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Cleft Lip-Palate CNV Analysis Uncovers New Clefting Genes

NEW YORK – A team led by researchers at the University of Iowa has characterized copy number variants that contribute to cleft lip with or without cleft palate (CL/P), a group of relatively common birth defects affecting craniofacial development.

"It is established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy number variants (CNVs) to cleft formation remains relatively unstudied," senior and corresponding author John Manak, a genetics and neurobiology researcher at the University of Iowa, and his colleagues explained in the American Journal of Human Genetics on Thursday.

By focusing on lower-frequency CNVs and those expected to produce the most pronounced or deleterious effects, the researchers tracked down CL/P-associated CNVs affecting known Mendelian genes, while identifying additional clefting genes that influenced craniofacial development in subsequent animal model experiments.

Using high-resolution comparative genomic hybridization arrays, the team profiled more than 64,100 CNVs in 869 individuals from the Philippines, including 77 participants with syndromic CL/P (SCL/P) and 792 non-syndromic CL/P (NSCL/P) patients, analyzing the chromosome loss and gain patterns along with those found in 233 CL/P patients of European descent.

In particular, the authors explained, they "assessed the total number of CNVs, CNV load, and CNV burden between cleft type and within NSCL/P subgroups."

Although the researchers did not find CNV differences that distinguished syndromic from non-syndromic CL/P cases, they noted that large gains spanning 300 kb to 400 kb were slightly more common in the syndromic clefting cases.

The team's results also pointed to the presence of CL/P-related duplications or deletions in Mendelian disease genes linked to non-syndromic conditions and to syndromes such as DiGeorge syndrome in more than two dozen of the syndromic or non-syndromic CL/P cases.

From there, the team filtered the CNVs found in CL/P-affected individuals against population genetic data — with array-based CNV profiling on nearly 1,800 female participants from the Cebu Longitudinal Health and Nutrition Survey — to find the variants that were rare across the general population but overrepresented in individuals with CL/P.

That search led to rare CNVs in and around the COBLL1, RIC1, and ARHGEF38 genes, the researchers reported. A potential craniofacial development role for those genes was supported by subsequent CRISPR-Cas9-based gene editing experiments, performed in the Xenopus laevis African clawed frog and Danio rerio zebrafish model organisms.

"Intriguingly, our top three candidate genes are involved in either the Rho or Rab GTPase signaling pathways, which have been implicated in a wide array of cellular dynamics including the formation of adhesion junctions, actin organization, cell division, cell migration, and membrane trafficking," the authors noted.