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FFPE Samples Rescue


The Challenge of Working with FFPE Samples

In pathology, Formalin-Fixed Paraffin-Embedded (FFPE) biopsies represent the universal standard in cancer diagnostics.

Some tumor samples, however, are very small or characterized by an overwhelming amount of stromal cells relative to the tumor cells, compromising molecular analysis by Next-Generation Sequencing (NGS) or other techniques.

Between 5 and 15% of FFPE samples are not suitable for NGS analysis, and this is mainly due to the low content of tumor cells. The presence of targetable mutations in the tumor cannot be retrieved from those samples, resulting in missing therapeutic opportunities for the patient.


Isolate Tumor Cells from FFPE samples with low tumor content

The DEPArray system isolates low numbers of tumor cells from any FFPE sample with high precision, even when the content of tumor cells is very low or the starting specimen is small. This unique feature can be exploited to rescue those samples normally excluded from conventional molecular testings due to low cellularity or sample exhaustion, making them suitable for clinical NGS.

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Small pools of only a few hundreds DEPArray-sorted tumor cells can be tested by DEPArray OncoSeek or other cancer gene panels to identify molecular drivers with high specificity and provide crucial information on the presence of targetable mutations or copy number variations in the tumor.


DEPArray FFPE Application Workflow 

FFPE tissue sample is first deparaffinized and disaggregated, then the resulting cell suspension is stained and loaded on the DEPArray cartridge. Target cells are identified by a combination of intracellular and extracellular immunofluorescent markers, relative DNA content and morphological features detected by image analysis. DEPArray immunofluorescent selection ensures high reliability in the accurate identification of the target cells.

DEPArray sorted FFPE cells contain highly pure tumor DNA in sufficient amounts for NGS library preparation, allowing precise and reproducible genomic analysis, from targeted cancer gene panels up to whole genome sequencing with moderate coverage needs.


The complete FFPE application workflow includes a sample preparation kit and a DNA quality control assay for FFPE samples - DEPArray FFPE SamplePrep Kit and 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. Finally the data analysis solution - MSBiosuite - automates analysis of data generated by the sequencing of libraries obtained with DEPArray OncoSeek Panel.


You can easily access our FFPE rescue through our lab service 


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