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Sequencing Analysis Support Core LUMC

Contact Details

Leiden University Medical Center

Office: LUMC T6-32

Dr. H. Mei

0031 (0)71 5268498 0031 (0)6 41709231

Hotel Description

SASC is a specialized team at LUMC to support LUMC researchers and clinicians to analyze their Next Generation Sequencing data. SASC team focuses on building scalable, maintainable, user-friendly, reproducible, and flexible data analysis pipelines by selecting and integrating algorithms and tools developed by academic institutes. The current SASC generic pipelines include single nucleotide polymorphism (SNP) detection and annotation, structure variants (Insertions, deletions, translocations) detection, annotation and visualization, gene expression analysis using RNAseq, epigenetics analysis, etc. To address the challenge on data computation and storage, SASC have access to both the LUMC local computer cluster and centralized computing resource hosted by SURFsara (Life Science Grid and HPC cloud). For all data analysis projects performed by SASC, SASC guarantees result reproducibility based on a rigorous project logging standard and backups of data provenance information.
SASC team also has a strong collaboration with several nation-wide expertise platforms on Next Generation Sequencing data analysis: NBIC Next Generation Sequencing Taskforce, DTL/DISC, CTMM/TraIT, BBMRI, Galaxy-WG, SASC expects to adopt and adapt the best practice on data analysis and setting up supporting IT infrastructure verified by these national platforms.

Bioinformatics
Public
  • Biomedical & health
  • Industrial biotech
  • Biodiversity & ecology
  • Genomics
  • Bio-informatics
  • Big data infrastructure
  • Diagnositic sequencing
  • Cancer genomics
  • Structure variants detection
  • Genomics database
  • Sequencing quality control

Expertise and Track Record

435000026 Development of standard microbial SNP typing pipeline with Prof. dr. E.J. Kuijper (LUMC)

LUMC and in particular LGTC (a current close collaborator of SASC) has been leading the adoption of the NGS technology in the Netherlands. LGTC was one of the first groups using NGS technology and lately the first adopter of 3rd generation sequencers (Helicos in 2011, PacBio in 2012). Thus, SASC has the advantage of leveraging the extensive bioinformatics expertise from LGTC and bring it further to satisfy the ever growing specific requirements from LUMC researchers.
SASC and LGTC have been actively participating the discussion in the NBIC BioAssist program and has established itself as a major knowledge center on NGS data analysis.

Not yet. We mainly focused on Genomics projects.

  • van Dijk, T., Rudnik-Schöneborn, S., Senderek, J., Hajmousa, G., Mei, H., Dusl, M., Aronica, E., Barth, P., Baas, F., 2017. Pontocerebellar hypoplasia with spinal muscular atrophy (PCH1): identification of SLC25A46 mutations in the original Dutch PCH1 family. Brain.
  • Pasteuning-Vuhman, S., Boertje-van der Meulen, J. W., van Putten, M., Overzier, M., ten Dijke, P., Kiełbasa, S. M., Arindrarto, W., Wolterbeek, R., Lezhnina, K. V., Ozerov, I. V., Aliper, A. M., Hoogaars, W. M., Aartsma-Rus, A. & Loomans, C. J. M. New function of the myostatin/activin type I receptor (ALK4) as a mediator of muscle atrophy and muscle regeneration. The FASEB Journal 31, 238–255 (2017).
  • BIOS consortium, Slieker, R. C., van Iterson, M., Luijk, R., Beekman, M., Zhernakova, D. V., Moed, M. H., Mei, H., van Galen, M., Deelen, P., Bonder, M. J., Zhernakova, A., Uitterlinden, A. G., Tigchelaar, E. F., Stehouwer, C. D. A., Schalkwijk, C. G., van der Kallen, C. J. H., Hofman, A., van Heemst, D., de Geus, E. J., van Dongen, J., Deelen, J., van den Berg, L. H., van Meurs, J., Jansen, R., ‘t Hoen, P. A. C., Franke, L., Wijmenga, C., Veldink, J. H., Swertz, M. A., van Greevenbroek, M. M. J., van Duijn, C. M., Boomsma, D. I., Slagboom, P. E. & Heijmans, B. T. Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms. Genome Biology 17, (2016).
  • Bonder, M. J., Luijk, R., Zhernakova, D. V., Moed, M., Deelen, P., Vermaat, M., van Iterson, M., van Dijk, F., van Galen, M., Bot, J., Slieker, R. C., Jhamai, P. M., Verbiest, M., Suchiman, H. E. D., Verkerk, M., van der Breggen, R., van Rooij, J., Lakenberg, N.,Arindrarto, W., Kielbasa, S. M., Jonkers, I., van ’t Hof, P., Nooren, I., Beekman, M., Deelen, J., van Heemst, D., Zhernakova, A., Tigchelaar, E. F., Swertz, M. A., Hofman, A., Uitterlinden, A. G., Pool, R., van Dongen, J., Hottenga, J. J., Stehouwer, C. D. A., van der Kallen, C. J. H., Schalkwijk, C. G., van den Berg, L. H., van Zwet, E. W., Mei, H., Li, Y., Lemire, M., Hudson, T. J., Slagboom, P. E., Wijmenga, C., Veldink, J. H., van Greevenbroek, M. M. J., van Duijn, C. M., Boomsma, D. I., Isaacs, A., Jansen, R., van Meurs, J. B. J., ’t Hoen, P. A. C., Franke, L. & Heijmans, B. T. Disease variants alter transcription factor levels and methylation of their binding sites. Nature Genetics 49, 131–138 (2016).
  • Zhernakova, D. V., Deelen, P., Vermaat, M., van Iterson, M., van Galen, M., Arindrarto, W., van ’t Hof, P., Mei, H., van Dijk, F., Westra, H.-J., Bonder, M. J., van Rooij, J., Verkerk, M., Jhamai, P. M., Moed, M., Kielbasa, S. M., Bot, J., Nooren, I., Pool, R., van Dongen, J., Hottenga, J. J., Stehouwer, C. D. A., van der Kallen, C. J. H., Schalkwijk, C. G., Zhernakova, A., Li, Y., Tigchelaar, E. F., de Klein, N., Beekman, M., Deelen, J., van Heemst, D., van den Berg, L. H., Hofman, A., Uitterlinden, A. G., van Greevenbroek, M. M. J., Veldink, J. H., Boomsma, D. I., van Duijn, C. M., Wijmenga, C., Slagboom, P. E., Swertz, M. A., Isaacs, A., van Meurs, J. B. J., Jansen, R., Heijmans, B. T., ’t Hoen, P. A. C. & Franke, L. Identification of context-dependent expression quantitative trait loci in whole blood. Nature Genetics 49, 139–145 (2016).
  • Ruben G. de Bruin, Lily Shiue, Jurriën Prins, Hetty C. de Boer, Anjana Singh, W. Samuel Fagg, Janine M. van Gils, Jacques M. G. J. Duijs, Sol Katzman, Adriaan O. Kraaijeveld, Stefan Böhringer, Wai Y. Leung, Szymon M. Kielbasa, John P. Donahue, Patrick H.J. van der Zande, Rick Sijbom, Carla M. A. van Alem, Ilze Bot, Cees van Kooten, J. Wouter Jukema, Hilde Van Esch, Ton J. Rabelink, Hilal Kazan, Erik A. L. Biessen, Manuel Ares Jr., Anton Jan van Zonneveld & Eric P. van der Veer. "Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression" Nature Communications 7, Article number: 10846, doi:10.1038/ncomms10846
  • ask others Peter van't Hof, Szymon M. Kielbasa, Wibowo Arindrarto, Jeroen F. J. Laros, Sander Bollen, Hailiang Mei: BIOPET: towards Scalable, Maintainable, User-friendly, Robust and Flexible NGS data analysis pipelines. CCGrid 2017: 823-829
  • Punt, Simone, Willem E. Corver, Sander A.J. van der Zeeuw, Szymon M. Kielbasa, Elisabeth M. Osse, Henk P.J. Buermans, Cornelis D. de Kroon, Ekaterina S. Jordanova, & Arko Gorter. "Whole-transcriptome analysis of flow-sorted cervical cancer samples reveals that B cell expressed TCL1A is correlated with improved survival." Oncotarget, 6.36 (0): 38681-38694. 2015
  • Wai Y. Leung, Tobias Marschall, Yogesh Paudel, Laurent Falquet, Hailiang Mei, Alexander Schoenhuth and Tiffanie Yael Maoz. "The new face of SV detection and tool development for all species SV-AUTOPILOT: Structural Variation AUTOmated PIpeLine Optimization Tool." BMC Genomics, 2015
  • Marvyn T. Koning, Sander A.J. van der Zeeuw, Marcelo Navarrete, Cornelis A.M. van Bergen, Valeri Nteleah, Marieke Griffioen, Szymon M. Kiełbasa, Hendrik Veelken. "Massive Parallel Sequencing of Full-Length B-Cell Receptor Sequences Reveals HLA-Dependent Shaping of the B-Cell Immune Repertoire." Blood Dec 2014, 124 (21) 4143
  • Chair, DTL/Elixir-NL Galaxy working group
  • Chair, DTL NGS interest group
  • Chair, data management group, BBMRI-BIOS project

 

Hotel Characteristics

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ENA, EGA, GEO