TY - JOUR
T1 - Detecting Gene-Gene Interaction among DNA Repair Genes in Chinese non-Syndromic Cleft lip with or Without Palate Trios
AU - Chen, Xi
AU - Zhou, Zhibo
AU - Li, Yixin
AU - Wang, Siyue
AU - Xue, Enci
AU - Wang, Xueheng
AU - Peng, Hexiang
AU - Fan, Meng
AU - Wang, Mengying
AU - Qin, Xueying
AU - Wu, Yiqun
AU - Li, Jing
AU - Zhu, Hongping
AU - Chen, Dafang
AU - Hu, Yonghua
AU - Beaty, Terri H.
AU - Wu, Tao
N1 - Publisher Copyright:
© 2024, American Cleft Palate Craniofacial Association.
PY - 2024
Y1 - 2024
N2 - Objective: The objective of this study is to investigate the gene-gene interactions associated with NSCL/P among DNA repair genes. Design: This study included 806 NSCL/P case-parent trios from China. Quality control process was conducted for genotyped single nucleotide polymorphisms (SNPs) located in six DNA repair genes (ATR, ERCC4, RFC1, TYMS, XRCC1 and XRCC3). We tested gene-gene interactions with Cordell's method using statistical package TRIO in R software. Bonferroni corrected significance level was set as P = 4.24 × 10–4. We also test the robustness of the interactions by permutation tests. Setting: Not applicable. Patients/Participants: A total of 806 NSCL/P case-parent trios (complete trios: 682, incomplete trios: 124) with Chinese ancestry. Interventions: Not applicable. Main Outcome Measure(s): Not applicable. Results: A total of 118 SNPs were extracted for the interaction tests. Fourteen pairs of significant interactions were identified after Bonferroni correction, which were confirmed in permutation tests. Twelve pairs were between ATR and ERCC4 or XRCC3. The most significant interaction occurred between rs2244500 in TYMS and rs3213403 in XRCC1(P = 8.16 × 10–15). Conclusions: The current study identified gene-gene interactions among DNA repair genes in 806 Chinese NSCL/P trios, providing additional evidence for the complicated genetic structure underlying NSCL/P. ATR, ERCC4, XRCC3, TYMS and RFC1 were suggested to be possible candidate genes for NSCL/P.
AB - Objective: The objective of this study is to investigate the gene-gene interactions associated with NSCL/P among DNA repair genes. Design: This study included 806 NSCL/P case-parent trios from China. Quality control process was conducted for genotyped single nucleotide polymorphisms (SNPs) located in six DNA repair genes (ATR, ERCC4, RFC1, TYMS, XRCC1 and XRCC3). We tested gene-gene interactions with Cordell's method using statistical package TRIO in R software. Bonferroni corrected significance level was set as P = 4.24 × 10–4. We also test the robustness of the interactions by permutation tests. Setting: Not applicable. Patients/Participants: A total of 806 NSCL/P case-parent trios (complete trios: 682, incomplete trios: 124) with Chinese ancestry. Interventions: Not applicable. Main Outcome Measure(s): Not applicable. Results: A total of 118 SNPs were extracted for the interaction tests. Fourteen pairs of significant interactions were identified after Bonferroni correction, which were confirmed in permutation tests. Twelve pairs were between ATR and ERCC4 or XRCC3. The most significant interaction occurred between rs2244500 in TYMS and rs3213403 in XRCC1(P = 8.16 × 10–15). Conclusions: The current study identified gene-gene interactions among DNA repair genes in 806 Chinese NSCL/P trios, providing additional evidence for the complicated genetic structure underlying NSCL/P. ATR, ERCC4, XRCC3, TYMS and RFC1 were suggested to be possible candidate genes for NSCL/P.
KW - case-parent trios
KW - cleft lip with or without palate
KW - DNA repair genes
KW - gene-gene interaction
KW - genome-wide association study
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U2 - 10.1177/10556656241228124
DO - 10.1177/10556656241228124
M3 - Article
C2 - 38303570
AN - SCOPUS:85184265805
SN - 1055-6656
JO - Cleft Palate Journal
JF - Cleft Palate Journal
ER -