Unknown

Dataset Information

0

Gene-gene interaction of single nucleotide polymorphisms in 16p13.3 may contribute to the risk of non-syndromic cleft lip with or without cleft palate in Chinese case-parent trios.


ABSTRACT: Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex and heterogeneous etiology. A recent genome-wide association study (GWAS) among Chinese populations has identified a new region at 16p13.3 as being associated with NSCL/P, which requires further replication. Here, we attempted to replicate and further clarify the genetic association between this region and NSCL/P, as well as testing for potential gene-gene (G?×?G) and gene-environment (G?×?E) interactions. We conducted transmission disequilibrium tests on 69 single nucleotide polymorphisms (SNPs) mapping to 16p13.3 among 806 Chinese case-parent trios ascertained through an international consortium where a GWAS of oral clefts was conducted. G?×?G, as well as G?×?E interactions involving maternal environmental tobacco smoke (ETS) and multivitamin supplementation, were explored using conditional logistic regression model. We applied Cordell's method as implemented in the R package TRIO to test for possible interactions. While no SNPs showed evidence of linkage and association with NSCL/P after Bonferroni correction, we found signals of G?×?G interactions between SNPs in 16p13.3. Nine pairs of SNP-SNP interactions attained significance after Bonferroni correction, among which the most significant interaction was found between rs2072346 (ADCY9) and rs11646137 (intergenic region, P?=?7.2?×?10-5 ). Linkage disequilibrium (LD) analysis revealed only low level of LD between these SNPs. This study failed to confirm the significant association between SNPs within 16p13.3 and the risk of NSCL/P, but underlined the importance of taking into account potential G?×?G interactions for the genetic association analysis of NSCL/P.

SUBMITTER: Liu D 

PROVIDER: S-EPMC5559727 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

altmetric image

Publications

Gene-gene interaction of single nucleotide polymorphisms in 16p13.3 may contribute to the risk of non-syndromic cleft lip with or without cleft palate in Chinese case-parent trios.

Liu Dongjing D   Wang Hong H   Schwender Holger H   Marazita Mary L ML   Wang Zhuqing Z   Yuan Yuan Y   Wang Ping P   Liang Kung Yee KY   Wu-Chou Yah Huei YH   Wang Mengying M   Shi Bing B   Zhu Hongping H   Wu Tao T   Beaty Terri H TH  

American journal of medical genetics. Part A 20170412 6


Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex and heterogeneous etiology. A recent genome-wide association study (GWAS) among Chinese populations has identified a new region at 16p13.3 as being associated with NSCL/P, which requires further replication. Here, we attempted to replicate and further clarify the genetic association between this region and NSCL/P, as well as testing for potential gene-gene (G × G) and gene-environment (G × E) in  ...[more]

Similar Datasets

| S-EPMC6785639 | biostudies-literature
| S-EPMC1885468 | biostudies-literature
| S-EPMC6207999 | biostudies-literature
| S-EPMC4164844 | biostudies-literature
| S-EPMC10957387 | biostudies-literature
| S-EPMC7653437 | biostudies-literature
| S-EPMC4623215 | biostudies-literature
| S-EPMC9197716 | biostudies-literature
| S-EPMC4564499 | biostudies-literature
| S-EPMC9449191 | biostudies-literature