Core Facility Genomics

Core Facility Genomics - Amsterdam UMC - AMC

Our team of specialists:

  • Peter Henneman; expert on (epi)genetics and epidemiology
  • Marcel Mannens, Head genome diagnostic and analysis
  • Janneke Weiss, expert on implementation and interpretation of genetic data
  • Marja Jakobs; expert for questions related to (research) NGS applications
  • Daoud Sie; expert on molecular biology, bio-informatics and IT infrastructure
  • Alex Postma; expert on applied bioinformatics

    Location/Contact

    You can find the Core Facility Genomics (CFG) at K2 / G2-105.3 and reach us via e-mail address: CFG@amc.nl

    Availability

    All equipment and services are available during normal working days between 08.30 and 17.00 hours.

    Application highlights

    The Core Facility Genomics (CFG) is involved in many projects, mainly within the AMC and VUmc, but also outside these institutes (UMCU, PMC, LUMC, EMC, HMF, GenomeScan). As such CFG not only provides services and consultation, but most importantly the CGF acts as a hub of knowledge and expertise which allows synergetic connections to be made between experts.

    Whole Genome Sequencing

    In the foreseeable future deep whole genome sequencing (WGS) will come within reach of many research and diagnostic applications. Already many scientist have utilized WGS data for research purposes (Molenaar / Koster) and diagnostic labs are taking their first steps with WGS in collaboration with the Hartwig Medical Foundation (Weiss et al.). In the meantime, low pass/shallow WGS is heavily being used for copy number analysis in non-invasive prenatal diagnostics (Oudejans / Weiss / Sistermans) and cancer research (Ylstra).

    Whole Exome Sequencing

    The coding regions of the human genome is routinely interrogated with Whole Exome Sequencing (WES). Diagnostics labs utilize WES for genetic counseling by analyzing a subset of the targets, called a Virtual Panel (Weiss.). WES is also utilized on specific sub populations to provide unique characteristics for genetic hereditary research (Jansen / Holstege / Posthuma).

    Targeted Sequencing

    Compared to WES, targeted sequencing presents an even more focused approach to interrogate your locus of interest. There are many hybrid selection panels and amplicon assays routinely utilized both in diagnostic (Mook / Gille / Heideman) and research setting (Smit / de Jong / Noesel.)

    RNA sequencing

    There are many different protocols available for RNA sequencing. The most straight forward protocol is stranded mRNA sequencing which is used in many projects where differential gene expression analysis is the main interest. However, RNAseq can cater many niche applications, from small non coding RNA (Koppers / Steenbergen / Pegtel) to splice isoforms ( Cloos ), to fusion genes ( … ). Choosing the right protocol is essential for your RNAseq experiment.

    Single Cell sequencing

    The main challenge with single cell analysis is to isolate each individual cell and to optimize conditions for their own reaction chamber. There are a number of ways to make this possible. The CFG provides a fluidic circuit (Fluidigm C1) approach where each chamber can automatically be stained and examined before they are processed for sequencing. In addition the CFG also provides a droplet based approach (10X Genomics Chromium Controller – expected Q2/Q3 2018), where the reaction chamber is provided as an emulsion droplet, containing all the necessary reagents.

    CRISPR Screens

    CRISPR-Cas9 was discovered as an immune system in prokaryotes and archaea that confers resistance to bacteriophages and invading nucleic acids by providing a form of acquired immunity. It provides biomedical research with a toolbox for genome editing in mammalian cells. The technology is rapidly changing biomedical science and is expected to form the basis of personalized medicine in the future. The VUmc and AMC have jointly setup a CRISPR Facility (Wolthuis / de Lint / Warmerdam) where the CFG is providing robotics, sequencing and data analysis support.

    Liquid Biopsy

    Non Invasive Prenatal Testing (Weiss / Sistermans / Oudejans) is a very effective and minimally invasive method to diagnose the unborn child for birth defects. It is currently implemented in routine diagnostics at the VUmc. Given our experience with processing and sequencing blood samples on a large scale, a collaboration is initiated with the Liquid Biopsy Center (Pegtel / Wurdinger), which opened its doors in Oktober 2017. The CFG is providing expertise in robotics, sequencing and data analysis to support efforts in early detection and monitoring of cancer (Pegtel /  Wurdinger / Ylstra / Brakenhoff )

    Our equipment and services

    Services:

    Sanger sequencing:

    1. Sanger sequencing (2x 3730XL DNA Analyzer):
    • Intake of sequence samples
    • Registration in laboratory management system (LIMS), tracking and tracing of supplied sequence samples
    • Cleanup of sequence samples using Cleanseq beads and Biomek FX pipetting robots
    • Quality assurance
    2. Possibility of large scale purification of fragments using SAP/Exo & BDT for either 96 wells or 384 wells plates, using robotics.

    Fragment length Analysis with 3730XL DNA Analyzer:

    • Intake of samples and verification
    • Registration in laboratory management sytem (LIMS), tracking and tracing
    • Running of samples, and help in scoring and interpreting results

    Sub-processes of nextgen applications:

    Biomek FX pipetting robots to help support components of Nextgen sequencing:
    • Size selection using Ampure beads.
    • Library preparation for Illumina platforms
      o Kapa chemistry (using DNA as starting material)
    • DNA quantification and concentration measurements

    RNA sequencing:

    Support and help with regard to various RNA seq kits. Per research question we will discuss which kits are best suited for your application (contact Marja Jakobs).

    Regular RNA-seq kits:
    • Ovation RNA-Seq System V2 kit combined with
    • Ovation Ultralow V2 kit (Nugen) for Illumina library prep

    Current kits under testing (Roche):
    • Kapa RNA Hyperprep with RiboErase HMR kit
    • Kapa mRNA Hyperprep kit

    DNA/RNA isolation:
    We support (research) in-house projects:
    3x Qiagen Autopure DNA isolator
    2x Qiaqube RNA isolator

    Equipment:

    Biomek FX pipeting robots
    Machines available for PCR(2x) and Post PCR(3x).
    Can automate many routine (and laborious) pipetting protocols, e.g.:

    • Multiplex PCR BRCA(VUMC)
    • Large projects that involve plate sample (re)distribution, concentration measurements, qPCR (lightcycler)
    • Hemolytic assays
    • Drug screening
    • Cherry picking

    LAS 4000 (viewing of gels and membranes).

    Bioanalyser (2x) + management of  chips and kits
    An automatic capillary electrophorese machine that is employed to measure size and quality/purity of DNA and RNA.
    Tapestation 4200: An automatic capillary electrophorese machine that is employed to measure size and quality/purity of DNA and RNA.

    Lightcycler and Caliper twister
    Automatic arm fitted to the lightcycler that can load and exchange plates from stacks. Each plate can have a barcode, and a specialized protocol can be run per plate.

    Nanodrops
    DNA concentration measurement using UV absorption.

    Qubit
    DNA concentration measurement using fluorometric quantification.

    Fluorstar
    Determine concentration using fluorometric quantification in 96 wells plates (using the Biomek FX pipeting robot).

    FluidX rackscanner
    2D scanner for both 96 wells plate as well as 2d labelled tubes.

    Covaris (2x)
    Sonicators used to reproducibly fragments DNA using sound waves

    Fluidigm C1 (Single cell preparation system)
    • Research
    o Approved customers can operate the machine themselves
    o Otherwise run by employees of the CFG
    o New project can be run only after discussion and clearance from department head or PI of the department.

    10x Genomics Chromium Controller for both single cell  as DNA linked read application

    Nextgen sequencers
    • Illumina MiSeq
    • Illumina HiSeq 4000
    • Lontorrent  and OT2, CHEF emulsion PCR, and PGM
    • S5XL sequencer

    Approved customers can operate the machine themselves (excluding HiSeq 4000). Otherwise run by employees of the CFG. New projects can be run only after discussion and clearance from department head or PI.

    Chemicals

    For certain (often used) chemicals we purchase centralized and in bulk, and therefore we can
    provide a discount to our customers. The following chemicals are available on discount:
    • Bigdye Terminator
    • Hidi formamide for fragment analysis
    • Ampure XP for purification and / size selection
    • Qubit chemicals for concentration measurements
    • Bioanalyser chips and chemicals

    Costs:

    Soon here will be an overview from the costs that are applicable for the various tests. These are “activity” based costs, which means they include the costs of the chemicals used, the direct hands-on time,  and the maintenance and purchase costs of the machines.