DNA Methylation Array Service
DNA Methylation arrays provide quantitative querying of specific methylation sites in the genome, allowing for high-throughput capabilities at a low cost per sample.
The epigenome is the primary focus of contemporary multi-omics research, and DNA methylation modification research is the most important subfield within the science of epigenetics. The modification of DNA by methylation is an important approach for regulating gene expression. This mechanism is involved in a variety of activities, including differentiation, development, the inactivation of chromosomes, and the specialization of tissue. Moreover, DNA methylation is also associated with the development and progression of a wide variety of complicated diseases, including diabetes, neurological system disorders, and cancer.
DNA Methylation
The biological process of DNA methylation refers to the addition of methyl groups to the molecule of DNA. A DNA region's activity can be modified by the process of methylation without affecting the sequence in any way. When DNA methylation takes place in the promoter region of a gene, its typical effect is to dampen the activity of the gene. DNA methylation is necessary for proper development in mammals and is associated with a number of important processes, including genomic imprinting, X-chromosome inactivation, transposable element suppression, aging, and cancer. And DNA methylation is also required for the prevention of cancer.
Fig.1 Typical DNA methylation landscape in mammals. (Wikipedia)
Methylation Array Services at Creative Biolabs
DNA methylation microarrays complement other methods. Microarrays can be used for bisulfite conversion, MBD-based capture, and many more methods. Microarrays target methylated or potentially methylated areas in methylation investigations. CpG island arrays target all known CpG islands. Common promoter arrays cover all RefSeq promoters in the species of interest (human, mouse, or rat). Although microarrays are less powerful than next-generation sequencing (NGS), their low cost and high throughput make them helpful for large-scale and high-throughput studies.
Fig.2 Workflow of the methylation array assay. (Wikipedia)
Creative Biolabs offers mainstream DNA methylation microarrays and comprehensive array-based DNA methylation testing tools. We also offer customized methylation microarrays. For more information, please contact us.
Published Data
| Paper Title | Host methylation predicts SARS-CoV-2 infection and clinical outcome |
| Journal | Communications Medicine |
| Published | 2021 |
| Abstract | They modified Illumina's Infinium Methylation EPIC array to improve immune response detection and profiled peripheral blood samples from 164 COVID-19 patients with longitudinal disease severity measurements and 288 patient controls. In conclusion, the strong COVID-19-specific epigenetic signature in peripheral blood driven by key immune-related pathways associated with infection status, disease severity, and clinical deterioration provides diagnostic and prognostic information for patients with the viral infection. |
| Result |
They first conducted an EWAS (Epigenome-Wide Association Study) to identify biological signals associated with the disease status of COVID-19. After adjusting for age, sex, array position (batch effect), cell proportions via ReFACTOR, ancestry via EPISTRUCTURE components, and EWAS of COVID-19 disease status in 164 SARS-CoV-2+ compared to 296 controls yielded 13,033 significant CpGs mapping to 6117 unique genes with a false discovery rate (FDR)-adjusted P value < 0.05 and moderate inflation typical of EWAS. Then they observed a total of 35 probes with an unadjusted P value < 10-20 and 183 probes with an unadjusted P value < 10-10. 1625 CpG islands and 1001 FANTOM5 enhancers are overlapped by significant probes. 52.1 percent of all significant probes were found to be hypermethylated; however, 78 percent of the top 100 probes ranked by adjusted P value were hypomethylated (Fisher's Exact Test P value = 9.46 x 10-8). Custom probes on the EPIC+ chip have a higher proportion of significant EWAS results (P value = 9.94 x 10-7, Fisher's Exact Test): 1.72 percent of EPIC probes are significant compared to 2.51 percent of custom probes. An analysis of the principal components of the leading associations reveals clustering by COVID-19 disease status. Concerned that population admixture might confound results, the COVID-19 disease status EWAS was repeated with EHR-defined race and ethnicity as additional covariates in addition to those modeled by EPISTRUCTURE and mixed-effects modeling. This had a minimal impact on the outcomes.
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Fig.3 Differentially methylated CpGs associated with SARS-CoV-2 infection. (Konigsberg, 2021)
Features
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Comprehensive Genome Coverage
DNA Methylation Arrays provide extensive coverage of CpG sites across the genome, including gene promoters, enhancers, and intergenic regions.
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High-Throughput Capability
The arrays offer high-throughput capabilities, allowing simultaneous analysis of multiple samples.
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Single-Nucleotide Resolution
High resolution ensures precise identification of methylation sites, allowing detailed epigenetic mapping and accurate detection of methylation changes associated with various diseases, enhancing the depth and reliability of research findings.
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Versatile Sample Compatibility
The arrays can analyze various sample types, including fresh-frozen tissues, formalin-fixed paraffin-embedded (FFPE) tissues, and blood samples.
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Integrated Data Analysis Tools
The service includes access to advanced bioinformatics tools for comprehensive data analysis. These tools support various functions such as SNP calling, copy number variation analysis, and functional annotation, ensuring that researchers can efficiently interpret and utilize the genetic data generated from their studies.
Q&As
Q: How does DNA methylation influence gene expression?
A: DNA methylation typically suppresses gene expression by adding methyl groups to cytosine residues in CpG dinucleotides. This modification can regulate gene activity, affect chromatin structure, and maintain genome stability, playing critical roles in development and disease.
Q: What kind of samples can be analyzed using DNA Methylation Arrays?
A: DNA Methylation Arrays can analyze various sample types, including fresh-frozen tissues, formalin-fixed paraffin-embedded (FFPE) tissues, and blood samples. This versatility makes them suitable for a wide range of research and clinical applications.
Q: How is data from the DNA Methylation Array Service analyzed?
A: Data analysis involves several steps, including normalization, identification of differentially methylated regions, and integration with gene expression data. Advanced bioinformatics tools are used to interpret methylation patterns and their biological significance.
Q: Can the DNA Methylation Array Service be used for longitudinal studies?
A: Yes, the service is ideal for longitudinal studies, allowing researchers to monitor changes in DNA methylation over time. This is particularly useful in studying disease progression, treatment response, and the effects of environmental exposures.
Q: How do DNA Methylation Arrays contribute to personalized medicine?
A: DNA Methylation Arrays can identify individual-specific methylation patterns that may influence disease risk, treatment response, and drug efficacy. This information can guide personalized treatment plans, ensuring that therapies are tailored to the unique epigenetic makeup of each patient.
Resources
Reference
- Konigsberg, I.R.; et al. Host methylation predicts SARS-CoV-2 infection and clinical outcome. Communications Medicine. 2021, 1(1):42.
