Get high quality results from FFPE specimens

Specimen Preparation

The recovery of quality DNA and RNA from FFPE (formalin-fixed, paraffin-embedded) specimens can be challenging. A number of factors can impact the overall quality and yield of nucleic acids isolated from these preparations.

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Download these guidelines (PDF)

Download a PDF of Paradigm’s guidelines for FFPE specimen preparation for your convenience.

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Smarter DNA/RNA/Protein recovery

Our specimen preparation recommendations address several key factors:
Tissue procurement and processing

Tissues should be fixed within one hour of surgical resection. The optimal total fixation time is 12-24 hours, using only neutral-buffered formalin. Fixed tissues should be thoroughly dehydrated prior to the embedding process.

Block storage

Storage of blocks without cut faces prevents ongoing damage from exposure to oxygen, water, light and other environmental factors.

Tissue type, size, and content

Excess non-malignant starting material will result in an effective dilution of targeted nucleic acids. When required, Paradigm employs Laser Capture Enrichment (LCE) to isolate and increase the specific microscopic subpopulations from FFPE tissue blocks.

Follow these guidelines for optimal results:

 

Sample Type

  • FFPE Block: Standard formalin-fixed, paraffin-embedded (FFPE) block from most recent surgery or biopsy, containing the most amount of tissue, excluding bone.
  • Shaves/Curls: 6-10 10μm thick freshly cut curls along with H&E stained section of same block.
  • Slides:  (7-25) 4 micrometer, freshly cut, unstained, unbaked, sections on positively charged slides, or (1) Slide per IHC selected +1
 
 

Sample Size

  • Optimal: 75mm3 (5mm x 5mm x 3mm) or 4 to 6 needle biopsies
  • Minimum: One core needle with 10% tumor* (10mm x 2mm x 1mm)
    (*risk that full profile cannot be completed)
 
 

Sample Tumor Content*

  • Optimal: 40% and higher
  • Minimum: 10% *Laser Capture Enrichment (LCE) will aid in specimen optimization

Solid tumor samples vary greatly from patient to patient and you may have unique challenges not covered here. Medical and scientific colleagues are available to answer questions about your specimen prior to sending sample. Please Client Services at (844) 232-4719.

Specimen Preparation
 

Shipping instructions

1

Freeze the Polar Pack included in shipping kit for a minimum of 4 hours.

2

Place FFPE Block with Paradigm Requisition Form and all patient insurance materials and pathology reports into Specimen Kit.

3

Place the Paradigm Specimen Kit into the pre-addressed shipping pack provided and seal.

4

Complete the pre-printed FedEx shipping label and affix to shipping pack.

5

Ship completed Specimen Kit (FFPE sample, requisition form, other documents) “Priority Overnight” to the following address:

Paradigm Diagnostics

445 N. 5th Street, Suite 300

Phoenix, AZ 85004

(844) 232-4719

Start getting better results, faster.

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