BACKGROUND DNA methylation is a part of epigenetic modification,that is closely related to the growth and development of colorectal cancer(CRC).Specific methylated genes and methylated diagnostic models of tumors have...BACKGROUND DNA methylation is a part of epigenetic modification,that is closely related to the growth and development of colorectal cancer(CRC).Specific methylated genes and methylated diagnostic models of tumors have become current research focuses.The methylation status of circulating DNA in plasma might serve as a potential biomarker for CRC.AIM To investigate genome-wide methylation pattern in early CRC using the Illumina Infinium Human Methylation 850K BeadChip.METHODS The 850K Methylation BeadChip was used to analyze the genome-wide methylation status of early CRC patients(n=5)and colorectal adenoma patients(n=5).Gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways enrichment analyses were performed on the selected differentially methylated sites to further discover candidate methylation biomarkers in plasma.RESULTS A total of 1865 methylated CpG sites with significant differences were detected,including 676 hypermethylated sites and 1189 hypomethylated sites.The distribution of these sites covered from the 1^(st) to 22^(nd) chromosomes and are mainly distributed on the gene body and gene promoter region.GO and KEGG enrichment analysis showed that the functions of these genes were related to biological regulation,molecular binding,transcription factor activity and signal transduction pathway.CONCLUSION The study demonstrated that the Illumina Infinium Human Methylation 850K BeadChip can be used to investigate genome-wide methylation status of plasma DNA in early CRC and colorectal adenoma patients.展开更多
【目的】检测隆林猪的全基因组拷贝数变异。【方法】采集33头隆林猪的耳组织样本,通过酚-氯仿法提取DNA后,使用猪中芯一号50K SNP芯片进行基因分型,得到的原始数据通过Genomestudio软件和Linux系统进行处理,使用CNVPartition和PennCNV...【目的】检测隆林猪的全基因组拷贝数变异。【方法】采集33头隆林猪的耳组织样本,通过酚-氯仿法提取DNA后,使用猪中芯一号50K SNP芯片进行基因分型,得到的原始数据通过Genomestudio软件和Linux系统进行处理,使用CNVPartition和PennCNV软件分别检测拷贝数变异(copy number variation,CNV),并利用Bedtools软件将CNV合并为拷贝数变异区域(copy number variation region,CNVR),使用Biomart对CNVR进行基因定位,利用David网站对定位到的基因进行GO和KEGG富集分析,使用猪QTL数据库对共同CNVR进行QTL注释。【结果】CNVPartition软件共检测到260个CNVs,合并为47个CNVRs,其中缺失型40个、获得型5个、混合型2个,共定位到84个基因,显著富集到13条信号通路;PennCNV软件共检测到96个CNVs,合并为15个CNVRs,其中缺失型9个、获得型1个、混合型5个,共定位到8个基因,显著富集到8条信号通路;2个软件检测结果定位到的基因主要富集在嗅觉相关通路和G-蛋白偶联相关通路中,其中INPP5B、NEURL1和GAPDHS基因显著富集到精子活力通路;2个软件获得了3个共同CNVRs,其中缺失型、获得型和混合型均为1个,共定位到8个基因,显著富集到涉及嗅觉感官知觉的化学刺激检测通路、嗅觉受体活性通路、嗅觉转导通路、G-蛋白偶联受体活性通路、G-蛋白偶联受体信号通路、膜整体组件通路和质膜通路共7条信号通路;共有130个QTLs与3个共同CNVRs重叠,其中与背膘厚、肉质和乳头数相关的QTLs分别有11、9和6个。【结论】隆林猪CNV可能与嗅觉功能、繁殖性能、背膘厚、肉质和乳头数性状相关。展开更多
基金Supported by National Natural Science Foundation of China,No. 81972010the National Key Research and Development Program of China,No. 2020YFC2002700, and No. 2020YFC2004604
文摘BACKGROUND DNA methylation is a part of epigenetic modification,that is closely related to the growth and development of colorectal cancer(CRC).Specific methylated genes and methylated diagnostic models of tumors have become current research focuses.The methylation status of circulating DNA in plasma might serve as a potential biomarker for CRC.AIM To investigate genome-wide methylation pattern in early CRC using the Illumina Infinium Human Methylation 850K BeadChip.METHODS The 850K Methylation BeadChip was used to analyze the genome-wide methylation status of early CRC patients(n=5)and colorectal adenoma patients(n=5).Gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways enrichment analyses were performed on the selected differentially methylated sites to further discover candidate methylation biomarkers in plasma.RESULTS A total of 1865 methylated CpG sites with significant differences were detected,including 676 hypermethylated sites and 1189 hypomethylated sites.The distribution of these sites covered from the 1^(st) to 22^(nd) chromosomes and are mainly distributed on the gene body and gene promoter region.GO and KEGG enrichment analysis showed that the functions of these genes were related to biological regulation,molecular binding,transcription factor activity and signal transduction pathway.CONCLUSION The study demonstrated that the Illumina Infinium Human Methylation 850K BeadChip can be used to investigate genome-wide methylation status of plasma DNA in early CRC and colorectal adenoma patients.
文摘【目的】检测隆林猪的全基因组拷贝数变异。【方法】采集33头隆林猪的耳组织样本,通过酚-氯仿法提取DNA后,使用猪中芯一号50K SNP芯片进行基因分型,得到的原始数据通过Genomestudio软件和Linux系统进行处理,使用CNVPartition和PennCNV软件分别检测拷贝数变异(copy number variation,CNV),并利用Bedtools软件将CNV合并为拷贝数变异区域(copy number variation region,CNVR),使用Biomart对CNVR进行基因定位,利用David网站对定位到的基因进行GO和KEGG富集分析,使用猪QTL数据库对共同CNVR进行QTL注释。【结果】CNVPartition软件共检测到260个CNVs,合并为47个CNVRs,其中缺失型40个、获得型5个、混合型2个,共定位到84个基因,显著富集到13条信号通路;PennCNV软件共检测到96个CNVs,合并为15个CNVRs,其中缺失型9个、获得型1个、混合型5个,共定位到8个基因,显著富集到8条信号通路;2个软件检测结果定位到的基因主要富集在嗅觉相关通路和G-蛋白偶联相关通路中,其中INPP5B、NEURL1和GAPDHS基因显著富集到精子活力通路;2个软件获得了3个共同CNVRs,其中缺失型、获得型和混合型均为1个,共定位到8个基因,显著富集到涉及嗅觉感官知觉的化学刺激检测通路、嗅觉受体活性通路、嗅觉转导通路、G-蛋白偶联受体活性通路、G-蛋白偶联受体信号通路、膜整体组件通路和质膜通路共7条信号通路;共有130个QTLs与3个共同CNVRs重叠,其中与背膘厚、肉质和乳头数相关的QTLs分别有11、9和6个。【结论】隆林猪CNV可能与嗅觉功能、繁殖性能、背膘厚、肉质和乳头数性状相关。
