Overcoming Challenges in Sequence Analysis of FFPE Tissue Due to Heterogeneity: Silicon Biosystems DEPArray™ Technology Offers a Revolutionary Approach to Understanding Complex Cancer Genomics in FFPE Samples

BOLOGNA, Italy

Silicon Biosystems, a Bologna (Italy) and San Diego (CA, USA) based biotech company that is part of the pharmaceutical Menarini Group, presented recent findings obtained with its breakthrough state-of-the-art DEPArray™ technology in the characterization of pure tumor cell subpopulations derived from formalin fixed paraffin embedded (FFPE) tissue samples at the European Association of Cancer Research Meeting in Florence (June 20-23).

DEPArray™ technology resolves heterogeneity in solid tumors by digitally sorting 100% pure subpopulations of cells from FFPE samples, thus allowing differential analysis and characterization of tumor vs stromal cell populations resulting in unprecedented data in the subsequent Next Generation Sequencing (NGS) analysis. With DEPArray™ technology, exquisite precision in the molecular characterization of tumor cells is achieved and is no longer compromised by the unwanted admixture of normal cells in biopsied tissue specimens. Further, with the identification and separation of different sub-populations of tumor cells, scientists now have a unique tool to resolve heterogeneity of cell populations revealing their true genetic profiles. The data presented at the meeting show how important genetic features such as loss-of-heterozygosis in cancer related genes, or somatic mutations zygosis, are revealed clearly by a simple targeted NGS test with this new approach but would be missed or misinterpreted analysing DNA extracted from the same clinical sample without DEPArray™ separation.

Recent DEPArray™ studies have reported a reproducible and reliable workflow for the isolation and characterization of circulating tumor cells (Polzer B et al, EMBO Molecular Medicine 2014, “Molecular profiling of single circulating tumor cells with diagnostic intention”; Hodgkinson C.L. et al, Nature Medicine 2014, “Tumorigenicity and genetic profiling of Circulating Tumor Cells in Small Cell Lung Cancer”). These pivotal studies demonstrate the power of the DEPArray™ as a tool to improve preparation of complex tissue specimens routinely used for molecular analysis.

Giuseppe Giorgini, Chief Executive Officer of Silicon Biosystems, said, “Resolving tumor heterogeneity is a major step forward in delivering precision to precision medicine. DEPArray™ technology leaves no sample behind. Regardless of tumor burden levels, all samples can be subjected to NGS to obtain meaningful genomic information. This revolutionary approach is beneficial to translational cancer researchers, the development of new cancer drugs and biomarker discovery.”

DEPArray™ technology combined with NGS analysis can reveal more comprehensive genomic information derived from FFPE specimens, as already demonstrated in posters presented recently at AMP (Washington D.C., November 2014), AGBT (Marco Island, February 2015), and AACR (Philadelphia, April 2015).

Presentation Details: Poster # 108

Time and Date: Sunday, June 21, 13:15-14:30
Title: “Genetic characterization of pure tumor cell sub-populations from FFPE samples”
Location: Firenze Fiera Piazza Adua 1, Florence

About Silicon Biosystems S.p.A.

Silicon Biosystems, with offices in Bologna, Italy, and San Diego, CA, has developed an instrument platform for cell and molecular biology, which can sort, manipulate, and collect individual cells or groups of cells with 100% purity.

Using a proprietary electronic chip-based microfluidic cartridge and automated microscopic image-based analysis, the DEPArray™ system can recover as little as a single cell from a suspension of tens of thousands of cells with 100% purity, allowing downstream molecular analyses using molecular assays such as whole genome amplification and sequencing.

DEPArray™ technology developed by Silicon Biosystems has applications in the molecular characterization of circulating tumor cells (CTCs), tumor-infiltrating cells, stem cells, and circulating fetal cells, and in the recovery of multiple cell phenotypes to study putative EMT cells, identify potential markers of metastasis, assess biomarker expression in distinct cell populations, and monitor the effects of therapy on tumor cell and CTC subpopulations. The technology can also separate tumor cells from stromal cells in FFPE and FNA biopsy tissue, and fresh or frozen sample tissue.

In July 2013, Silicon Biosystems became part of the Menarini Group, the first global Italian pharmaceutical company. The Menarini Group ranks 17th in Europe out of 5,389 companies, and 37th in the world out of 19,992 companies, with a turnover of more than 3 billion Euro and nearly 17,000 employees.

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