DEPArray™ FFPE QC Kit

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 difference in quantification cycles (Cq) obtained with the long amplicon assay and the short amplicon assay for a given sample.

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.

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