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"If you have access to a real-time PCR instrument, you can analyze
the methylation status of multiple genes at the same time using the
Methyl-Profiler PCR technology."
The Methyl-Profiler DNA Methylation PCR Array System is a fast, reliable
technology that profiles the DNA methylation status of a panel of genes.
These PCR Arrays can help you discover and validate cancer or developmental
biomarkers useful for both basic and applied research. No bisulfite
conversion is required, and the challenges of real-time PCR primers design
and optimization has already been done for you. Achieve ten-fold higher
throughput than bisulfite sequencing and bisulfite PCR with the same
reliability and sensitivity expected from these methods.
You can use any 96-well or 384-well real-time PCR instrument.
Click below for detailed information.
How it Works
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.
Same Results as Bisulfite Sequencing
Methyl-Profiler DNA Methylation PCR Yields Results Identical 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. The matching results suggest that the easy-to-use DNA Methylation PCR
Array System can readily replace more tedious bisulfite PCR methods typically
used to validate bisulfite sequencing.
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 each
major type of cancer is still rapidly growing. However, even the most relevant
genes have not yet been correlated to individual cancer types or subtypes in
order to better define biological pathways and mechanisms leading to oncogenesis
and in order to properly develop DNA methylation biomarkers. The tedious and
low-throughput nature of the current bisulfite-based methods are not practical
for analyzing large numbers of genes in large numbers of tumor samples
simultaneously. The Methyl-Profiler PCR System provides an ideal reagent for
such studies. The following experiments demonstrate that DNA Methylation PCR
Arrays can both validate known and discover new DNA methylation cancer
biomarkers.
Biomarker Validation
Methyl-Profiler DNA Methylation PCR Arrays Validate Breast Cancer Gene
Methylation Status in Breast Cancer Cell Lines.
The heat map compares the hypermethylation status of 24 genes in the genomic DNA
of three breast cancer cell lines and blood genomic DNA (used as an unmethylated
control) determined with the Human Breast Cancer Signature Panel DNA Methylation
PCR Arrays. The results further strengthen the correlation of these biomarkers
with breast cancer.
Biomarker / Pathway Discovery
Cancer progresses through aberrant cell differentiation due to alterations in
gene expression. Transcription factors regulate gene expression, and many tumor
suppressor genes and oncogenes, defined by classical genetic methods, encode
transcription factors. Do 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.
The heat map compares the hypermethylation status of a panel of 79 transcription
factor genes in six different breast cancer cell lines (some in duplicate) and a
normal epithelial cell line as determined using 384-well Custom DNA Methylation
PCR Arrays. These breast cancer cell lines also hypermethylate this gene panel
potentially providing a new source of cancer biomarkers.
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.
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