Streamline FFPE Samples Analysis

The DEPArray™ Kits streamline and optimize the analysis of FFPE samples by providing DEPArray™ users a fast and easy workflow, for a precise genetic analysis on pure cancer and stromal cell populations.

The workflow includes a kit for disaggregation and staining of FFPE tissue sections – DEPArray™ FFPE SamplePrep Kit ; a DNA quality control assay for FFPE samples - DEPArray™ FFPE QC Kit ; a cell lysis kit downstream of DEPArray™ sorting - DEPArray™ LysePrep Kit ; and an oncology panel library preparation kit for Next Generation Sequencing (NGS) – DEPArray™ OncoSeek Panel.


DEPArray™ FFPE SamplePrep Kit

The DEPArray™ FFPE SamplePrep Kit is intended for the dissociation of FFPE human tissue sections into a cell suspension and the subsequent immunofluorescence staining by anti-keratin and anti-vimentin antibodies.

The kit allows the detection, identification and isolation of vimentin-positive stromal cells and keratin-positive putative cancer cells with DEPArray™ system.

Main Features

  • Dissociation of formalin-fixed, paraffin-embedded tissue sections down to single cell suspension;
  • Cell-specific staining of stromal compartment cells and epithelial putative cancer cells;
  • Identification and recovery of different cell populations by DEPArray™ system based on specific immunofluorescent staining and DNA content.

This product contains reagents that are subjected to specific Limitations of Use*.


Formalin-fixation causes fragmentation and chemical modifications in DNA, posing significant challenges for molecular assays, such as downstream NGS applications. The DEPArray™ FFPE QC Kit has been developed to assess the DNA integrity of cell suspensions obtained from formalin-fixed paraffin-embedded (FFPE) samples of human origin prior to DEPArray™ experiments and NGS library preparation.

DNA quality assessment is performed by a qPCR-based assay using two different primer pairs that produce amplicons of 54 bp and 132 bp. The quality of DNA is inferred by the ratio between the quantification using the long amplicon and the short amplicon (QC score).

The QC score, coupled with ploidy information, allows to predict the outcome of NGS library preparation, providing a useful tool to infer the minimum recommended number of cells to obtain a given NGS performance level.

DEPArray™ LysePrep Kit

DEPArray™ LysePrep Kit has been optimized for the lysis of up to 1500 fresh or fixed cells in order to release genomic DNA. The cells lysate obtained can be used directly for subsequent DNA analysis (Targeted PCR, NGS library preparation for Ion Torrent and Illumina platforms).

Sample Types

  • Fresh/live cells
  • Fixed with paraformaldehyde (1%-2% PFA, 10’-20’ at RT)
  • Cells isolated from blood samples collected in CellSave/Streck tubes
  • Inside Stain (Inside Fix/Inside Perm) from Miltenyi
  • Biotec GmbH
  • Cell suspension obtained from FFPE tissue specimens

Main Features

  • Simple one-step cell lysis procedure
  • There are no sample transfers, columns or washes, which can lead to loss and⁄or dilution of the precious sample
  • The entire lysate can be used in downstream reactions ensuring maximum sensitivity and accuracy in your experiments

DEPArray™ OncoSeek Panel

The DEPArray™ OncoSeek Panel enables the preparation of high-quality targeted NGS libraries from FFPE cell populations isolated with the DEPArray technology or from fresh tissue. It allows the simultaneous detection of SNVs, indels and CNAs from 63 oncology relevant genes starting from very low amount of input DNA, such as 60 fresh/unfixed cells corresponding to about 400pg DNA and around 100-300 FFPE cells depending on quality according to DEPArray FFPE QC Kit results.

The kit utilizes Illumina-compatible adapter sequences and has been validated on Illumina platforms.

Main Features

  • Input as low as 60 fresh cells (400 pg DNA). Around 100-300 FFPE cells (660-1980 pg).
  • Single Tube, 4 hours workflow
  • Coverage of 63 oncology relevant genes
  • Detection of SNPs, indels and CNAs
  • Leverages the high fidelity of the Illumina Platform
  • Enables multiplexing of up to 96 unique libraries