Methyl-Profiler™ DNA Methylation PCR Arrays

The Methyl-Profiler DNA Methylation PCR Arrays allows the DNA methylation profiling of a panel of 24 (96-well format) or 96 (384-well format) genes promoters simultaneously. These genes have been carefully selected based on their reported hypermethylation in a variety of experimental settings. Profiling your biological DNA samples with these arrays will allow you to correlate CpG island methylation status with biological phenotypes or disease outcomes, and the results can provide insights into the molecular mechanisms and biological pathways critical for disease development. With a simple restriction enzyme digestion followed by real-time PCR, you can analyze the DNA methylation levels of 24 or 96 different genes simultaneously using DNA Methylation PCR Arrays.

List of PCR Arrays Available:

How It Works

DNA methylation plays an important role in gene expression and it occurs almost exclusively in the context of CpG dinucleotides in the form of a covalent attachment of a methyl residue to the cytosine residue. CpG islands (CGIs) are regions with an elevated GC content and a high frequency of CpG dinuleotides which overlap the promoter region of 60-70% of all human genes. Hypermethylation of CpG islands at gene promoters is mostly associated with gene silencing.

The Methyl-Profiler PCR Array System relies on the differential cleavage of target sequences by two different restriction endonucleases whose activities require either the presence or absence of methylated cytosines in their respective recognition sequences. As real-time PCR quantifies the relative amount of DNA remaining after each enzyme digestion, the methylation status of individual genes and the methylation profile across a gene panel are reliably and easily calculated. The high yield of DNA from the restriction digests and PCR amplification allow the analysis of smaller, more heterogeneous samples.

Download User Manual           Tour the FREE Data Analysis Template

What It Offers:

• Guaranteed Performance - Ready-to-use for DNA methylation analysis
• Time & Cost Savings - Less than 30 min hands-on time to analyze 24 or 96 genes
• Easy Data Analysis - FREE Excel-based data analysis template available

You can easily perform a Methyl-Profiler experiment in your own laboratory using any 96-well or 384-well real-time PCR instrument that you have access to.
Or you can send your DNA samples to us and take advantage of our PCR Array Services.

Array Layout:
The PCR Arrays are available in both 96- and 384-well plate formats to analyze the methylation status of 24 or 96 genes related to a disease state, such as specific types of cancer, or development pathways related to specific cells or tissues. The signature panels of 24 genes are arranged on either 96-well or 384-well plates to simultaneously characterize all four restriction digests from either one or four different DNA samples, respectively. The more complete panels of 96 genes are arranged on 96- or 384-well plates to characterize all four restriction digests from one DNA sample either on four plates or all on the same plate, respectively.

For more detail on PCR Array layout, see the "Gene Table" link for the individual array products.

Performance Data

To validate the reliability of the Methyl-Profiler DNA Methylation PCR Array System, its results and sensitivity were compared with bisulfite sequencing, the gold standard in DNA methylation analysis.

Similar Result as Bisulfite Sequencing

Methyl-Profiler DNA Methylation PCR Assays Yield Results Similar to Bisulfite Sequencing
The methylation status of the cadherin 1 (CDH1) gene promoter was analyzed using either bisulfite sequencing or DNA Methylation PCR Assays in three different breast cancer cell lines known to have very different CDH1 methylation patterns.

Same Sensitivity as Bisulfite Sequencing
Primary tumors are typically very heterogeneous, containing a mixture of both cancerous and noncancerous cells. Therefore, reliable tumor characterization requires detecting smaller amounts of hypermethylated DNA diluted in an unmethylated background.

Methyl-Profiler DNA Methylation PCR Detects Hypermethylation in Heterogeneous Samples Containing As Little As Five Percent Tumor DNA.
SKBR3 breast cancer cell line and normal blood genomic DNA (encoding hypermethylated and unmethylated HIC1, respectively) were mixed in different ratios. Using Human HIC1 DNA Methylation qPCR Primers, the percentage of hypermethylated HIC1 relative to total promoter DNA in each mixture was detectable even down to five percent of the total DNA sample.

Application Data

Gene promoter methylation is the most common epigenetic mechanism silencing tumor suppressor genes during oncogenesis. Almost all cancer-related signaling pathways are affected by methylation, and the number of genes affected in cancer is growing rapidly. However, even the most cancer type-relevant gene is not sufficient to define individual cancer types. In order to better define biological pathways and mechanisms leading to oncogenesis, the DNA methylation profiling of a large number of genes is required. The labor-intensive and time-consuming bisulfite-based DNA methylation analysis methods are not practical for analyzing a large number of genes in a large number of tumor samples simultaneously. The Methyl-Profiler PCR Array System provides an ideal tool for such studies. The following experiments demonstrate that DNA methylation PCR Arrays not only validate known but also discover new DNA methylation cancer biomarkers.

Biomarker Validation

Methyl-Profiler PCR Arrays Validate Breast Cancer Gene Methylation Status in Breast Cancer Cell Lines.
Heat map representation of the methylation status of 24 genes in the genomic DNA of three breast cancer cell lines and blood genomic DNA as determined by Human Breast Cancer Signature Panel DNA Methylation PCR Arrays.

Biomarker / Pathway Discovery
Cancer progresses through aberrant cell differentiation due to alterations in gene expression. Tumor suppressor genes and oncogenes, defined by classical genetic methods, encode transcription factors that play an important role in gene regulation. Does the methylation status of transcription factor genes differ between cancer and normal cells?

Methyl-Profiler DNA Methylation PCR Arrays Discover New Candidate Breast Cancer DNA Methylation Biomarkers.
Heat map representation of the methylation status of a panel of 79 transcription factor genes in six breast cancer lines and a normal epithelial cell line as determined with Custom DNA Methylation PCR Arrays.

These results are consistent with the notions that aberrant expression of transcription factors controlling cell differentiation plays key roles in oncogenesis and that transcription factors can be tumor suppressors.

Resources:

Methyl-Profiler DNA Methylation PCR Array Manual

Methyl Profiler Enzyme Kit
To prepare DNA samples for Methyl-Profiler DNA Methylation PCR Arrays or qPCR Primers of choice

RT² SYBR® Green qPCR Master Mixes
Instrument-specific PCR master mixes insure high-efficiency, sequence-specific amplification

Data Analysis Software (Excel template)

Attend a Webinar to have dialects with our Application Scientists