Developing next-generation approaches and bioinformatics solutions for comprehensive single-cell analysis

Next-generation sequencing (NGS) of single cells is of high importance to understand complex biological processes, such as the heterogeneity during disease progression in cancer. At Fraunhofer ITEM in Regensburg, these methods are used to identify hallmarks of cancer cells at defined stages of systemic cancer progression, thereby opening new entry points for therapeutic interventions. Rare tumor cells are detected, enriched and isolated by using different technologies.


Isolated single cells are prepared for subsequent amplification of the genome and/or transcriptome of single cells. Specially developed quality control assays are applied after amplification to assess the quality of the amplified material. This ensures that only high-quality amplified single-cell samples yielding reliable data are forwarded to downstream NGS applications. NGS quality workflows provide a set of quality parameters independent of the assay and sequencing technology. Adapted open-source tools and in-house developed scripts enable NGS data analysis tailored to the special requirements of single-cell amplification technologies. The Fraunhofer team in Regensburg has extensive experience in developing and optimizing workflows from single cells to adapted NGS workflows and bioinformatics evaluation.