Preanalytics & diagnostics

Single circulating tumor cells (CTCs) from blood or disseminated tumor cells (DTCs) from lymph nodes or CSF are a valuable source for the molecular and functional analyses of systemic cancers. In order to find and analyze these very rare cells, we have developed different strategies for enrichment and isolation of single cells.

Following standardized tissue processing, we offer both marker-dependent methods (CellSearch, FACS sorting) and marker-independent methods (microfluidics, leukocyte depletion) for enriching the desired target cells. Afterward, they can be isolated as single cells using either micromanipulation, so called single cell printing or by automatic dielectrophoretic deposition (DEPArray™ PLUS). The isolated single cells are then available for further studies such as single-cell genomic and transcriptomic analyses or for generating innovative cell models and functional assays.

In many cases, the molecular analysis of FFPE tissue is hampered or even prevented by a small sample size or low tumor cell content surrounded by a large number of non-malignant cells (e.g., connective tissue).

In our laboratories, we have established semi-automated workflows to isolate either defined areas from tissue sections by means of laser microdissection or — after preparing a single-cell suspension — highly purified cell populations using dielectrophoretic deposition. DNA can even be isolated from very small cell and tissue quantities before checking its quality and feed it into our molecular analysis methods.

The analysis of chromosomal copy number alterations (CNAs) is a rapid and cost-effective method for the molecular characterization of tumor cells. It is used to confirm the malignant origin of the isolated cells, thereby making it an ideal tool for validating new technologies for the detection of rare circulating tumor cells, for example. Besides that,  it allows treatment effects to be evaluated over time, such as selection of resistant subclones.

Using high-throughput methods, we produce sequencing libraries of single cells, specific cell populations, tumor tissue, or cell-free DNA. The quality of the individual libraries is carefully checked before the whole genome is sequenced.

Our bioinformatic evaluation

• logs certain quality characteristics of the sequenced samples as standard procedure throughout the course of the analysis,
• includes the graphical representation of chromosomal aberrations, and
• tabulates the overall results for the affected chromosomes and for the genes localized on these chromosomes.

All work steps can be adapted to the needs of our customers on request. We provide assistance for interpreting the data and performing additional bioinformatic analyses.

The goal of personalized medicine is to enable treatment that is tailored to the patient and therefore more efficient. Compared to the primary tumor, tumor cells from liquid biopsies and metastatic tissue may carry additional disease-relevant mutations promoting spreading or systemic progression. These cells can also be characterized with respect to therapeutically relevant and useful mutations for the purpose of targeted therapeutic strategies at the current stage of disease. We have developed or adapted various gene panels of different sizes (ranging from approx. 50 to over 400 cancer-related genes) for use in single-cell analysis. Many of the genes studied have a causal relationship to targeted therapies. In our laboratories, we compile libraries, monitor their quality, and routinely sequence them for the molecular analysis of single cells, such as CTC. At the same time, we have been developing a process of evaluation and analysis that, among other things, minimizes the number of false positive mutation predictions, which is a methodological challenge when analyzing single cells (error-free sequencing). The bioinformatic evaluations we offer include comprehensive quality control, the compilation of relevant mutations with their associated attributes, and, ideally, indications of their clinical usability.

When seeking answers to research questions, the integrity of the biospecimens analyzed is a fundamental requirement for obtaining meaningful results. Our researchers have many years of experience in setting up biomarker studies for a large number of tumor entities and different sample types (e.g., blood and other body fluids as well as different tissue types). We design optimal workflows for sample logistics and for preanalytical and analytical sample preparation — tailor-made for the our customer’s needs — in order to achieve the best possible data quality and meaningful results.