On December 16, 2021 Menarini Silicon Biosystems (MSB), a pioneer of single cell technologies, reported its new FFPE Rescue Application, to enable molecular testing on formalin-fixed, paraffin-embedded (FFPE) samples with low tumor cell contents (Press release, Menarini Silicon Biosystems, DEC 16, 2021, View Source [SID1234597345]). Thanks to the sorting capabilities of the recently launched DEPArray PLUS instrument, it is possible to isolate a sufficient number of tumor cells to generate relevant molecular data, even from FFPE tissues that were previously discarded from conventional Next Generation Sequencing (NGS) processing. Thus, the DEPArray PLUS workflow can reduce the failure rates of FFPE molecular analyses and provide clinical researchers with valuable information about actionable mutations, potentially improving clinical trial recruitment and allowing more patients to access new targeted therapies.
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Formalin fixation and paraffin embedding remains the gold standard preservation method of human tissue for molecular diagnostics. NGS of FFPE tissue is becoming increasingly important to identify targetable mutations and has greatly enhanced the ability of physicians to optimize treatment strategies.
However, not all FFPE samples are suitable for molecular analyses. The failure rate for molecular testing of FFPE tissues ranges between 5 and 15%, with the primary driver being low tumor content. The precise digital sorting capability of DEPArray PLUS allows for the isolation of small pools of only a few hundred tumor cells that are then suitable for NGS library preparation and sequencing.
According to Dr Javier Hernández Losa, Director of the Molecular Biology Laboratory within the Pathology Department at the Vall d´Hebron University Hospital in Barcelona, Spain "the DEPArray platform allows us to conduct unambiguous genetic analyses on FFPE samples that failed the standard NGS procedure and identify potentially targetable mutations". MSB and the Vall d’Hebron University Hospital have recently engaged in a research collaboration to expand the types of complex samples that can be analyzed by DEPArray, such as cytologic samples. The Vall d’Hebron University Hospital Pathology lab provides molecular testing for many hospitals throughout Catalonia. It aims to establish a NGS testing service across the entire region to provide the information that will help physicians improve their decision-making and patient care.
Prof Lorenzo Leoncini, MD, Head of the Department of Medical Biotechnology and Director of the Pathological Anatomy Division at the University of Siena, Italy adds that: "the DEPArray technology helped to rescue tissue samples with less than a 5% tumor cell content to generate robust data on cancer mutations. We are now planning to use this technology in different new research projects. For example, we will use DEPArray to study tumor cells in classical Hodgkin Lymphoma tissue biopsies, a setting in which isolation of these rare cells is extremely challenging, as they are present in a very low percentage compared to normal cells".
"We are excited to be able to deliver such a unique technology for the analysis of FFPE biopsies with low tumor cellularity," said Fabio Piazzalunga, President and CEO of MSB. "Our DEPArray platform could help pathology labs reduce the significant burden, caused by FFPE biopsies that are rejected from molecular analysis and support pharma companies involved in clinical trials to expedite recruitment".