IKP Core Facility

Molecular Analytics


The core facility Molecular Analytics provides various analytical methods and platforms for genotyping and gene expression analysis, DNA sequencing as well as array-based genomic analyses. Our facility runs a MALDI-TOF mass spectrometer (Sequenom System), real-time PCR instrumentation including 7900HT and OpenArray Systems, LightCycler, and a BioMark HD system (Fluidigm) for a broad range of micro-fluid based genomic applications. Moreover, we operate an 8-Capillary 3500DX ABI Genetic Analyzer to be used in both research and diagnostic setting, and a GeneChip Affymetrix microarray platform equipped with two Fluidics 450 stations.

The core facility team is responsible for the device maintenance and for the establishment and validation of new technologies and methods. The team also provides technical support for users at the IKP / RBK regarding experimental setup, implementation of methods for a certain research question and for data analyses. For certain applications that require error-free operation, e.g. MALDI-TOF mass spectrometer based genotyping systems are exclusively operated by the core facility team.

Bild Molecular Analytics


Dr. Elke Schaeffeler
Research Group Leader Integrative Omics Analyses and Cancer Therapy
Head of Molecular Analytics
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Genotyping and Gene Expression Analysis (selection)


  • MALDI-TOF mass spectrometry (MassARRAY System (Agena Bioscience)) is used for genotype analysis, tumour profiling and for the quantitative detection of epigenetic changes (DNA methylation). Genotyping by the iPLEX method provides a very cost-effective method because of its multiplexing capacity of up to 40 SNPs in a single sample and its high-throughput scalability. The latter is a prerequisite for the participation of IKP in international collaborative projects and third-party funded networks for the analyses of large cohorts. The additional use of the MALDI-TOF mass spectrometer for DNA methylation analysis is a unique feature at IKP.
  • Several real-time PCR instruments (7500, QuantStudio Dx and QuantStudio 12K Flex Systems (Thermo Fisher Scientific)) for different applications and formats (96-well, 384-well, Array Card and OpenArray format): These systems allow for a cost-effective TaqMan based genotyping in e.g. a 384-well, single or low-plex assay format, making them particularly useful for small to medium-sized projects. These devices can also be used for the determination of copy number variations (CNV) and microRNAs expression analysis in the context of epigenetic research. There is also a unit for gene expression analysis using low-density arrays capable of simultaneously measuring up to 384 different genes or miRNAs (custom made). In addition, a genotyping panel for pharmacogenetic testing based in part on the OpenArray format is available.
  • BioMark HD System (Fluidigm): This platform is a flexible and cost-effective system for a broad number of genomic applications including genotyping, gene expression, digital PCR, amplicon-based NGS library preparation, and single cell analyses in the nanoliter range. The BioMark system is a versatile platform for the preparation and low-to-high-throughput analyses of limited-sample material (e.g. biopsies).
  • QX200 Droplet Digital PCR System (Bio-Rad) for digital PCR and absolute quantification of DNA molecules.
  • GeneChip microarray platform (GeneChip Scanner/Autoloader, 2 x Fluidic 450 Station (DX), Hybridization Oven (Thermo Fisher Scientific)). This system is used for any microarray experiments based on the GeneChip format including whole-gene/transcriptome and microRNA expression profiling, hybridization based genotyping and CNV analyses, and disease related mutation screening.

Sequencing & Fragment Analyses


  • An 8-Capillary-sequencer (Genetic Analyzer 3500DX, Thermo Fisher Scientific) is available for DNA sequencing as well as for various fluorescence-detection based fragment analyses. Our system is approved for diagnostic applications (Dx System).
  • A MiniSeq System (Illumina) is available and used for panel based next-generation sequencing (NGS).


DNA and RNA Isolation


  • The Facility has a pipetting robot (Genesis RSP 150/8, Tecan) for fully automated and parallel DNA isolation of up to 96 blood samples using the QIAamp MDx kits (Qiagen). For quantification and quality control of DNA and RNA, two NanoDrop 2000 spectrophotometers and a Bioanalyzer (Agilent Technologies) are available.


Other instruments


  • The facility provides a number of PCR devices for different reaction volumes and plate formats (single tubes, 96-well / 384-well plates). For automated pipetting in 96- and 384-well format the facility operates various pipetting robots (MassARRAY Nanodispenser (Agena Bioscience), CyBi-Well and CyBi-disk devices (CyBio/Analytik Jena).