ENCOMPASS™ Services for FFPE tissues
Services for Formalin-fixed, Paraffin-embedded (FFPE) tissues
The first integrated service for clinically reliable data from FFPE tissues.
Formalin-fixed, paraffin-embedded (FFPE) tissue samples can be a valuable resource
for retrospective and prospective discovery studies because large numbers of samples
with associated clinical data can be readily acquired and analyzed. However, the
nucleic acid degradation typical of FFPE samples has historically presented challenges
for gene expression studies. Although FFPE-derived RNA or DNA is not suited for
all downstream applications, Asuragen scientists have now refined the methods required
to achieve clinically reliable, data from this important resource.
Description of Services
Features of the ENCOMPASS™Services for FFPE tissues:
- Compatible with all sample formats - Blocks, slices, or slides
- Pathology confirmation
- Tumor enrichment via macrodissection
- RNA/DNA Sample Preparation - RNA isolation methods verified to
recover mRNA and miRNA fractions.
Accurate Downstream Analysis
Deliverables
Informative Bioinformatics
Asuragen’s bioinformatics team is experienced with Affymetrix Gene 1.0 ST and Exon
1.0 ST analysis. As part of the Standard Service for gene expression profiling,
our team summarizes the data and provides you with a report that outlines each step
of the analysis project and presents your findings so that you can advance to the
next stage of investigation and experimentation.
Consult with our experts to discuss your tissue types, tissue processing, and any
downstream applications required for your experimental design.
Learn more about how
we qualify our methods and staff.
Quality Control
No matter how robust the downstream processes, good data is dependent on sample
quality; consequently, accurate measurement of sample quality is essential before
deciding if a sample merits further analysis. All samples prepared by Asuragen Services
are routinely qualified by spectrophotometry with the NanoDrop spectrophotometer. Due to the partially degraded
nature of RNA and DNA from FFPE tissues, special quality control measurements are
used. Concentration and QC pass/fail information are provided. If a sample does
not pass the recommended QC metrics for analysis, you will be contacted promptly
to discuss possible solutions. These may include replacing the sample or re-isolating
the RNA or DNA, excluding the sample from further analysis, or proceeding at-risk.
Electropherograms of (A) highly intact RNA and (B) partially degraded RNA typical
of FFPE tissues.
Asuragen’s rigorous procedures enable Asuragen to be the only service provider to
offer a Data Quality Guarantee:
If, for any reason, a qualified sample does not pass our process control specifications,
we will re-run the sample at no additional charge.
Read more about our
commitment to the best possible data quality, or read about our contributions to
in-process controls and
standardization.
Turn-around Time
Most projects are completed in one to two weeks. If you have a critical time requirement,
we can often meet your need for no additional charge.
Read more about our commitment to prompt turn-around times.
Typical Yields
Asuragen recommends characterizing the tissue area and histology adjacent to the
slices sent for RNA isolation to better estimate potential RNA yield and enable
correlation with conventional pathology assessment.
While it is very difficult to predict RNA yield from FFPE tissue with great accuracy,
Asuragen can provide guidance on RNA yield per tissue volume (area x thickness)
for a wide array of common human tissues. RNA yield and quality from FFPE is heavily
influenced by methods of purification, storage, and age of block.
Catalog Numbers for ENCOMPASS™Services
for FFPE tissues
Isolation and Prep Services
|
CA0063
|
Sample Prep, Slicing FFPE Block, per Sample (up to 5 slices or slides)
|
|
CA0064
|
Sample Prep, Descriptive Pathology; per Slide (Includes H&E staining)
|
|
CA0076
|
Sample Prep, Macrodissection (up to 5 Slides per sample)
|
|
CA0008
|
Isolation, Total RNA from FFPE (up to 80μm thickness total)
|
|
CA0062
|
Isolation, DNA from FFPE (up to 80μm thickness total)
|
Gene Expression Profiling
|
CC0240
|
Affymetrix, Whole-Transcript Analysis (WTA), Gene 1.0 ST
|
|
CC0250
|
Affymetrix, Whole-Transcript Analysis (WTA), Exon 1.0 ST
|
|
CC0220
|
Illumina Sentrix DASL Universal 96 Array Matrix, for 96 Samples
|
|
CC0230
|
Illumina Sentrix Universal Beadchip, for 16 Samples
|
|
CA0030
|
AB TaqMan Service for mRNA, Individual Assays, RT-PCR
|
|
CA0035
|
AB TaqMan Assay Validation, mRNA
|
miRNA Expression Services
|
CC0290
|
Agilent Human miRNA Microarray V2 (Sanger 10.1)
|
|
CC0280
|
Agilent Mouse miRNA Microarray V2 (Sanger 10.1)
|
|
CA0042
|
AB TaqMan Service for miRNA, Individual Assays, RT-PCR, Absolute Quantitation
|
|
CA0028
|
AB TaqMan Service for miRNA, Individual Assays, RT-PCR, Relative Abundance
|
|
CA0044
|
Affymetrix DiscovArray Service (Array Processing & Scanning)
|
DNA Analysis Services
|
CC0400
|
Agilent Human 244A aCGH Array (1x244K)
|
|
CC0440
|
Agilent Human 105A aCGH Array (2x105K)
|
|
CC0390
|
Agilent Human 44K aCGH Array (4x44K)
|
|
CC0410
|
Agilent Mouse 244A aCGH Array (1x244K)
|
|
CC0460
|
Agilent Mouse 105A aCGH Array (2x105K)
|
|
CC0420
|
Agilent Mouse 44K aCGH Array (4x44K)
|
|
CC0430
|
Agilent Rat 244A aCGH Array (1x244K)
|
|
CC0450
|
Agilent Rat 105A aCGH Array (2x105K)
|
Data Analysis Services
|
CS0001
|
Fee, Initial Consult, Design Plan
|
|
CS0002
|
Data Analysis, mRNA, Standard Service Premium
|
|
CS0010
|
Data Analysis, per Custom SOW
|
|
CS0020
|
miRInform™, Data Delivery System for DiscovArray and Agilent miRNA Expression
Service
|
Requirements for FFPE Sample Prep and Related Services
Sample Input Requirements for the services listed above are found in the Sample Submission Form and Shipping Instructions.