从Illumina Infinium人类甲基化微阵列中检测多态CpG的现有方法中的差距,并在多EWAS分析中探索它们的潜在影响
Basharat Bhat1, Gregory T Jones1
1Departments of Surgical Sciences, University of Otago, Dunedin, New Zealand.
Epigenetics
|November 20, 2023
概括
整个表观基因组的关联研究 (EWAS) 可以被遗传变异混. 目前的工具很难在不同人群中识别这些甲基化定量特征位点 (meQTL),这限制了它们在多民族EWAS中的有效性.
科学领域:
- 遗传学 是一个遗传学.
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 生物信息学是一种生物信息学.
背景情况:
- 全表观基因组关联研究 (EWAS) 识别疾病的DNA甲基化 (DNAm) 生物标志物.
- 遗传多态性可以影响DNAm水平,产生甲基化定量特征位点 (meQTLs).
- meQTL频率在不同的人群中存在差异,可能会混多民族EWAS.
研究的目的:
- 评估两个工具 (GapHunter和MethylToSNP) 在识别meQTLs方面的性能.
- 评估这些工具在检测多态CpG遗址跨多种祖先群体的一致性.
主要方法:
- 对来自6个祖先群体的1342个个体的公开可用的DNA甲基化概况 (450K阵列) 的分析.
- 利用GapHunter和MethylToSNP来识别受遗传变异影响的CpG位点.
- 在不同小等位基频率 (MAF) 上研究了工具性能.
主要成果:
- 无论是GapHunter还是MethylToSNP,都未能一致识别meQTL,特别是对于较罕见的变体 (MAF<0.05).
- 超过一半的与常见变异相关的部位 (MAF>0.2) 没有被检测到.
- 在检测多态CpG时,GapHunter和MethylToSNP之间观察到较低的一致性.
结论:
- 目前的工具不太可能在EWAS中全面识别所有遗传混影响.
- 使用这些工具选EWAS关联可能不够强大来检测meQTLs.
- 为了在多民族研究中准确检测meQTL,需要进一步开发.
相关概念视频
Comparing Copy Number Variations and SNPs
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
DNA Microarrays
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...


