Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common complex orofacial birth defect associated with significant morbidity and increased mortality. Surgical correction is always required and the multidisciplinary health interventions cost approximately a half billion dollars each year. Candidate gene studies and GWAS have identified a number of putative NSCLP genes and loci that are estimated to account for only ~20% of the genetic variation. While this represents an important starting point, the majority of genetic risk for NSCLP remains undiscovered and represents a frontier to be explored. We have used both candidate gene and GWAS approaches to define genetic variation in NSCLP;a previously unsuspected gene, CRISPLD2, was found to be associated with NSCLP and, when knocked down in zebrafish, causes palatal and jaw abnormalities. The goal of this project is to continue identifying and understanding the undiscovered variation that contributes to the genetic architecture of NSCLP. To accomplish this goal, we will apply the newest technologies, whole exome next generation sequencing (WES) and chromosomal microarray analysis (CMA) to our well-characterized extensive family-based NSCLP dataset. We will use the WES that detects coding and noncoding variants (Agilent 50Mb v.4 exon content +UTR) because we have shown that both types of variation contribute to NSCLP. In addition, CMA will detect copy number variants (CNVs) that would be missed by WES. This will provide the most complete coverage and the family-based design will allow for detection familial causes of NSCLP. Candidate genes will be prioritized, functionally tested in zebrafish to determine biological significance and analyzed in our case controls for spectrum variation and risk modeling. The results will provide important information about risk variants, individually and in aggregate. During the entire study period, we will continue to expand our NSCLP dataset for this and future genetic studies. Application of the newest technology to our extensive family-based dataset is a powerful method for uncovering the genetic variation contributing to this common birth defect. This approach is a significant step forward;the results will add important new information to the developing knowledge base of genetic variation responsible for NSCLP, which will translate into genetic counseling for at-risk families.

Public Health Relevance

Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect affecting 4000 newborns in the US and 135,000 worldwide each year. The etiology is poorly understood and currently, only 20% of the NSCLP genetic liability has been identified, limiting our ability to identify at-risk individuals or provide accurate counselin for families. In these studies, we apply the newest technology to identify the genetic variation underlying NSCLP in families with multiple cases, will test the variants for expression and functionality in a fish model and develop ethnic-specific risks. The results of this study will ultimately be utilized to identify and test for potential at-risk genotypes.

National Institute of Health (NIH)
National Institute of Dental & Craniofacial Research (NIDCR)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-GGG-E (03))
Program Officer
Harris, Emily L
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Texas Health Science Center Houston
Schools of Medicine
United States
Zip Code
Chiquet, Brett T; Yuan, Qiuping; Swindell, Eric C et al. (2018) Knockdown of Crispld2 in zebrafish identifies a novel network for nonsyndromic cleft lip with or without cleft palate candidate genes. Eur J Hum Genet 26:1441-1450
Carlson, Jenna C; Nidey, Nichole L; Butali, Azeez et al. (2018) Genome-wide interaction studies identify sex-specific risk alleles for nonsyndromic orofacial clefts. Genet Epidemiol 42:664-672
Rodriguez, Nicholas; Maili, Lorena; Chiquet, Brett T et al. (2018) BRCA1 and BRCA2 gene variants and nonsyndromic cleft lip/palate. Birth Defects Res 110:1043-1048
Yuan, Qiuping; Zhao, Min; Tandon, Bhavna et al. (2017) Role of WNT10A in failure of tooth development in humans and zebrafish. Mol Genet Genomic Med 5:730-741
Leslie, Elizabeth J; Carlson, Jenna C; Shaffer, John R et al. (2017) Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate. Am J Med Genet A 173:1531-1538
Ruegg, Teresa A; Cooper, Margaret E; Leslie, Elizabeth J et al. (2017) Ear Infection in Isolated Cleft Lip: Etiological Implications. Cleft Palate Craniofac J 54:189-192
Leslie, Elizabeth J; Carlson, Jenna C; Shaffer, John R et al. (2017) Genome-wide meta-analyses of nonsyndromic orofacial clefts identify novel associations between FOXE1 and all orofacial clefts, and TP63 and cleft lip with or without cleft palate. Hum Genet 136:275-286
Leslie, E J; Koboldt, D C; Kang, C J et al. (2016) IRF6 mutation screening in non-syndromic orofacial clefting: analysis of 1521 families. Clin Genet 90:28-34
Leslie, Elizabeth J; Carlson, Jenna C; Shaffer, John R et al. (2016) A multi-ethnic genome-wide association study identifies novel loci for non-syndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q13. Hum Mol Genet 25:2862-2872
Leslie, Elizabeth J; Liu, Huan; Carlson, Jenna C et al. (2016) A Genome-wide Association Study of Nonsyndromic Cleft Palate Identifies an Etiologic Missense Variant in GRHL3. Am J Hum Genet 98:744-54

Showing the most recent 10 out of 34 publications