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.

CCA-DryLab

Dr. Yongsoo Kim has been recruited to head the drylab and started October 1st 2018. The drylab 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 (tgac-vumc), R/Bioconductor and Galaxy while data is deposited in community supported and access controlled data repositories (GEO, EGA, TranSMART). 

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

Members

Head Tumor Genome Analysis Core (TGAC)
Prof. Dr. Bauke Ylstra (researcherID)
Room: CCA 1 – 22

Principal Investigator, Bioinformatics
Dr. Yongsoo Kim
Room: CCA 1 – 28

Principal Investigator, Gastrointestinal oncology
Prof. Dr. Nicole van Grieken

Principal Investigator, Lymphoma
Prof. Dr. Daphne de Jong

Senior Research Technician
Paul P. Eijk
Room: CCA 1 – 26

PhD candidates
Tanya Soeratram
Irene Caspers
Barbara Barbosa
Jurriaan Janssen
Mischa Steketee
Min Wu

Principal Investigators

Teodora Radonic, MD. PhD

Nicole van Grieken, MD. PhD

Gastric cancer

Bauke Ylstra, PhD

Full professor in Tumor Genome Analysis

Yongsoo Kim, PhD

Bioinformatics

Postdoc Researchers

Bernard Stikker
Shiva Najjary

PhD Candidates

Dominika Martinovicova
Jeltje Rommens
Barbara Andrade Barbosa
Stef Elings
Jurriaan Janssen

PhD Student

Mischa Steketee