← Back to list

Tumor Genome Analysis Core

Contact Details

Amsterdam UMC location VUmc

De Boelelaan 1117, 1081 HV Amsterdam

https://www.tgac.nl/

Bauke Ylstra

B.Ylstra@vumc.nl

+31204442495

Hotel Description

 

TGAC

The core expertise of the Tumor Genome Analysis Core (TGAC) is to sequence, assemble, and analyse the function and structure of cancer genomes.

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 to perform translational  research and provide patients with optimal, individualised medical care through precision diagnostics. 

NGS

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 (WGS), whole exome sequencing (WES), capture panels and (small) RNA sequencing.

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.

DryLab

Dr. Yongsoo Kim has been recruited to head the CCA-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, R/Bioconductor and Galaxy while data is deposited in community supported and access controlled data repositories (GEO, EGA, TranSMART). 

Genomics
Public
  • Biomedical & health
  • Bioinformatics - deconvolution
  • Archival - formalin fisxed specimens
  • Liquid biopsy
  • Droplet Digital PCR
  • Combined copy number, mutation and translocation sequencing
  • oncology

Expertise and Track Record

Routine laboratory and bioinformatics under ISO 15189 accreditation for copy number analysis from FFPE materials

5 central publications underlining the expertise

[1]. Sequencing Structural Variants in Cancer for Precision Therapeutics. Macintyre G, Ylstra B, Brenton JD. Trends Genet. 2016 Sep;32(9):530-42.

[2]. Loss of chromosome 18q11.2-q12.1 is predictive for survival in patients with metastatic colorectal cancer treated with bevacizumab. E. van Dijk, H. D. Biesma, M. Cordes, D. Smeets, M. Neerincx, S. Das, P. P. Eijk, V. Murphy, A. Barat, O. Bacon, J. H. M. Prehn, J. Betge, T. Gaiser, B. Fender, G. A. Meijer, D. A. McNamara, R. Klinger, M. Koopman, M. P. A. Ebert, E. W. Kay, B. T. Hennessey, H. M. W. Verheul, W. M. Gallagher, D. P. O’Connor, C. J. A. Punt, F. Loupakis, D. Lambrechts, A. T. Byrne, N. C. T. van Grieken, and B. Ylstra. J Clin Oncol. 2018 Jul 10;36(20):2052-2060.

[3]. Genomic landscape of metastatic colorectal cancer. Haan JC, Labots M, Rausch C, Koopman M, Tol J, Mekenkamp LJ, van de Wiel MA, Israeli D, van Essen HF, van Grieken NC, Voorham QJ, Bosch LJ, Qu X, Kabbarah O, Verheul HM, Nagtegaal ID, Punt CJ, Ylstra B*, Meijer GA*. Nat Commun. 2014 Nov 14;5:5457.

[4] Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy. Smeets D, Miller IS, O’Connor DP, Das S, Moran B, Boeckx B, Gaiser T, Betge J, Barat A, Klinger R, van Grieken NCT, Cremolini C, Prenen H, Mazzone M, Depreeuw J, Bacon O, Fender B, Brady J, Hennessy BT, McNamara DA, Kay E, Verheul HM, Maarten N, Gallagher WM, Murphy V, Prehn JHM, Koopman M, Punt CJA, Loupakis F, Ebert MPA, Ylstra B, Lambrechts D*, Byrne AT*. Nat Commun. 2018 Oct 5;9(1):4112

[5] DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B. Genome Res. 2014 Dec;24(12):2022-32.

No

  • Copy number signatures and mutational processes in ovarian carcinoma. Macintyre G, Goranova TE, De Silva D, Ennis D, Piskorz AM, Eldridge M, Sie D, Lewsley LA, Hanif A, Wilson C, Dowson S, Glasspool RM, Lockley M, Brockbank E, Montes A, Walther A, Sundar S, Edmondson R, Hall GD, Clamp A, Gourley C, Hall M, Fotopoulou C, Gabra H, Paul J, Supernat A, Millan D, Hoyle A, Bryson G, Nourse C, Mincarelli L, Sanchez LN, Ylstra B, Jimenez-Linan M, Moore L, Hofmann O, Markowetz F, McNeish IA, Brenton JD. Nat Genet. 2018 Sep;50(9):1262-1270.
  • Decoy receptor 1 (DCR1) promoter hypermethylation and response to irinotecan in metastatic colorectal cancer. Bosch LJW, Trooskens G, Snaebjornsson P, Coupé VMH, Mongera S, Haan JC, Richman SD, Koopman M, Tol J, de Meyer T, Louwagie J, Dehaspe L, van Grieken NCT, Ylstra B, Verheul HMW, van Engeland M, Nagtegaal ID, Herman JG, Quirke P, Seymour MT, Punt CJA, van Criekinge W, Carvalho B, Meijer GA. Oncotarget. 2017 Jun 27;8(38):63140-63154.
  • Assessment of concordance between fresh-frozen and formalin-fixed paraffin embedded tumor DNA methylation using a targeted sequencing approach. Moran B, Das S, Smeets D, Peutman G, Klinger R, Fender B, Connor K, Ebert M, Gaiser T, Prehn JH, Bacon O, Kay E, Hennessy B, Murphy V, Ylstra B, Lambrechts D, Byrne AT, Gallagher WM, O'Connor DP. Oncotarget. 2017 Jul 18;8(29):48126-48137.
  • Condensin II mutation causes T-cell lymphoma through tissue-specific genome instability. Woodward J, Taylor GC, Soares DC, Boyle S, Sie D, Read D, Chathoth K, Vukovic M, Tarrats N, Jamieson D, Campbell KJ, Blyth K, Acosta JC, Ylstra B, Arends MJ, Kranc KR, Jackson AP, Bickmore WA, Wood AJ. Genes Dev. 2016 Oct 1;30(19):2173-2186.
  • Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets. Best MG, Sol N, In 't Veld SGJG, Vancura A, Muller M, Niemeijer AN, Fejes AV, Tjon Kon Fat LA, Huis In 't Veld AE, Leurs C, Le Large TY, Meijer LL, Kooi IE, Rustenburg F, Schellen P, Verschueren H, Post E, Wedekind LE, Bracht J, Esenkbrink M, Wils L, Favaro F, Schoonhoven JD, Tannous J, Meijers-Heijboer H, Kazemier G, Giovannetti E, Reijneveld JC, Idema S, Killestein J, Heger M, de Jager SC, Urbanus RT, Hoefer IE, Pasterkamp G, Mannhalter C, Gomez-Arroyo J, Bogaard HJ, Noske DP, Vandertop WP, van den Broek D, Ylstra B, Nilsson RJA, Wesseling P, Karachaliou N, Rosell R, Lee-Lewandrowski E, Lewandrowski KB, Tannous BA, de Langen AJ, Smit EF, van den Heuvel MM, Wurdinger T. Cancer Cell. 2017 Aug 14;32(2):238-252.e9.
  • Combination of a six microRNA expression profile with four clinicopathological factors for response prediction of systemic treatment in patients with advanced colorectal cancer. Neerincx M, Poel D, Sie DLS, van Grieken NCT, Shankaraiah RC, van der Wolf-de Lijster FSW, van Waesberghe JTM, Burggraaf JD, Eijk PP, Verhoef C, Ylstra B, Meijer GA, van de Wiel MA, Buffart TE, Verheul HMW. PLoS One. 2018 Aug 3;13(8):e0201809.
  • Endogenous C1-inhibitor production and expression in the heart after acute myocardial infarction. Emmens RW, Baylan U, Juffermans LJ, Karia RV, Ylstra B, Wouters D, Zeerleder S, Simsek S, van Ham M, Niessen HW, Krijnen PA. Cardiovasc Pathol. 2016 Jan-Feb;25(1):33-9.
  • Reduced rate of copy number aberrations in mucinous colorectal carcinoma. Hugen N, Simmer F, Mekenkamp LJ, Koopman M, van den Broek E, de Wilt JH, Punt CJ, Ylstra B, Meijer GA, Nagtegaal ID. Oncotarget. 2015 Sep 22;6(28):25715-25.
  • Select item 26287660 29. Variant Rett syndrome in a girl with a pericentric X-chromosome inversion leading to epigenetic changes and overexpression of the MECP2 gene. Vieira JP, Lopes F, Silva-Fernandes A, Sousa MV, Moura S, Sousa S, Costa BM, Barbosa M, Ylstra B, Temudo T, Lourenço T, Maciel P. Int J Dev Neurosci. 2015 Nov;46:82-7.
  • Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. Faddeeva A, Studer RA, Kraaijeveld K, Sie D, Ylstra B, Mariën J, op den Camp HJ, Datema E, den Dunnen JT, van Straalen NM, Roelofs D. PLoS One. 2015 Jun 15;10(6):e0130600.

N/A

Hotel Characteristics

  • 0.5 FTE facility Coordinator
  • 2 FTE dedicated technicians incl lab manager (2.0 FTE)
  • 1 FTE Tenure track PI in Bioinformatics
  • 0.3 FTE Bioinformatics maintenance

50%

  • Droplet Digital PCR (ddPCR, BioRad QX200) equipment
  • Illumina sequencing HiSeq, MiSeq, NextSeq etc.

ISO 15189 for diagnostic activities

European Genome-phenome Archive (EGA) and TranSMART