Format

Send to

Choose Destination
Am J Hum Genet. 2015 Mar 5;96(3):397-411. doi: 10.1016/j.ajhg.2015.01.004. Epub 2015 Feb 19.

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.

Author information

1
Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA. Electronic address: ejl40@pitt.edu.
2
Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.
3
Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA; State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 430072 Wuhan, China.
4
The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
5
Department of Statistical Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.
6
Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA.
7
Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.
8
Department of Biochemistry and Molecular Biology, College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824, USA.
9
Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
10
Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
11
Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
12
Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
13
Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA.
14
Department of Epidemiology, Institute of Public Health, University of Southern Denmark, 5230 Odense, Denmark.
15
Foundation for the Community Control of Hereditary Diseases, Budapest 1148, Hungary.
16
Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO 80045, USA.
17
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
18
Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
19
Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA.
20
The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06117, USA.
21
Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Human Genetics, Graduate School of Public Health, and Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA. Electronic address: marazita@pitt.edu.

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.

PMID:
25704602
PMCID:
PMC4375420
DOI:
10.1016/j.ajhg.2015.01.004
[Indexed for MEDLINE]
Free PMC Article

Publication types, MeSH terms, Substances, Supplementary concept, Secondary source ID, Grant support

Publication types

MeSH terms

Substances

Supplementary concept

Secondary source ID

Grant support

Supplemental Content

Full text links

Icon for Elsevier Science Icon for PubMed Central
Loading ...
Support Center