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Sample analysis

Next Generation Sequencing and Data Analysis
The department of Clinical Genetics currently operates an HiSeq2500 sequencer from Illumina . The department has developed a pipeline in-house for the purpose of analysing the sequencing data generated by the HiSeq. Right after demultiplexing the data, the pipeline starts by generating a report on the quality of the raw data, per sample. If this quality meets the customer's requirements, then the analysis is continued. For human DNA sample analysis, the pipeline involves a range of tools that align the reads to the reference genome, mark duplicates, perform realignments, recalculates base qualities and calls SNPs and indels with respect to certain filters. The last step is to perform an annotation of the variants that are called, which generates an overview of the most likely candidates.
Some examples of projects that we are currently running on the HiSeq and for which we have developed in-house pipelines are non-invasive prenatal testing, targeted sequencing, and exome sequencing.
Additional applications that can be performed at our NGS facility include Haloplex, CAGE, Whole Genome Sequencing, Bisulphite sequencing, miRNA, and RNASeq.
We are open to discussions of other sequencing application options. For more details about the above projects or about how to set up your own project, please contact us at this e-mail adress .

RNA Interference Functional Oncogenomics Laboratory (RIFOL)
The RIFOL is the core facility for RNAi library screening in the VUmc Cancer Center Amsterdam. The RIFOL supports RNAi high-throughput screening projects by providing access to whole genome and custom human siRNA libraries, by operating and maintaining HTS equipment, by providing guidance in designing and performing functional assays and by advising on data analysis. See this website for more details. RIFOL primarily serves researchers from VUmc departments that participate in the VUmc CCA. Other academic research groups can obtain access to RIFOL facilities through collaborative ventures with VUmc CCA departments. A VUmc CCA program advisory committee prioritizes proposals for new screening projects. Dr. V.  van Beusechem is the contact for RIFOL.

OncoProteomics Laboratory
The Department of Medical Oncology's The Onco Proteomics Laboratory (OPL) performs biomarker research involving high resolution tandem mass spectrometry-based proteomics. This work is carried out in the context of numerous core and collaborative projects within CCA/V-ICI, VUmc, as well as at national and international level (EU projects) The focus is on discovering protein biomarkers for the early detection and personalized treatment of cancer, as well as on CSF biomarkers for neurodegenerative diseases. The OPL has developed and implemented robust label-free mass spectrometry-based strategies for biomarker discovery in tumour tissue and biofluids, including workflows for phosphoproteomics, subcellular and proximal fluid proteomics as well as workflows for cerebrospinal fluid, sputum and faeces proteomics. Dedicated statistical methods developed for the spectral count data have proved to be a versatile strategy for label-free protein quantitation and biomarker discovery. Further details can be found at the OncoProteomics Laboratory website. Collaborative ventures are established on a project-by-project basis. Before submitting samples for analysis, you should first discuss the details of the research project in question with the head OPL (Dr. Connie R Jimenez ).

Biological samples
Do you need to have a biological sample analysed? If so, take a look at the overview of the Clinical Chemistry laboratories  . Contact the Clinical chemistry department for details about the ordering procedure .

Microbiology
The department of medical microbiology, MMI  ,has in-house expertise on microbiology and infective microorganisms.

Molecular Cell Biology and Immunology Technology Centre
The MCBI Technology Centre has outstanding state-of-the-art research facilities, including advanced cellular identification and imaging systems (such as FACS sorting and analysis, confocal microscopy, and live cell imaging) as well as biochemical design and analysis by peptide synthesis and mass spectrometry. The Centre uses well characterized in vivo and in vitro models in efforts to identify a number of crucial molecules and processes involved in the development of chronic inflammatory diseases. The Technology Centre comprises three units: Microscopy, Flow Cytometry, and Biochemistry. The techniques used include well validated in vitro and in vivo models, with the option of validating findings in patient material.

Micro Array Facility
The Microarray Core Facility's services range from specimens to final data, including histochemistry, micro-array-tailored DNA/RNA isolations and data analysis. The Facility is world renowned for its expertise in processing clinical archival material (FFPE) for microarray CGH.
The Facility places no restrictions on a project's subject, sample origin, or sample size.

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