Targeted Sequencing of GWAS Loci in Cleft Lip and Palate

Nonsyndromic cleft lip and palate (NSCL/P) is a complex disorder caused by both genetic and environmental factors and has been the focus of an extensive effort to identify genetic risk factors. A number of candidate gene studies have been performed but have not been widely replicated. To date, four independent genome wide association studies have been performed as well as a meta-analysis. Together these studies have identified many loci associated with NSCL/P. The goal of this project is to use targeted sequencing to further characterize these regions and to progress from the association signals identified by GWAS to the identification of causative genes and/or variants.

This study is part of the GWASeq project, a collaboration of five disease studies, which will sequence genomic regions from GWAS to characterize the genetic variation underlying these diseases and to compare study design and methods for the follow-up of GWAS studies by sequencing.

The goal of this study is to sequence 1000+ NSCL/P case-parent trios from China and the Philippines and 400 trios of European ancestry. Targeted sequencing was performed on intervals ranging between 60kb to 1Mb surrounding 13 genes/loci previously associated with NSCL/P including: IRF6, MAFB, ARHGAP29, 8q24, PAX7, VAX1, NTN1, NOG, FOXE1, MSX1, BMP4, FGFR2, PTCH1.

• Study Design:
  • Family/Twin/Trios
• Study Type:
  • Parent-Offspring Trios
  • Multiplex Families
  • Twin
• Total number of consented subjects: 6122
• Subject Sample Telemetry Report (SSTR)

• BioProject
• Sequence Read Archive
• BioSample
• MeSH

Inclusion/Exclusion criteria: Primary inclusion criteria were a case with non-syndromic cleft lip and/or palate with DNA from both parents also available. Secondary analyses were also performed on twin pairs concordant or discordant for NSCL/P and syndromes with features that overlapped with NSCL/P. Other variables available for analyses include some samples with sub-phenotype data for NSCL/P including 3-D facial images, orbicularis oris ultrasounds and GWA data from 1782 cases done in a prior GENEVA GWAS study of Beaty et al. (phs000094.v1.p1) and Marazita et al. (phs000440.v1.p1).

This study consists of samples derived from multiple sources and ancestral backgrounds with 1782 case having had prior GWA data generated in the GENEVA study. The data for these samples are connected to the GWA data through common anonymized identifier numbers. Research groups contributing samples are:
University of Iowa (Murray, JC; Lidral, AC; Wehby, G)
University of Pittsburgh (Marazita, ML)
Johns Hopkins (Beaty, TH)
University of Texas-Houston (Hecht, J)
University of Southern Denmark (Christensen, K)

• Primary Phenotype: Orofacial Cleft, Nonsyndromic
• Cleft Lip
• Cleft Palate

• Prinicipal Investigators
  • Richard K. Wilson. Washington University School of Medicine, St. Louis, MO, USA.
  • George Weinstock. Washington University School of Medicine, St. Louis, MO, USA.
  • Jeff Murray. University of Iowa, Iowa City, IA, USA.
• Funding Sources
  • 3U54HG003079-07S1. Center for Large-Scale Genome Sequencing and Analysis, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.