FFPE DNA and RNA Extraction

Formalin-fixed, paraffin-embedded (FFPE) tissue samples are the most abundant resource for retrospective discovery studies. One of the big challenges for downstream applications related to RNA analysis are RNA degradation and variability. Nevertheless, these samples can be used in accordance with dedicated SOPs and QCs.

Description of services

Overview

Depending on the requirements of our customers, we can extract genomic DNA and RNA (including miRNAs) together or sequentially . This allows the use of several genomic applications using the same sample without any sampling biases.

RNA extraction work flow:FFPE slides

Slide preparation work flow:

In addition to our core service for RNA extraction, we can also perform some sections in order not to use the whole biopsy and extract only the RNA or DNA required for further experiments

Some of these sections can also be fixed and colored with hematoxilin-eosin stain (or other, if required) and therefore analyzed for their cell contents. This protocol is very useful and even  crucial in diagnostics to check the concordance between the RNA extracted and the cells supposed to be analyzed.

RNA deliverables and QCs

For every extraction, we provide you with the spectrophotometric data (including the 260/280 and 260/230 ratios), the RNA Integrity Number (RIN) values and the original electropherogram. The RNA can either be stored in our Biobank or shipped to your facility after the downstream process.

All samples prepared by DNAVision are routinely qualified with a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer. For anything concerning FFPE samples, the RIN method is not applicable. For downstream applications related to either Next Gen Sequencing or Microarray; an RIN value of minimum 7.5 is recommended.

Some specific buffers are used to meet the requirements. of downstream applications like SNP genotyping , Sanger DNA Sequencing , Next Gen Sequencing or DNA Copy number analysis.

Turn-around Time

Most projects are completed in one to two weeks. If you have a critical time requirement, we can often meet your needs.

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