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Association of low‐frequency genetic variants in regulatory regions with nonsyndromic orofacial clefts
Author(s) -
Shaffer John R.,
LeClair Jessica,
Carlson Jenna C.,
Feingold Eleanor,
Buxó Carmen J.,
Christensen Kaare,
Deleyiannis Frederic W. B.,
Field L. Leigh,
Hecht Jacqueline T.,
Moreno Lina,
Orioli Ieda M.,
Padilla Carmencita,
Vieira Alexandre R.,
Wehby George L.,
Murray Jeffrey C.,
Weinberg Seth M.,
Marazita Mary L.,
Leslie Elizabeth J.
Publication year - 2019
Publication title -
american journal of medical genetics part a
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.064
H-Index - 112
eISSN - 1552-4833
pISSN - 1552-4825
DOI - 10.1002/ajmg.a.61002
Subject(s) - craniofacial , enhancer , biology , genetics , genome wide association study , branchial arch , heritability , genetic association , missing heritability problem , allele , allele frequency , gene , single nucleotide polymorphism , genotype , transcription factor , embryo
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.