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Genome-wide meta-analyses of nonsyndromic orofacial clefts identify novel associations between FOXE1 and all orofacial clefts, and TP63 and cleft lip with or without cleft palate

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Abstract

Nonsyndromic orofacial clefts (OFCs) are a heterogeneous group of common craniofacial birth defects with complex etiologies that include genetic and environmental risk factors. OFCs are commonly categorized as cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP), which have historically been analyzed as distinct entities. Genes for both CL/P and CP have been identified via multiple genome-wide linkage and association studies (GWAS); however, altogether, known variants account for a minority of the estimated heritability in risk to these craniofacial birth defects. We performed genome-wide meta-analyses of CL/P, CP, and all OFCs across two large, multiethnic studies. We then performed population-specific meta-analyses in sub-samples of Asian and European ancestry. In addition to observing associations with known variants, we identified a novel genome-wide significant association between SNPs located in an intronic TP63 enhancer and CL/P (p = 1.16 × 10−8). Several novel loci with compelling candidate genes approached genome-wide significance on 4q21.1 (SHROOM3), 12q13.13 (KRT18), and 8p21 (NRG1). In the analysis of all OFCs combined, SNPs near FOXE1 reached genome-wide significance (p = 1.33 × 10−9). Our results support the highly heterogeneous nature of OFCs and illustrate the utility of meta-analysis for discovering new genetic risk factors.

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Abbreviations

OFC:

Orofacial cleft

CL:

Cleft lip

CLP:

Cleft lip and palate

CL/P:

Cleft lip with or without cleft palate

CP:

Cleft palate

TDT:

Transmission disequilibrium test

OR:

Odds ratio

SNP:

Single nucleotide polymorphism

GWAS:

Genome-wide association study

POFC:

Pittsburgh orofacial cleft study

PCA:

Principal components analysis

PC:

Principal component

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Acknowledgements

Many thanks to the participating families world-wide who made this project possible. The tireless efforts by the dedicated field staff and collaborators were similarly essential to the success of this study. This work was supported by grants from the National Institutes of Health (NIH) including: K99-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 [LMM], R01-DE012472 [MLM], R01-DE011931 [JTH], R01-DE011948 [KC], U01-DD000295 [GLW], K99 -DE024571 [CJB], R25-MD007607 [CJB], R01-DE014581 [TB], U01-DE018993 [TB]. 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 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-26/102.797/2012, E-26/110.140/2013; grants through CNPq, Brazil [IMO]: grant numbers: 481069/2012-7, 306396/2013-0, 400427/2013-3.

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Leslie, E.J., Carlson, J.C., Shaffer, J.R. et al. Genome-wide meta-analyses of nonsyndromic orofacial clefts identify novel associations between FOXE1 and all orofacial clefts, and TP63 and cleft lip with or without cleft palate. Hum Genet 136, 275–286 (2017). https://doi.org/10.1007/s00439-016-1754-7

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