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Leiden Genome Technology Centre

Contact Details

LUMC

Albinusdreef 2 2333 ZA Leiden

https://www.lumc.nl/org/lgtc/

Dr. Susan Kloet

info@lgtc.nl

0031 (0)71 526 9500

Hotel Description

Leiden Genome Technology Center (LGTC), the genomics facility of the LUMC. The aim of the LGTC is to make things possible, through the development and facilitation of advanced, high-throughput methods, technology and equipment, biological resources and bioinformatic tools for genomic research by academic and industrial parties. Anybody in- and outside (world-wide) the LUMC, especially researchers and diagnostic laboratories performing (high-throughput) DNA and RNA analysis. The LGTC has state-of-the-art technology to perform (high-throughput) genomics and transcriptomics analysis. Instruments include two PacBio single molecule sequencers (the Sequel and the Sequel II), the 10x Genomics Chromium system for genomic assembly and high-throughput single cell analysis, and a Dolomite Bio Nadia platform for single cell analysis. In addition to providing access to the technology, the LGTC can be contacted for advice; technology options, best methodological approach, cost analysis and training (for details www.LGTC.nl). The LGTC organises and participates in many courses where the focus is on new technologies and ways to analyse the data. To disseminate knowledge to the general public, the LGTC joined the LeveDNA! initiative (www.LeveDNA.nl).

Genomics
Public
  • Agri & Food
  • Biodiversity & ecology
  • Biomedical & health
  • Next-generation sequencing
  • genomic assembly
  • Single cell analysis
  • (Small)RNA sequencing
  • bioinformatics
  • Genomics technology
  • Transcriptomics technology
  • Single cell analysis
  • Genetics

Expertise and Track Record

43500985028 Visualization of the Reversibility of Apoptosis Using Annexin A5 with P. Taschner (Hogeschool Leiden). 43500984086 Full-length sequencing of the gene encoding the drug metabolizing enzyme CYP2D6 to explore the contribution of rare and structural variants to pharmacogenetics with J.J. Swen (LUMC). 43500984066 Characterization of nasal dendritic cells in allergic rhinitis patients following controlled allergen challenge with A.L. Voskamp (LUMC). 43500984051 RENEW: REsequencing Nasonia vitripennis to Enhance its Workability with E.C. Verhulst (Wageningen University). 43500984027 Integrated whole genome and transcriptome analysis of cutaneous anaplastic large T-cell lymphomas (C-ALCL); new clues for diagnostic/prognostic markers and therapeutic targets with C.P. Tensen (LUMC). 435000006 Epigenetic reprogramming of mycobacterium-infected host cells with dr. A.H. Meijer (U Leiden). 435002029 Dissection of human mesenchymal stem cell population heterogeneity using single cell gene expression analysis to improve bone regenerative therapies With Van Leeuwen (Erasmus MC).

We provide the infrastructure and expertise to facititate genomics-based research projects. The added value is not just in the range of instruments that we have, but also the high-quality biological expertise we can offer.

The LGTC has taken part in a number of projects. Examples of large consortia include:

  • Genome of the Netherlands (GoNL) (involvement included data analysis)
  • gEUVADIS (involvement included data generation (transcriptome) and analysis)

No

  • van den Oever et al., 2012. Single molecule sequencing of free DNA from maternal plasma for noninvasive trisomy 21 detection. Clin Chem PMID:22278607
  • Nolte-'t Hoen et al., 2012 Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucl Acid Res PMID:22821563
  • Lappaleinen et al., 2013. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. PMID:24037378
  • 't Hoen et al., 2013. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotech. PMID:24037425
  • Rong J, et al. 2014. New insights into domestication of carrot from root transcriptome analyses. BMC Genomics PMID:25311557
  • Liang et al., 2014 Detecting authorized and unauthorized genetically modified organisms containing vip3A by real-time PCR and next-generation sequencing. Anal Bioanal Chem PMID:24553665
  • Kraaijeveld et al. 2015. Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing. Mol Ecol Resour. PMID:24893805
  • Browne et al. 2015. Complete genome sequence of BS49 and draft genome sequence of BS34A, Bacillus subtilis strains carrying Tn916. FEMS Microbiol Lett. PMID:25673660
  • Kolder et al. 2016. A full-body transcriptome and proteome resource for the European common carp. BMC Genomics PMID:27590662
  • Buermans et al., 2017. Flexible, scalable and cost efficient full-length CYP2D6 long amplicon PacBio sequencing. Hum Mut PMID:28044414

Centre for Genome Diagnostics
Centre for Medical Systems Biology
gEUVADIS
GoNL

Hotel Characteristics

  • 1 lab head
  • 4 technicians
  • 1 lab manager
  • 1 biostatistician

50%

  • PacBio Sequel II Sequencer
  • PacBio Sequel Sequencer
  • 10x Genomics Chromium instrument
  • Dolomite Bio Nadia platform plus Innovate module
  • Fluidigm BioMark HD, plus C1
  • Agilent FEMTO Pulse
  • Illumina HiSeq4000, NextSeq500, MiSeq

No

SRA