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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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Komiyama Y, Koshiji C, Yoshida W, Natsume N, Kawamata H. 5,10-Methylenetetrahydrofolate reductase ( MTHFR) C677T/A1298C polymorphisms in patients with nonsyndromic cleft lip and palate. Biomed Rep 2020; 13:57. [PMID: 33123371 PMCID: PMC7583695 DOI: 10.3892/br.2020.1364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/21/2020] [Indexed: 11/06/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is considered a multifactorial genetic disorder. Folic acid metabolism has been suggested to underlie the development of CL/P. The gene for the enzyme 5,10-methylentetrahydrofolate reductase (MTHFR) contributes to folic acid metabolism, and polymorphisms of this gene at C677T (rs1801133) and A1298C (rs1801131) are reported to alter its enzyme activity and are suggested to be involved in CL/P development. We investigated C677T and A1298C polymorphisms of the MTHFR gene in Japanese patients with nonsyndromic CL/P and cleft palate only (CPO). We examined 240 patients with CL/P, 103 fathers and 153 mothers of the patients, and 68 healthy controls. Restriction fragment length polymorphisms (RFLPs) of C677T and A1298C of MTHFR were analyzed. We determined the frequencies of the polymorphisms in the patients and controls and performed a transmission equilibrium test and haplotype analysis of both MTHFR C677T and A1298C. There were no significant differences in the frequencies of MTHFR C677T and A1298C polymorphisms between the patients and controls. We did not observe transmission equilibrium or linkage equilibrium among the cases. In this experimental condition, we did not detect an association of MTHFR C677T and/or A1298C polymorphisms with the development of CL/P in this Japanese cohort.
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Affiliation(s)
- Yuske Komiyama
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Mibu, Tochigi 321-0293, Japan
| | - Chikako Koshiji
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Mibu, Tochigi 321-0293, Japan
| | - Waka Yoshida
- Department of Oral Pathology, School of Dentistry, Aichi-Gakuin University, Nagoya, Aichi 464-8650, Japan
| | - Nagato Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, School of Dentistry, Aichi-Gakuin University, Nagoya, Aichi 464-8650, Japan
| | - Hitoshi Kawamata
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Mibu, Tochigi 321-0293, Japan
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