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, Terri L Beaty

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number557
JournalInternational journal of environmental research and public health
Volume16
Issue number4
DOIs
StatePublished - Feb 2 2019

Fingerprint

Haplotypes
Single Nucleotide Polymorphism
Population
Genome-Wide Association Study
Mothers
Genes
Cleft Lip
Environmental Exposure
Cleft Palate
Smoke
Quality Control
Tobacco
China
Software

Keywords

  • Aplotypes
  • Case-parent trios
  • Cleft lip and palate
  • Gene-environmental interaction
  • Genetic association study

ASJC Scopus subject areas

  • Public Health, Environmental and Occupational Health
  • Health, Toxicology and Mutagenesis

Cite this

Haplotype and haplotype-environment interaction analysis revealed roles of SPRY2 for NSCL/P among Chinese populations. / Zhou, Ren; Wang, Mengying; Li, Wenyong; Wang, Siyue; Zheng, Hongchen; Zhou, Zhibo; Hu, Yonghua; Li, Jing; Wu, Tao; Zhu, Hongping; Beaty, Terri L.

In: International journal of environmental research and public health, Vol. 16, No. 4, 557, 02.02.2019.

Research output: Contribution to journalArticle

Zhou, Ren ; Wang, Mengying ; Li, Wenyong ; Wang, Siyue ; Zheng, Hongchen ; Zhou, Zhibo ; Hu, Yonghua ; Li, Jing ; Wu, Tao ; Zhu, Hongping ; Beaty, Terri L. / Haplotype and haplotype-environment interaction analysis revealed roles of SPRY2 for NSCL/P among Chinese populations. In: International journal of environmental research and public health. 2019 ; Vol. 16, No. 4.
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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.",
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