The Tumor Genome Analysis Core
The Tumor Genome Analysis Core (TGAC) is housed in the VUmc Cancer Center Amsterdam (CCA) as part of the Department of Pathology. Its core responsibility is to sequence, assemble, and analyze the function and structure of cancer genomes. High quality genome data is a prerequisite for personalised cancer medicine. To deliver this high quality data, we develop and provide laboratory and bioinformatics solutions to capture as much molecular information from the tumor as possible using next generation sequencing (NGS). Elimination of technical noise to recognise true genomic alterations is combined with systematic annotation procedures that discriminate molecular characteristics of the tumor from heritable biological variation. Our focus is on NGS solutions for FFPE archival material and liquid biopsies applied to a broad spectrum of cancer types in collaboration with corresponding disease specialists. With these aims and focus, we adhere to the greater goal of the CCA to perform translational cancer research and provide patients with optimal, individualised medical care through precision diagnostics.
Next Generation Sequencing
In collaboration with the Clinical Genetics department we are now employing two Illumina HiSeq 2500 and two Illumina MiSeq sequencers to offer a wide range of next gen sequencing services. We now support whole genome sequencing, whole exome sequencing and small RNA sequencing with many other NGS applications to follow. The sequencers enable us to bring diagnostic applications to a next level in terms of speed and cost effectiveness. For the analysis of NGS data we join forces with the CCA Drylab bioinformatics facility.
Droplet Digital PCR
Droplet Digital PCR (ddPCR, BioRad QX200) equipment was installed to provide us with the ultimate technology for mutation testing and is being applied for absolute quantification of target DNA and RNA in liquid biopsies and for validation of NGS mutation analysis.
The CCA-Drylab project was installed to handle the BIG data NGS produces, which requires solid computing power, reliable data storage and retrieval, fast transport and granular access rights management. To facilitate reproducible research, tools are made available through GitHub, R/Bioconductor and Galaxy while data is deposited in community supported and access controlled data repositories (GEO, EGA, TranSMART).
The Tumour Genome Analysis Core is ISO 15189:2007 certificate 111