In the last years, high-throughput sequencing (HTS) has become an integral part of translational cancer research. The DKTK Cancer Genomics & Epigenomics Core Facility was established in 2014 to respond to the growing demand for HTS services from researchers and clinicians at the Goethe University Medical School. The core unit offers access to state-of-the-art equipment for high-throughput sequencing (Illumina MiSeq) and whole-genome methylation analysis (Illumina IScan). In addition, we provide help with the design and execution of HTS experiments as well as with data analysis. Larger sequencing efforts that cannot be handled locally can be executed in collaboration with the Genomics and Proteomics Core Facility at the DKFZ in Heidelberg.
The applications that are currently supported include targeted resequencing, deconvolution of genetic screens and whole-genome methylation analysis.
Targeted resequencing can be employed to identify genetic variants in a selected subset of genes. The target enrichment is typically achieved using amplicon- or hybridization-based approaches and is chosen depending on the research project. Common applications of targeted resequencing include:
- Identification of somatic hotspot mutations in solid tumors
- Identification of somatic hotspot mutations in myeloid malignancies
- Identification of germline mutations in selected genes that predispose to cancer
- Microbiome analysis (16S sequencing)
Deconvolution of genetic screens
In the last years, genetic screens using pooled lentiviral shRNA or sgRNA libraries have been successfully employed to decipher diverse oncogenic mechanisms. HTS is typically used to compare the representation of the targeting constructs in different conditions or cell pools.
DNA methylation regulates gene expression and is involved in the development of cancer. Chip-based whole-genome methylation analysis can help to access methylation patterns at the genome or gene level. Methylation analysis in the core unit is performed using the Illumina Infinium MethylationEPIC BeadChip on the Illumina IScan platform. Apart from the DNA methylation analysis, this technique also allows determination of copy number profiles.
Illustration of hierarchical cluster analysis of differentially methylated CpGs in different brain tumor entities including principal component analysis of the same specimen: