摘要
目的运用生物信息学方法对肝癌易感基因ARID1A的低频遗传变异进行功能初探,为后续肝癌遗传关联研究提供线索。方法运用1000 genomes、db SNP、UCSC等数据库检索ARID1A的低频遗传变异名录;通过Regulome DB、SNPinfo、F-SNP等功能注释数据库预测低频变异的功能。结果在1000 genomes的中国汉族南方人群和中国汉族北方人群数据中,ARID1A基因上MAF≤0.05的遗传变异各有141和139个,其中135个低频变异位于调控区或编码区。Regulome DB、SNPinfo、F-SNP等数据库预测出9个潜在功能变异,分别为rs12685、rs60798877、rs6598860、rs12739212、rs139907456、rs34618114、rs191813608、rs182858322和rs78520390。结论所识别的ARID1A基因的9个低频潜在功能变异,可作为肝癌遗传关联研究的目标变异,以助于系统阐明ARID1A低频变异对肝癌易感性的影响。
Objective To analyze the low-frequency variations in the liver cancer susceptibility gene ARID1A using a comprehensive bioinformatics strategy, and provide a clue for the genetic association studies of liver cancer. Methods 1000 Genomes Project, dbSNP, UCSC and other databases were applied to query the list of low-frequency variants. Allele frequency calculator was used to select the variants with the minor allele frequency （MAF） ≤ 5%. RegulomeDB, SNPinfo, F-SNP and other tools were utilized to predict the function of low-frequency variants. Results There were 141 and 139 variants with the MAF ≤ 5% in the CHS and CHB data of 1000 genomes, respectively, in which 135 variants were located in the regulatory region or coding region. Nine variants had been predicted to be potential functional by RegulomeDB, SNPinfo, F-SNP and other tools. Conclusion The potentially functional variants in AR1DIA with low- frequency could be used as targets in the genetic association studies of liver cancer, which may provide an evidence for exploring the effect of ARID1A low-frequency variants on the development of liver cancer.
出处
《广东药科大学学报》
CAS
2017年第2期270-274,共5页
Journal of Guangdong Pharmaceutical University
基金
国家青年科学基金项目(81302493)
