Association of low‐frequency genetic variants in regulatory regions with nonsyndromic orofacial clefts
Abstract
Genome‐wide scans have shown that common risk alleles for orofacial clefts (OFC) tend to be located in noncoding regulatory elements and cumulatively explain only part of the heritability of OFCs. Low‐frequency variants may account for some of the “missing” heritability. Therefore, we scanned low‐frequency variants located within putative craniofacial enhancers to identify novel OFC risk variants and implicate new regulatory elements in OFC pathogenesis. Analyses were performed in a multiethnic sample of 1,995 cases of cleft lip with or without cleft palate (CL/P), 221 cases with cleft palate (CP) only, and 1,576 unaffected controls. One hundred and nineteen putative craniofacial enhancers identified from ChIP‐Seq studies in craniofacial tissues or cell lines contained multiple low‐frequency (0.01–1%) variants, which we genotyped in participants using a custom Illumina panel. Two complementary statistical approaches, sequence kernel association test and combined multivariate and collapsing, were used to test association of the aggregated low‐frequency variants across each enhancer region with CL/P and CP. We discovered a significant association between CP and a branchial arch enhancer near FOXP1 (mm60; p‐value = .0002). Additionally, we observed a suggestive association between CL/P and a forebrain enhancer near FOXE1 (hs1717; p‐value = .001). These findings suggest that low‐frequency variants in craniofacial enhancer regions contribute to the complex etiology of nonsyndromic OFCs.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Dec 24, 2018
- Source ID
- 10.1002/ajmg.a.61002
Entities
People
- Alexandre R. Vieira
- Carmen J. Buxó
- Carmencita Padilla
- Eleanor Feingold
- Elizabeth J. Leslie
- Frederic W. B. Deleyiannis
- George L. Wehby
- Iêda M Orioli
- Jacqueline T. Hecht
- Jeffrey C. Murray
- Jenna C. Carlson
- Jessica Leclair
- John R. Shaffer
- Kaare Christensen
- L. Leigh Field
- Lina Moreno
- Mary L. Marazita
- Seth M Weinberg
Organizations
- Boston University
- Emory University
- Federal University of Rio de Janeiro
- Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro
- National Council for Scientific and Technological Development
- National Institutes of Health
- National Science Foundation
- Robert Wood Johnson Foundation
- United States Department of Defense
- University of British Columbia
- University of Colorado
- University of Iowa
- University of Pittsburgh
- University of the Philippines