Targeted Sequencing of Orofacial Clefts

In this study the CCDG and collaborators at the University of Iowa undertook a targeted sequencing study of regions associated with orofacial clefts, specifically focusing on nonsyndromic cleft lip with or without cleft palate (NSCL/P). As is true for many complex human traits, substantial progress in gene identification has recently occurred, largely as a result of genome-wide association studies (GWAS). Prior to GWAS only one gene, IRF6, had been consistently shown to have common variants associated with increased risk of NSCL/P.  After genome-wide linkage studies, four GWAS and a GWAS meta-analysis, multiple loci associated with NSCL/P are now identified and replicated.  We sequenced more than 4,000 participants for thirteen genomic intervals implicated in NSCL/P. The thirteen regions included nine regions selected as high priority candidates from GWAS and/or genome-wide linkage studies and four regions containing genes with prior compelling evidence of rare variants contributing to NSCL/P. This is the first study to perform targeted sequencing of NSCL/P GWAS regions and is among the first to sequence the complete GWAS intervals, including non-coding and coding DNA, for any complex disease or trait. Our international cohort of participants consists of case-parent trios, which allows us to accurately identify de novo variants and makes it possible to search for the contributions of both rare and common variants as risk alleles for NSCL/P.   In addition, variants identified have also been investigated in vitro and in vivo.

Targeted Sequencing of Orofacial Clefts Publication


Figures from Identification of functional variants for cleft lip with or without

cleft palate in or near PAX7, FGFR2, and NOG by targeted

sequencing of GWAS loci.


A de novo mutation in PAX7 disrupts DNA binding

A de novo Mutation in an Enhancer 254 kb Downstream of FGFR2 Disrupts Enhancer Activity

Association and Immunostaining of NTN1

rs227727 Is a Functional Variant Associated with NSCL/P

Select any of the images above to see enlargements.
Referenced Publication: Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, Carlson JC, Hetmanski JB, Wang H, Larson DE, Fulton RS,Kousa YA, Fakhouri WD, Naji A, Ruczinski I, Begum F, Parker MM, Busch T, Standley J, Rigdon J, Hecht JT, Scott AF, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FW, Schutte BC, Wilson RK, Cornell RA, Lidral AC, Weinstock GM, Beaty TH, Marazita ML, Murray JC. Am J Hum Genet. 2015 Mar 5;96(3):397‐411. doi: 10.1016/j.ajhg.2015.01.004. Epub 2015 Feb 19. PMID: 25704602