Next-Generation Sequencing (NGS) has the potential to revolutionize clinical oncology by providing direct, actionable molecular information about tumor cells. Such information could be used to stratify patients for appropriate clinical trials assignment, select of efficacious, personalised therapies, and, in routine use, to monitor therapy.
The potential power of NGS, however, is largely neutralized by current sample preparation practices, which allow mixtures composed of tumor cells and normal cells to enter the NGS assay workflow. The background of normal diploid cells in the analyzed tumor sample dilutes signals associated with clinically relevant, quantifiable genetic features, such as copy-number variation and loss of heterozygosity. With an admixture of normal cells present in the sample, the prevalence of a mutation within a tumor cannot be assessed. Resolving sample heterogeneity prior to NGS analysis would eliminate the ambiguity that precludes productive clinical utilization of NGS data, but conventional methods of cell separation cannot produce the 100% pure preparations of tumor cells required. Flow-based methods require large cell loads, typically unavailable in real life clinical specimens, and are capable only of producing enriched cell preparations, because flow itself is indiscriminate. Similarly, labor-intensive microdissection methods can yield enriched tumor preparations, but irregular, branching tumor cell infiltration patterns make pure tumor cell separation, isolation, and recovery impossible.
The DEPArray™ system from Silicon Biosystems resolves cellular heterogeneity, enabling NGS-based molecular characterization of pure cell subpopulations. The system can sort, manipulate, and collect individual cells, or groups of cells, with 100% specificity and purity. Compatible with a variety of clinical oncology samples, such as enriched blood, and fresh, frozen, or formalin-fixed paraffin-embedded (FFPE) tissue, the DEPArray™ system enables separation, isolation, and recovery of pure cell preparations composed of phenotypically distinct cell types. Any cell that can be identified using positive or negative selection of fluorescent markers or probes can be isolated by the DEPArray™ system. Morphological features, such as size and circularity can be included in the selection criteria. A pure preparation of tumor cells can be recovered from a dissociated cells prepared from an FFPE tumor biopsy, or fresh or frozen tissue, and a pure preparation blood sample.
The DEPArray™ platform consists principally of a fluorescence microscope, a digital camera, a single-use microfluidic cartridge, computer hardware, and software. Image- based fluorescence and brightfield microscopy are combined with dielectrophoresis to enable interrogation and direct manipulation of thousands of individual cells. Dielectrophoretic forces induced between upper and lower electrodes embedded in the cartridge trap suspended cells into a grid formation. Thus immobilized, the cells can be rapidly interrogated for phenotypic characteristics, such as size, shape, and the presence or absence of one or moretarget surface proteins. For recovery, cells of interest are mobilized and isolated by stepwise transfer to adjacent cages leading to a separate clean buffer volume in a separate area within the cartridge, and subsequently eluted from there without contamination of other cells.
The DEPArray™ system unleashes the power of NGS for diagnostic assays by enabling preanalytical cell type purification from enriched blood, and fresh, frozen, and FFPE-preserved clinical samples. NGS assay workflow sample input composed of 100% pure tumor cells enables facile resolution of genetic alterations present in assayed cells. By enabling the addition of precise sample preparation to the NGS assay workflow, the DEPArray™ system brings precision medicine concepts such as personalized therapy, molecular monitoring of response to therapy, and liquid biopsy into the realm of practical possibility. Pre-analytical resolution of tumor heterogeneity is a major step forward for precision medicine. of circulating tumor cells (CTCs) can be isolated from an enriched
By Farideh Bischoff
Executive Director of Scientific Affairs and Member of the Board
Chief Technology Officer
Chief Scientific Officer