling, of the most promising loci.
Effective start/end date9/27/118/31/12


  • National Institute of Dental and Craniofacial Research: $185,000.00


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