Haplotype and Haplotype-Environment Interaction Analysis Revealed Roles of SPRY2 for NSCL/P among Chinese Populations

Ren Zhou, Mengying Wang, Wenyong Li, Siyue Wang, Hongchen Zheng, Zhibo Zhou, Yonghua Hu, Jing Li, Tao Wu, Hongping Zhu and Terri H. Beaty
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Ren Zhou: School of Public Health, Peking University, Beijing 100191, China
Mengying Wang: School of Public Health, Peking University, Beijing 100191, China
Wenyong Li: School of Public Health, Peking University, Beijing 100191, China
Siyue Wang: School of Public Health, Peking University, Beijing 100191, China
Hongchen Zheng: School of Public Health, Peking University, Beijing 100191, China
Zhibo Zhou: School of Stomatology, Peking University, Beijing 100081, China
Yonghua Hu: School of Public Health, Peking University, Beijing 100191, China
Jing Li: School of Public Health, Peking University, Beijing 100191, China
Tao Wu: School of Public Health, Peking University, Beijing 100191, China
Hongping Zhu: School of Stomatology, Peking University, Beijing 100081, China
Terri H. Beaty: School of Public Health, Johns Hopkins University, Baltimore, MD 21218, USA

IJERPH, 2019, vol. 16, issue 4, 1-7

Abstract: Non-syndromic cleft lip with or without cleft palate (NSCL/P) is one of common birth defects in China, with genetic and environmental components contributing to the etiology. Genome wide association studies (GWASs) have identified SPRY1 and SPRY2 to be associated with NSCL/P among Chinese populations. This study aimed to further explore potential genetic effect and gene—environment interaction among SPRY genes based on haplotype analysis, using 806 Chinese case—parent NSCL/P trios drawn from an international consortium which conducted a genome-wide association study. After the process of quality control, 190 single nucleotide polymorphisms (SNPs) of SPRY genes were included for analyses. Haplotype and haplotype—environment interaction analyses were conducted in Population-Based Association Test (PBAT) software. A 2-SNP haplotype and three 3-SNP haplotypes showed a significant association with the risk of NSCL/P after Bonferroni correction (corrected significance level = 2.6 × 10 −4 ). Moreover, haplotype—environment interaction analysis identified these haplotypes respectively showing statistically significant interactions with maternal multivitamin supplementation or maternal environmental tobacco smoke. This study showed SPRY2 to be associated with NSCL/P among the Chinese population through not only gene effects, but also a gene—environment interaction, highlighting the importance of considering environmental exposures in the genetic etiological study of NSCL/P.

Keywords: haplotypes; genetic association study; gene-environmental interaction; cleft lip and palate; case-parent trios (search for similar items in EconPapers)
JEL-codes: I I1 I3 Q Q5 (search for similar items in EconPapers)
Date: 2019
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