Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity

Yanqin Yu, Xianbo Zuo, Miao He, Jinping Gao, Yuchuan Fu, Chuanqi Qin, Liuyan Meng, Wenjun Wang, Yaling Song, Yong Cheng, Fusheng Zhou, Gang Chen, Xiaodong Zheng, Xinhuan Wang, Bo Liang, Zhengwei Zhu, Xiazhou Fu, Yujun Sheng, Jiebing Hao, Zhongyin Liu, Hansong Yan, Elisabeth Mangold, Ingo Ruczinski, Jianjun Liu, Mary L. Marazita, Kerstin U. Ludwig, Terri H. Beaty, Xuejun Zhang, Liangdan Sun () and Zhuan Bian ()
Additional contact information
Yanqin Yu: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University
Xianbo Zuo: Anhui Medical University
Miao He: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University
Jinping Gao: Anhui Medical University
Yuchuan Fu: School and Hospital of Stomatology, Wuhan University
Chuanqi Qin: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University
Liuyan Meng: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University
Wenjun Wang: Anhui Medical University
Yaling Song: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University
Yong Cheng: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University
Fusheng Zhou: Anhui Medical University
Gang Chen: Anhui Medical University
Xiaodong Zheng: Anhui Medical University
Xinhuan Wang: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University
Bo Liang: Anhui Medical University
Zhengwei Zhu: Anhui Medical University
Xiazhou Fu: College of Life Science, Wuhan University
Yujun Sheng: Anhui Medical University
Jiebing Hao: The Second Charity Hospital of Henan Province
Zhongyin Liu: Stomatological Hospital of Nanyang
Hansong Yan: Stomatological Hospital of Xiangyang
Elisabeth Mangold: Institute of Human Genetics, Life and Brain Center, University of Bonn
Ingo Ruczinski: Bloomberg School of Public Health, Johns Hopkins University
Jianjun Liu: Anhui Medical University
Mary L. Marazita: School of Dental Medicine, University of Pittsburgh
Kerstin U. Ludwig: Institute of Human Genetics, Life and Brain Center, University of Bonn
Terri H. Beaty: School of Public Health, Johns Hopkins University
Xuejun Zhang: Anhui Medical University
Liangdan Sun: Anhui Medical University
Zhuan Bian: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University

Nature Communications, 2017, vol. 8, issue 1, 1-11

Abstract: Abstract Non-syndromic cleft lip with palate (NSCLP) is the most serious sub-phenotype of non-syndromic orofacial clefts (NSOFC), which are the most common craniofacial birth defects in humans. Here we conduct a GWAS of NSCLP with multiple independent replications, totalling 7,404 NSOFC cases and 16,059 controls from several ethnicities, to identify new NSCLP risk loci, and explore the genetic heterogeneity between sub-phenotypes of NSOFC. We identify 41 SNPs within 26 loci that achieve genome-wide significance, 14 of which are novel (RAD54B, TMEM19, KRT18, WNT9B, GSC/DICER1, PTCH1, RPS26, OFCC1/TFAP2A, TAF1B, FGF10, MSX1, LINC00640, FGFR1 and SPRY1). These 26 loci collectively account for 10.94% of the heritability for NSCLP in Chinese population. We find evidence of genetic heterogeneity between the sub-phenotypes of NSOFC and among different populations. This study substantially increases the number of genetic susceptibility loci for NSCLP and provides important insights into the genetic aetiology of this common craniofacial malformation.

Date: 2017
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DOI: 10.1038/ncomms14364

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