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FFPE-rescue products

FFPE 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 characterized by an overwhelming amount of stromal cells relative to the tumor cells, compromising molecular analysis of cancer genetics by Next-Generation Sequencing (NGS) or other techniques.

Around 8% of FFPE samples are not suitable for molecular testing, mainly due to low tumor cellularity. The presence of targetable mutations in the tumor cannot be evaluated from those samples, resulting in missing therapeutic opportunities for the patient.

Our solution for low cellularity FFPE samples analysis

DEPArray FFPE Rescue: Isolate Tumor Cells from any FFPE sample

The DEPArray™ system isolates pure cancer cells from any FFPE sample with high precision, even when the percentage 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 genetic analysis due to low cellularity or sample exhaustion, making them suitable for clinical NGS.

Small numbers of pure DEPArray sorted cells can be tested by cancer gene panels to identify molecular drivers with high specificity and provide crucial information on the presence of targetable gene aberrations or copy number variations in the tumor.

For research use only and not for use in diagnostic procedures.

You can access the FFPE Rescue Application through our Lab Services

Tumor Breast Breast Lung Lung
Sample 1 2 3 4
N cells 100 178 113 208
Reads 2.535.672 1.656.682 995.888 978.912
Coverage 2.413 1.419 1.028 1.106
Gene         hotspot variant-type effect var
TP53 92,88 0,00 0,00 0,00 True SNV stop_gained chr17:7577142:C:A
PIK3CA 57,18 0,00 0,00 0,00 True SNV missense_variant chr3:178936091:G:A
TP53 0,00 85,12 0,00 0,00 True SNV missense_variant chr17:7578551:A:G
PTEN 0,00 50,38 0,00 0,00 False deletion frameshift_variant chr10:89690819:TA:-
EGFR 0,00 0,00 36,86 0,00 True deletion frameshift_variant chr7:55242468:ATTAAGAGAAGCAAC:-
TP53 0,00 0,00 0,00 29,12 True SNV missense_variant chr17:7577548:C:T

The table presents the variant frequencies detected in small tumor cells populations obtained with DEPArray sorting and subsequent analysis by NGS using the DEPArray OncoSeek Panel (internal data).

PRODUCT LITERATURE DOWNLOAD
FFPE rescue BROCHURE

Make every FFPE sample actionable

Rescue FFPE samples with low tumor cell content from analytical exclusion
Select target cells with high reliability by combined immunofluorescent and image-based identification
Collect pure tumor cell pools or single cells to analyze tumor heterogeneity
Identify mutations in 63 oncology relevant genes starting from very low amount of input DNA with the DEPArray OncoSeek Panel

Publications

Discover recently published articles featuring research enabled by our CELLSEARCH, DEPArray and Ampli1 technologies

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