Encompass Service for FFPE

Services for Formalin-fixed, Paraffin-embedded (FFPE) tissues

The first complete and reliable solution for global gene expression data from FFPE tissues


Click here for early access information

Formalin-fixed, paraffin-embedded (FFPE) tissue samples can be a valuable resource for retrospective discovery studies because large numbers of samples with associated clinical data can be readily acquired and analyzed. However, the severe RNA degradation typical of FFPE samples has historically presented challenges for gene expression studies. Although FFPE-derived RNA is not suited to all downstream applications, Asuragen scientists have now refined the methods required to achieve reliable, whole-transcript gene expression data from this important resource.


Convenient

Histology and RNA isolation
Blocks, slices, or slides

Accurate

Unbiased whole-transcript analysis
Full-genome coverage

Informative

Data analysis
Biomarker discovery

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.



Description of Services
Deliverables
Quality Control
Turn-around Time
Typical Yields
Additional Services Available
Catalog Numbers ENCOMPASS™ Services for FFPE

Description of Services

Features of the ENCOMPASS™ for FFPE Service:

Sample Prep services:

  • RNA isolation methods verified to recover mRNA
  • Asuragen-isolated RNA or DNA suitable for numerous downstream applications, including comprehensive expression profiling and genotyping studies (click here for additional services)
  • Histology and macrodissection services also available
  • RNA purity and yield measurements using NanoDrop spectrophotometer readings at 260 and 280 nm

Affymetrix Gene Expression services:


Deliverables

Data Analysis

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.


Additional Data Analysis

Standard Service Premium (SSP) For statistical analysis and graphical representation of your entire experiment, our SSP data analysis package offers additional analysis and these deliverables:


  • Hypothesis testing by one- or multi-way ANOVA of the summarized array data, providing p-value and fold-change information relevant to your experimental groups
  • Publication-quality figures and images, including:
    • Hierarchical clustering
    • Pair-wise volcano plot(s)
    • MA plot(s)
    • Box plot(s)
    • Principal components analysis (PCA) plot(s)

These are provided in electronic form on the data delivery DVD in addition to the standard deliverables provided with every gene expression profiling project.


With all SSP projects we will call you upon shipment of your data to arrange an informatics review of your data.

Full Service
Based on your initial consultation, Asuragen can define expert analysis for a custom informatics approach. See our Informatics section for more information on our capabilities.


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 degraded nature of RNA 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, excluding the sample from further analysis, or proceeding at-risk.

ffpe formalin fixed parafin embedded tissue quality control

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 two weeks or less. 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 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.


Additional Services Available


mRNA Analysis:

miRNA Analysis:


DNA Analysis:

Data Analysis:

Catalog Numbers for ENCOMPASS™ Services for FFPE


Sample Prep

CA0008 Isolation, Total RNA from FFPE (up to 4 slides or sections of up to 20 μm thickness)

Gene Expression

CA0010 QC, NanoDrop and Bioanalyzer, Total RNA, for mRNA applications
CA0061 Target Preparation, ENCOMPASS for FFPE  Service
CA0012 Array Processing and Scanning, Affymetrix Arrays Hybridization, Scanning, and Analysis of Affymetrix Array
CA0240 Affymetrix Gene 1.0 ST
CA0250 Affymetrix Exon 1.0 ST

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.