Breast Cancer DNA Methylation PCR Array

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Human Breast Cancer DNA Methylation PCR Array, Complete Panel MeAH-8010 (4 × 96-well) MeAH-3010 (384-well)
The Human Breast Cancer Methyl-Profiler DNA Methylation PCR Arrays profile the methylation status of 96 tumor suppressor gene promoters whose hypermethylation has been reported in the literature the most frequently in a variety of breast tumors. Profiling your tumor samples with these arrays will correlate CpG island methylation status with biological phenotypes or clinical outcomes like staging, therapy selection, metastasis, recurrence, and survival rate, among others. The results also provide insights into the molecular mechanisms and biological pathways behind oncogenesis and cancer pathology. With a simple restriction enzyme digestion and real-time PCR, you can analyze the methylation status of 96 different breast cancer genes with these DNA Methylation PCR Arrays. Both 96-well (duplicate set of four arrays) and 384-well formats are available.	User Manual

Functional Gene Grouping

How It Works

Manual & Resources

Reagents & Software

96 Well Gene Table 384 Well Gene Table

Cell Cycle, Growth, Differentiation & Development:

APC, ATM, BRCA1, BRCA2, CCNA1, CCND2, CDKN1B, CDKN1C, CDKN2A (p14ARF), CDKN2B, CHFR, GADD45A, GPC3, HOXD11, PALB2, RASSF1, SFN (14-3-3 sigma), TERT, TGFB2, TGFBI, TGFBR1, TP73, TWIST1, VHL, WIF1, WT1, WWOX.

Transcription Factors:

APC, BRCA1, BRCA2, MYOD1, CDKN2A (p14ARF), CDX2, HIC1, HOXA5, HOXD11, ID4, MSX1, PAX5, PLAGL1, PRDM2, PROX1, RB1, RUNX3, TP73, TWIST1, VHL, WT1, ZMYND10.

DNA Damage Repair:

APC, BRCA1, BRCA2, GADD45A, MLH1, RASSF1, TERT, VHL, WWOX.

Apoptosis & Anti-Apoptosis:

APC, BRCA1, BRCA2, DAPK1, PYCARD, TNFRSF10C, TNFRSF10D, TP73, VHL, WWOX.

Cell Adhesion:

APC, CDH1, CDH13, CADM1, DSC3, JUP, TACSTD1, THBS1.

Growth Factors:

BMP6, IGFBP7, IGFBPL1, WIF1.

Chemokine & Cytokine Signaling:

CXCL12, TNFRSF10C, TNFRSF10D.

Circadian Rhythm:

PER1, PER2.

Solute Carrier Family:

SLC5A8.

Drug Metabolism:

ABCB1, CYP1B1, GSTP1.

Fatty Acid Metabolism:

HSD17B4.

Heparan Sulfate Biosynthetic Enzymes:

HS3ST2, HS3ST3B1.

Extracellular Matrix:

LOX, MUC2, SLIT2, TGFBI, THBS1, TIMP3, WIF1.

Protein Kinase & Protein Kinase Adaptor Proteins:

DAB2IP, PRKCDBP, STK11, SYK.

Phosphatases:

PTEN.

Prostaglandin-Endoperoxide Synthase:

PTGS2.

DNA Methylation:

MGMT, PRDM2.

Proteases & Inhibitors:

ADAM23, CST6, KLK10, THBS1, TIMP3.

Caveolae Protein:

CAV1.

Nuclear Receptors:

ESR1, PGR, RARB, RBP1.

GTPase-Activating Protein:

DAB2IP.

Hormones & Receptors:

ESR1, PGR.

Histidine Triad Gene Family:

FHIT.

miRNA Genes:

mir-152, mir-663, mir-9-1.

Ras Associated Protein Superfamily:

RRAD, RASSF1.

Wnt Signaling Proteins:

SFRP1, SFRP2, WIF1.

Others:

CALCA, EPB41L3, PDLIM4, RARRES1.

96 Well Gene Table 384 Well Gene Table

Functional Gene Grouping

How It Works

Manual & Resources

Reagents & Software

"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 Performance Data Application Data

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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Functional Gene Grouping

How It Works

Manual & Resources

Reagents & Software

The complete Methyl-Profiler DNA Methylation PCR Array System insures that you will get good results from your DNA methylation analysis experiment the first time, and every time guaranteed.

The Complete Methyl-Profiler DNA Methylation PCR Array System Includes:

DNA Methylation PCR Arrays
Analyze the DNA Methylation Status of 24 or 96 Genes Simultaneously

DNA Methylation Enzyme Kit
Required for a complete and successful experiment
Includes enzymes and a digestion buffer optimized for complete digestion by both enzymes under the same conditions

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

Data Analysis Software (Excel template)

Our convenient and high-quality real-time RT-PCR accessory products complete the Methyl-Profiler PCR Array System. The other components needed for real-time PCR analyzing profiles of methylation status are a SYBR^® Green qPCR master mix matched to the instrument in your laboratory, and the DNA Methylation Enzyme Kit.

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