The Core Facility Genomics (CFG) provides state of the art genomics equipment to research groups and diagnostic labs, primarily in the Amsterdam UMC, but also to external parties. We facilitate the use of cutting-edge technology through centralized investment, management and maintenance of genomics equipment. The CFG combines a flexible research mindset with diagnostic grade quality and assurance. Most equipment is housed within the CFG laboratories, however, usage of equipment at research groups and diagnostic labs is often organized through the CFG.
CFG User Meetings
Every three months the CFG organizes a user meeting to update Amsterdam UMC researchers on the state of the art in genomics techniques and acquisitions. Experts, form research and industry are invited to present at these meetings. Examples of recent topics: Single Molecule Real Time (SMRT) sequencing, single cell technology/sequencing, Gene expression analysis: RNAseq and its data analysis
Facilities and services
The CFG houses multiple lab automation robots from Biomek, Mosquito and Hamilton to enhance reproducibility, cost efficiency and to allow handling of low amounts of input material and/or reagents. Standardized liquid handling workflows are available for DNA-seq and RNA-seq experiments. Custom workflows for your application can be developed in a collaborative setup.
Next Gen Sequencing
For NGS sequencing we offer both high throughput sequencing services (Illumina HiSeq 4000 / GeneStudio S5 Prime) as well as fast turnaround sequencing services (Illumina-MiSeq / IonTorrent-PGM).
Single Cell/Nuclei Sequencing
The CFG offers multiple workflows for single cell gene expression analysis. The most recent acquisition is the 10X Chromium controller, which offers a well-established and standardized platform for single cell analysis. Furthermore, we are working workflows for single cell ATAC sequencing and single nuclei sequencing.
Digital Droplet PCR
The newest acquisition of the CFG is a Biorad QX200 ddPCR machine for Rare Mutation Detection (RMD).
NGS data storage is provided. Raw fastq data is kept by default for 3 months; optionally, up to 5 years can be requested. The data is stored in a centralized computing facility where users can log in and apply analysis pipelines to their data. At current we offer a small number of data processing pipelines, including, variant calling, alignment, CNV calling and RNAseq analysis. Downstream analysis and interpretation is not included in our standard services.
The CFG is intended as the first point of contact for your genomics project. We offer advice on technical feasibility, experimental design and data analysis to optimize cost and outcome. We provide quotations of the cost and planning of laboratory and bioinformatics services which can be included in project proposals. Based on these initial discussions a project agreement is written, including cost, time. Furthermore, due to our combined expertise and many collaborations we can provide advise in many different fields and connect different groups.
The CFG is continuously looking to improve its offerings and services to facilitate high level research within the Amsterdam UMC. If you have specific equipment needs or ideas, let us know so we can see if and how we can help organize the acquisition of funding and support. We may also be aware of additional groups interested in the same techniques.