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

Author

Listed:
  • 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)

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.

Suggested Citation

  • Ren Zhou & Mengying Wang & Wenyong Li & Siyue Wang & Hongchen Zheng & Zhibo Zhou & Yonghua Hu & Jing Li & Tao Wu & Hongping Zhu & Terri H. Beaty, 2019. "Haplotype and Haplotype-Environment Interaction Analysis Revealed Roles of SPRY2 for NSCL/P among Chinese Populations," IJERPH, MDPI, vol. 16(4), pages 1-7, February.
    • Handle: RePEc:gam:jijerp:v:16:y:2019:i:4:p:557-:d:206065
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    References listed on IDEAS

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    1. Brendan Maher, 2008. "Personal genomes: The case of the missing heritability," Nature, Nature, vol. 456(7218), pages 18-21, November.
    2. Anshul Kundaje & Wouter Meuleman & Jason Ernst & Misha Bilenky & Angela Yen & Alireza Heravi-Moussavi & Pouya Kheradpour & Zhizhuo Zhang & Jianrong Wang & Michael J. Ziller & Viren Amin & John W. Whit, 2015. "Integrative analysis of 111 reference human epigenomes," Nature, Nature, vol. 518(7539), pages 317-330, February.
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