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Home > Products > DNA Methylation > PCR Array > Liver Cancer
Liver Cancer DNA Methylation PCR Array
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| Human Liver Cancer DNA Methylation PCR Array, Complete Panel
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MeAH-8030 (4 × 96-well)
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MeAH-3030 (384-well)
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| The Human Liver Cancer
EpiTect Methyl qPCR 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 liver 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 disease development and progression as well as its
pathology. With a simple restriction enzyme digestion and real-time
PCR, you can analyze the methylation status of 96 different liver
cancer genes with these DNA Methylation PCR Arrays.
Both 96-well (duplicate set of four arrays) and 384-well formats are available.
The EpiTect Methyl qPCR Arrays use the MethylScreen™
Technology provided under license from Orion Genomics,
LLC.
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User Manual
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Well Gene Table 384
Well Gene Table
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Angiogenesis: EP300.
Apoptosis & Anti-Apoptosis: APAF1, CADM1 (TSLC1), CDKN1B, CDKN1C
(p57Kip2), CDKN2A (p14ARF), CDKN2A (P16), CDKN2B (p15), CLU, DAPK1, EBF3, FHIT,
PYCARD (TMS1), SFN (14-3-3 sigma), TNFRSF10C, TNFRSF10D, TP73.
Calcium Channel Signaling: EDNRB.
Caveolae Proteins: CADM1 (TSLC1), CAV1, CD44, CDH1, CDH13.
Cell Adhesion & Migration: CADM1 (TSLC1), CD44, CDH1, CDH13, CTNNB1,
DAB2, DCC, DLC1, JUP (CTNNG), OPCML (aOBCAM), RELN, SPINT2, THBS1, TIMP3.
Cell Cycle, Growth, Differentiation & Development: CADM1 (TSLC1),
CCND2 (cyclin D2), CDKN1A, CDKN1B (p27KIP1), CDKN1C (p57Kip2), CDKN2A (p14ARF)
CDKN2A (P16), CDKN2B (p15INK4b), CHFR, CLU, DLC1, EBF3, EP300, FHIT, GATA4,
IGFBP3, MLH1, MYOD1, PRDM2 (RIZ1), PRDM5, PTGS2 (COX2), RARB, RASSF1, RASSF4,
RASSF5, SFN, SPRY2, TP73, WIF1, WT1.
Chemokines, Cytokines & Receptors: IRF7, TNFRSF10C, TNFRSF10D.
Neuronal Adaptor Proteins: APBA1 (MINT1), MINT27, MINT31.
Cytokine Signaling Inhibitors: SOCS1, SOCS4, SOCS5.
DNA Damage Repair: CDKN1A, CLU, MLH1, MSH2, MSH3, RASSF1, RASSF4, RASSF5.
DNA Methyltransferases: MGMT (AGT), PRDM2.
Drug Metabolism: ABCB1, GSTP1.
EGFRP Phosphotyrosine Signaling: SPRY2.
Extracellular Matrix Remodeling: CD44, LOX, RELN, SPINT2, THBS1, TIMP3,
WIF1.
Tumor Suppressor Gene Candidates: DIRAS3, DLEC1, NQO1, SCGB3A1 (HIN-1),
TSPY1.
Glycosyltransferase: B4GALNT2.
Growth Factors: IGFBP7, WIF1.
GTPase-Activating Protein: DAB2IP.
Histidine Triad Gene Family: FHIT.
Hormone receptor: AR, NR0B2, ESR1
Human Sd(a) & Cad Antigen Biosynthesis: B4GALNT2.
Hypoxia Response: EP300, NDRG2, SPINT2.
Inflammation: PTGS2 (COX2), PYCARD (TMS1/ASC).
Insulin-Like Growth Factor Signaling Pathway: IGFBP3.
Lipid Metabolism: HRASLS3 (PLA2G16).
Metal Ion Binding: MT1A.
miRNA Genes: has-miR-1, hsa-miR-34a.
Mitogenesis: PTGS2 (COX2).
Nuclear Receptors: AR, ESR1, NR0B2, RARB.
Oncogenes: CAV1, E2F1.
p53 Signaling Pathway: RPRM.
Proteases and protease inhibitors: SPINT2, THBS1, TIMP3.
Protein Kinase & Protein Kinase Adaptor Proteins: DAB2IP, SYK.
Retinoid Acid Signaling: RARB.
TGFbeta Signaling Pathway: SOCS4.
Transcription Factors or Cofactors: ALX4, CDKN2A (p14ARF), E2F1, EP300,
GATA4, GATA5, GATA6, HIC1, MYOD1, PDLIM4, PRDM2 (RIZ1), PRDM5, RUNX3, TP73, WT1.
Tumor Suppressors: CAV1, CDKN1A, CDKN1C (p57Kip2), CDKN2A (p14ARF),
CDKN2A (P16), CDKN2B (p15INK4b), CHFR DAB2, DCC, E2F1, MLH1, MSH2, MSH3, NDRG2,
RASSF1, RUNX3, SFN, TP73.
Wnt Signaling Pathway: DACT1, DKK1, DKK3, SFRP1, SFRP2, SFRP4, SFRP5.
Others: OGDHL, ZMYND10.
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Well Gene Table 384
Well Gene Table
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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
EpiTect Methyl qPCR technology."
The EpiTect Methyl qPCR 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 verify 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. EpiTect Methyl qPCR Arrays are ideal for fast,
high-throughput methylation analysis. For determining the exact methylation
level of individual and consecutive CpG sites, we recommend using bisulfite
Pyrosequencing on a PyroMark system.
You can use any 96-well or 384-well real-time PCR instrument.
Click below for detailed information.
How it Works
The EpiTect Methyl qPCR 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 DNA Methylation 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 verify the reliability of the EpiTect Methyl qPCR Array
System, its results and sensitivity were compared with bisulfite Sanger sequencing, the
gold standard in DNA methylation analysis.
Same Results as Sanger Bisulfite Sequencing
EpiTect Methyl qPCR Yields Results Identical to Sanger Bisulfite
Sequencing.
The methylation status of the cadherin 1 (CDH1) gene promoter was analyzed
using either bisulfite sequencing or EpiTect Methyl qPCR Primer Assays in three
different breast cancer cell lines known to have very different CDH1 methylation
patterns.
Same Sensitivity as Sanger 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.
EpiTect Methyl qPCR 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 EpiTect Methyl 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 expenses
related to screening large numbers of genes in many tumor samples simultaneously
using a bisulfite-based method are not practical. The EpiTect Methyl qPCR System
provides an ideal reagent for such studies. The following experiments
demonstrate that DNA Methylation PCR Arrays can both verify known and discover
new DNA methylation cancer biomarkers. For determining exact methylation levels
of specific CpG sites, we recommend using bisulfite Pyrosequencing on a PyroMark
system.
Biomarker Verification
EpiTect Methyl qPCR Arrays Verify 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. Does the methylation status of transcription factor genes
differ between cancer and normal cells?
EpiTect Methyl qPCR 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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The complete EpiTect Methyl qPCR Array System
insures that you will get good results from your DNA methylation
analysis experiment the first time, and every time guaranteed.
The Complete EpiTect Methyl qPCR Array System
Includes:
EpiTect Methyl qPCR
Arrays
Analyze the DNA Methylation Status of 24 or 96 Genes Simultaneously
EpiTect Methyl DNA Restriction 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 EpiTect Methyl qPCR 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 EpiTect Methyl DNA Restriction Kit.
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