The Tumor Genome Analysis Core

About

The Tumor Genome Analysis Core (TGAC) is housed in the Cancer Center Amsterdam (CCA), at Amsterdam UMC location VUmc and 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 employing Illumina sequencing 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.

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.

Bioinformatics

Dr. Yongsoo Kim leads Bioinformatics in TGAC. For a robust anlaysis of NGS data generated in house or obtained from public domain, we developed a number of reproducible pipelines based on Snakemake, available at through Github (tgac-vumc). In addition to pipelines that makes use of available tools, we also developed a number of novel tools such as: QDNAseq (DNA Copy number analysis), ACE (absolute copy number estimation tool), and BLADE/Statescope (RNA deconvolution methods).

Accreditation
The Tumour Genome Analysis Core is accredited according to ISO 15189 for its diagnostic activities.