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 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 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 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).
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.