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Chen X, Zhou Z, Li Y, Wang S, Xue E, Wang X, Peng H, Fan M, Wang M, Qin X, Wu Y, Li J, Zhu H, Chen D, Hu Y, Beaty TH, Wu T. Detecting Gene-Gene Interaction among DNA Repair Genes in Chinese non-Syndromic Cleft lip with or Without Palate Trios. Cleft Palate Craniofac J 2024:10556656241228124. [PMID: 38303570 DOI: 10.1177/10556656241228124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
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.
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Affiliation(s)
- Xi Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhibo Zhou
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yixin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Siyue Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Enci Xue
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xueheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hexiang Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Meng Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xueying Qin
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yiqun Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jing Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hongping Zhu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
| | - Dafang Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yonghua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
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Liu D, Wang M, Yuan Y, Schwender H, Wang H, Wang P, Zhou Z, Li J, Wu T, Zhu H, Beaty TH. Gene-gene interaction among cell adhesion genes and risk of nonsyndromic cleft lip with or without cleft palate in Chinese case-parent trios. Mol Genet Genomic Med 2019; 7:e00872. [PMID: 31419083 PMCID: PMC6785639 DOI: 10.1002/mgg3.872] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/27/2019] [Accepted: 07/08/2019] [Indexed: 01/07/2023] Open
Abstract
Background Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with complex etiology. One strategy for studying the genetic risk factors of NSCL/P is to consider gene–gene interaction (G × G) among gene pathways having a role in craniofacial development. The present study aimed to investigate the G × G among cell adhesion gene pathway. Methods We carried out an interaction analysis of eight genes involved in cell adherens junctions among 806 NSCL/P Chinese case‐parent trios originally recruited for a genome‐wide association study (GWAS). Regression‐based approach was used to test for two‐way G × G interaction, while machine learning algorithm was run for exploring both two‐way and multi‐way interaction that may affect the risk of NSCL/P. Results A two‐way ACTN1 × CTNNB1 interaction reached the adjusted significance level. The single nucleotide polymorphisms pair composed of rs17252114 (CTNNB1) and rs1274944 (ACTN1) yielded a p value of .0002, and this interaction was also supported by the logic regression algorithm. Higher order interactions involving ACTN1, CTNNB1, and CDH1 were picked out by logic regression, suggesting a potential role in NSCL/P risk. Conclusion This study suggests for the first time evidence of both two‐way and multi‐way G × G interactions among cell adhesion genes contributing to the NSCL/P risk.
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Affiliation(s)
- Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Yuan Yuan
- School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Hong Wang
- School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Jing Li
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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