Association of low-frequency genetic variants in regulatory regions with nonsyndromic orofacial clefts

• Type of Material: Article
• Authors: John R. Shaffer, University of Pittsburgh; Jessica LeClair, University of Pittsburgh; Jenna C. Carlson, University of Pittsburgh; Eleanor Feingold, University of Pittsburgh; Carmen J. Buxo, University of Puerto Rico; Kaare Christensen, University of Southern Denmark; Frederic W. B. Deleyiannis, University of Colorado; L. Leigh Field, University of British Columbia; Jacqueline T. Hecht, University of Texas Houston; Lina Moreno, University of Iowa; Ieda M. Orioli, Federal University of Rio de Janeiro; Carmencita Padilla, University of the Philippines Manila; Alexandre R. Vieira, University of Pittsburgh; George L. Wehby, University of Iowa; Jeffrey C. Murray, University of Iowa; Seth M. Weinberg, University of Pittsburgh; Mary L. Marazita, University of Pittsburgh; Elizabeth Leslie, Emory University
• Language: English
• Date: 2019-03-01
• Publisher: WILEY
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2018 Wiley Periodicals, Inc.
• Final Published Version (URL): http://dx.doi.org/10.1002/ajmg.a.61002
• Title of Journal or Parent Work: AMERICAN JOURNAL OF MEDICAL GENETICS PART A
• Volume: 179
• Issue: 3
• Start Page: 467
• End Page: 474
• Grant/Funding Information: This work was supported by grants from the National Institutes of Health (NIH) including: R00-DE025060 [EJL], X01-HG007485 [MLM, EF], R01-DE016148 [MLM, SMW], U01-DE024425 [MLM], R37-DE008559 [JCM, MLM], R01-DE009886 [MLM], R21-DE016930 [MLM], R01-DE014667 [LM], R01-DE012472 [MLM], R01-DE011931 [JTH], R01-DE011948 [KC], U01-DD000295 [GLW], R25-MD007607 [CJB], K99-DE024571 [CJB], S21-MD001830 [CJB], U54-MD007587 [CJB].; Genotyping and data cleaning were provided via an NIH contract to the Johns Hopkins Center for Inherited Disease Research: HHSN268201200008I.; Additional support provided by: the National Science Foundation Grant DBI-1263020, which was co-funded by the Department of Defense; the Robert Wood Johnson Foundation, AMFDP Grant 72429 [AB]; an intramural grant from the Research Institute of the Children’s Hospital of Colorado [FWD]; operating costs support in the Philippines was provided by the Institute of Human Genetics, National Institutes of Health, University of the Philippines, Manila [CP]; grants through FAPERJ, Brazil [IMO]: grant numbers: E-26/20300/2017; grants through CNPq, Brazil [IMO]: grant numbers: 310772/2017–6, 400427/2013–3.
• Keywords: genetic association; LIP; Genetics & Heredity; PALATE; FOXP1; cleft palate; EXPRESSION; INTELLECTUAL DISABILITY; LOCUS; RARE VARIANTS; cleft lip; orofacial cleft; Life Sciences & Biomedicine; ENHANCER; Science & Technology; CODING VARIANTS; GENOME-WIDE ASSOCIATION
• Research Categories: Biology, Genetics

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.