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

Elizabeth J. Leslie, Margaret A. Taub, Huan Liu, Karyn Meltz Steinberg, Daniel C. Koboldt, Qunyuan Zhang, Jenna C. Carlson, Jacqueline B. Hetmanski, Hang Wang, David E. Larson, Robert S. Fulton, Youssef A. Kousa, Walid D. Fakhouri, Ali Naji, Ingo Ruczinski, Ferdouse Begum, Margaret M. Parker, Tamara Busch, Jennifer Standley, Jennifer RigdonJacqueline T. Hecht, Alan F. Scott, George L. Wehby, Kaare Christensen, Andrew E. Czeizel, Frederic W.B. Deleyiannis, Brian C. Schutte, Richard K. Wilson, Robert A. Cornell, Andrew C. Lidral, George M. Weinstock, Terri H. Beaty, Mary L. Marazita, Jeffrey C. Murray

Research output: Contribution to journalArticle

Abstract

Although genome-wide association studies (GWASs) for nonsyndromic orofacial clefts have identified multiple strongly associated regions, the causal variants are unknown. To address this, we selected 13 regions from GWASs and other studies, performed targeted sequencing in 1,409 Asian and European trios, and carried out a series of statistical and functional analyses. Within a cluster of strongly associated common variants near NOG, we found that one, rs227727, disrupts enhancer activity. We furthermore identified significant clusters of non-coding rare variants near NTN1 and NOG and found several rare coding variants likely to affect protein function, including four nonsense variants in ARHGAP29. We confirmed 48 de novo mutations and, based on best biological evidence available, chose two of these for functional assays. One mutation in PAX7 disrupted the DNA binding of the encoded transcription factor in an in vitro assay. The second, a non-coding mutation, disrupted the activity of a neural crest enhancer downstream of FGFR2 both in vitro and in vivo. This targeted sequencing study provides strong functional evidence implicating several specific variants as primary contributory risk alleles for nonsyndromic clefting in humans.

Original languageEnglish (US)
Pages (from-to)397-411
Number of pages15
JournalAmerican journal of human genetics
Volume96
Issue number3
DOIs
StatePublished - Mar 5 2015

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ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Leslie, E. J., Taub, M. A., Liu, H., Steinberg, K. M., Koboldt, D. C., Zhang, Q., Carlson, J. C., Hetmanski, J. B., Wang, H., Larson, D. E., Fulton, R. S., Kousa, Y. A., Fakhouri, W. D., Naji, A., Ruczinski, I., Begum, F., Parker, M. M., Busch, T., Standley, J., ... Murray, J. C. (2015). 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. American journal of human genetics, 96(3), 397-411. https://doi.org/10.1016/j.ajhg.2015.01.004