Genomics

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22^nd Core Facility Genomics (CFG) user webinar

24^th of September 16:00-17:00

“The future of HPC compute” and “NovaSeq X Plus”

The CFG of the Amsterdam UMC frequently organizes an user webinar to update Amsterdam UMC researchers on the state of the art in genomics techniques and data acquisitions.

Experts, from diagnostics, research, or industry are invited to present at these meetings. Examples of recent topics: Single Molecule Real Time (SMRT) sequencing, single cell technology/sequencing, Spatial transcriptomics (Nanostring®). Recordings of previous CFG user webinars can be found at: https://cfg.amsterdamumc.nl

21^st Core Facility Genomics (CFG) user webinar

13^th of February 2024

Nanostring

Program:

1. Daisy Picavet – Havik (Core Facility Imaging, Amsterdam UMC) & Ingrid Bakker (Core Facility Genomics, Amsterdam UMC)

Title: “Practical info from the labs about the GeoMX DSP Nanostring”

2. Lieve van der Maarel & Otto Mulleners (Dept of Medical Biology, Amsterdam UMC)

Title: “Exploring regional gene expression during mouse heart development using the NanoString GeoMx”

20^th Core Facility Genomics (CFG) user webinar

12^th of December 2023

Nanopore

The speakers of this meeting were Desiree de Bruin and Norbert Moldovan.

Desiree de Bruin is an alumna of the master Forensic Science, who conducted her research thesis project at the department of Human Genetics at the AMC. She explored the current capabilities and potential application of Nanopore sequencing in the context of forensic DNA phenotyping, by combining forensic genetic, epigenetic, and phenotypic markers in a single assay following a direct sequencing approach. For her thesis project, Desiree received the Faculty Master’s Thesis Prize (Faculty of Science/University of Amsterdam) earlier this year.

Norbert Moldovan is a postdoc computational biologist affiliated with the Department of Pathology, Cancer Center Amsterdam. His research has centered around the innovative utilization of cell-free DNA fragmentomic features for cancer detection. He developed bioinformatic tools for long- and short-read genomic and transcriptomic data analysis. Norbert recently secured the ZonMw Off Road grant, to explore the usability of the Nanopore sequencing technology for full-length circular RNA characterization in liquid biopsies and self-collected samples.

Program:

1. Desiree de Bruin (MSc Forensic Science), Dept. of Human Genetics, Genome Diagnostic laboratory, Epigenetics of disease.

   Title: “Nanopore Sequencing: Towards an All-In-One Forensic DNA Analysis Technology”

2. Dr Norbert Moldovan, Dept. of Pathology, Cancer Center Amsterdam.

   Title: “Ouro-seq: Full-length circular RNA characterization in liquid biopsies and self-collected samples of cervical cancer patients”

19th Core Facility Genomics (CFG) user webinar

19^th of September 2023

Bioinformatics is the topic of this CFG webinar, entitled: “High Performance Compute and Bioinformatics”.

Program:

1. Daoud Sie/ Reinier Vleugels (dept. of Human Genetics, Amsterdam UMC) 

   Title: “Introduction and overview of the HPC Genomics resource” 

2. Roxanne Boyer (dept. of Human Genetics, Amsterdam UMC) 

   Title: “Pipeline development for the P2 Solo Nanopore sequencer”

3. User story 

   Using Graphical applications on HPC 

   Executing a workflow using RStudio on HPC 

18^th Core Facility Genomics (CFG) user webinar

2^nd of May

This webinar topic concerns Spatial transcriptomics, which is an emerging new technology. This technology enables to generate transcriptomic profiles and spatial information simultaneously. This technology allows researchers to pinpoint the tissue location of aberrant molecular processes in disease. Since this technology brings together the scientific fields of imaging and genomics, both the Core facility Imaging and the Core facility Genetics have put efforts to obtain the Digital Spatial Profiler GeoMX of Nanostring® within our institute. Obviously, the generation of such data requires also high standard bioinformatics.

Both the introduction of GeoMX and Bioinformatics will be the topics of the next webinar, which is scheduled for the 2^nd of May, 16:00, entitled: “Nanostring GeoMX DSP, designing my experiment and data processing and analysis”

Program:

1. Dr Yongsoo Kim (dept. of Pathology and CCA, Amsterdam UMC)

   Title: “BLADE: A Bayesian Deconvolution Approach and its Practical Use in Analyzing Spatial Transcriptome Data.”

2. Daisy Picavet - Havik (Core Facility Imaging, Amsterdam UMC)

   Marja Jakobs (Core Facility Genomics, Amsterdam UMC)

   Title: “Practical info from the labs about the GeoMX DSP Nanostring”

3. Discussion & closure

17^th Core Facility Genomics (CFG) user webinar

13^th December 2022

Topic: Robotics

The core facility genomics puts continuously much effort in developing and implementation of new and innovative techniques in order to offer state of the art technologies and methodologies to their users. This webinar is about such new methodology: “Robotics at the Core Facility Genomics”

The webinar starts with Patrick Ruizendaal, robotics specialist of the Core Facility Genomics. This presentation gives a broad overview of in-house robotics equipment and CFG services.

Next, Eva van der Linden, dept. Public & Occupational Health & dept. Internal Medicine, introduces the proRODAM study and the applications and implementations of robotics in this study. In this context a nice case report on the usage of robotics in a large longitudinal cohort.

Finally, Jörg Hamann, affiliated to the Amsterdam UMC Biobank, presents the biobanking workflow of banking and explains in that setting, as CFG user, robotic applications.

If you have any questions after watching this webinar, do not hesitate to contact your Core Facility Genomics at: cfg@amsterdamumc.nl

16^th Core Facility Genomics (CFG) user webinar

17th of September 2022

Topic: Functional gene expression analysis

15th Core Facility Genomics (CFG) user webinar

March 22nd 2022

CRISPR-Based Genome Engineering, Functional Genomics, and Compound-Genome Interaction Mapping in Human Cell Models.

Inventory of CRISPR-Based Research- and Translational Facility Services at Amsterdam UMC.

Rob Wolthuis (Associate Professor and Head of Oncogenetics, Co-Manager Amsterdam UMC CRISPR Expertise Center, Dept. of Human Genetics, Cancer Center Amsterdam, Amsterdam UMC).

14th Core Facility Genomics (CFG) user webinar

February 1st 2022

“Decoding cell-free DNA biology to boost liquid biopsy.”

“Cell Free Analyses implementation at the Core Facility Genomics”

13th Core Facility Genomics (CFG) user webinar

Nov 2021

Practical aspects of SARS-CoV-2 genomic surveillance and outbreak analysis

12th Core Facility Genomics (CFG) user webinar

Sept 2021

Next Generation Sequencing at the Core: What's new?

11th Core Facility Genomics (CFG) user webinar

March 2021

Data analysis and HPC solutions within AmsterdamUMC

10th Core Facility Genomics (CFG) user webinar

Morphology driven High Plex Spatial Analysis