Study on the association between TPM1 gene-related polymorphism and nonsyndromic orofacial clefts in the northern Chinese Han population

doi:10.3969/j.issn.1005-4979.2022.01.007

Abstract

Abstract:

Objective: To analyze the association between three single nucleotide polymorphisms(SNPs) in the upstream functional region of TPM1 and nonsyndromic orofacial clefts(NSOC) in northern Chinese Han population. Methods: The peripheral blood DNA in 335 NSOC samples and 572 control samples were examined. The target sites were amplified by polymerase chain reaction(PCR), sequenced and genotyped. The basic information of polymorphic loci were collected from PubMed database (https://www.ncbi.nlm.nih.gov/pubmed). The allele frequency, genotype and haplotype of SNPs loci were analyzed by SHEsis and SPSS 20.0 software. Results: TPM1-related rs1873147, rs7179658 and rs4775599 were in complete linkage, and the allele frequency difference of rs1873147 between the cleft lip and palate(CLP) group and the healthy control group was statistically significant(P=0.035). Conclusion: TPM1-related rs7179658, rs1873147 and rs477559 may be associated with NSOC in the northern Chinese Han population.

Key words: nonsyndromic orofacial clefts, TPM1, single nucleotide polymorphism

摘要：

目的：分析TPM1基因上游功能区3个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点与中国北方人群非综合征性唇腭裂（nonsynodromic orofacial clefts, NSOC）的关联。方法：通过对335个NSOC样本及572个健康对照样本外周血DNA的研究对目的位点行聚合酶链反应（polymerase chain reaction, PCR）扩增、DNA测序、基因分型。利用PubMed数据库（https://www.ncbi.nlm.nih.gov/pubmed）采集相关多态性位点基本信息。使用SHEsis在线软件、SPSS 20.0软件对SNPs位点的等位基因频率、基因型及单体型进行分析研究。结果：TPM1相关rs1873147、rs7179658和rs4775599完全连锁，rs1873147在唇腭裂（cleft lip and palate, CLP）组与健康对照组之间的等位基因频率差异有统计学意义（P=0.035）。结论：TPM1相关rs7179658、rs1873147和rs477559与中国北方汉族人群NSOC可能存在关联。

关键词: 非综合征性唇腭裂, TPM1基因, 单核苷酸多态性

HUI Xiang, JIANG Yuxin, LIU Tingting, SHI Xuheng, WANG Qi, SONG Tao. Study on the association between TPM1 gene-related polymorphism and nonsyndromic orofacial clefts in the northern Chinese Han population[J]. 《Journal of Oral and Maxillofacial Surgery》, 2022, 32(1): 34-41.

回翔, 姜宇欣, 刘婷婷, 时旭恒, 王琪, 宋涛. TPM1基因相关多态性与中国北方汉族人群非综合征性唇腭裂的相关研究[J]. 《口腔颌面外科杂志》, 2022, 32(1): 34-41.

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URL: https://journal06.magtech.org.cn/Jweb_joms/EN/10.3969/j.issn.1005-4979.2022.01.007

https://journal06.magtech.org.cn/Jweb_joms/EN/Y2022/V32/I1/34

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References 22

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名称	位置
rs4775599	Chr15: 63 019 296
rs1873147	Chr15: 63 020 433
rs7179658	Chr15: 63 020 496
TPM1	Chr15: 63 042 698~63 071 915
间距	22 202~23 402

名称	位置
rs4775599	Chr15: 63 019 296
rs1873147	Chr15: 63 020 433
rs7179658	Chr15: 63 020 496
TPM1	Chr15: 63 042 698~63 071 915
间距	22 202~23 402

SNP	项目	人群	组别	样本量	参考等位基因	变异等位基因
rs7179658	1000 Genomes	全球	全组别范围	5 008	T=0.498	C=0.502
	1000 Genomes	东亚	亚组	1 008	T=0.863	C=0.137
	本研究	中国北方	亚组	572	T=0.844	C=0.156
rs1873147	1000 Genomes	全球	全组别范围	5 008	G=0.496	A=0.504
	1000 Genomes	东亚	亚组	1 008	G=0.860	A=0.140
	本研究	中国北方	亚组	572	G=0.844	A=0.156
rs4775599	1000 Genomes	全球	全组别范围	5 008	A=0.496	G=0.504
	1000 Genomes	东亚	亚组	1 008	A=0.860	G=0.140
	本研究	中国北方	亚组	572	A=0.844	G=0.166

SNP	项目	人群	组别	样本量	参考等位基因	变异等位基因
rs7179658	1000 Genomes	全球	全组别范围	5 008	T=0.498	C=0.502
	1000 Genomes	东亚	亚组	1 008	T=0.863	C=0.137
	本研究	中国北方	亚组	572	T=0.844	C=0.156
rs1873147	1000 Genomes	全球	全组别范围	5 008	G=0.496	A=0.504
	1000 Genomes	东亚	亚组	1 008	G=0.860	A=0.140
	本研究	中国北方	亚组	572	G=0.844	A=0.156
rs4775599	1000 Genomes	全球	全组别范围	5 008	A=0.496	G=0.504
	1000 Genomes	东亚	亚组	1 008	A=0.860	G=0.140
	本研究	中国北方	亚组	572	A=0.844	G=0.166

rs1873147	分组	基因型/[n（%）]			Chi²值	P值
rs1873147	分组	CC	CT	TT	Chi²值	P值
	对照组	411（71.9）	142（24.8）	18（3.1）	1.72	0.19
	NSOC组	249（74.3）	80（23.9）	6（1.8）	0.02	0.88
	CLO组	77（75.5）	22（21.6）	3（2.9）	0.81	0.37
	CLP组	75（80.6）	18（19.4）	0	1.07	0.30
	CPO组	3（2.1）	40（28.6）	97（69.3）	0.23	0.63

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