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Liquid biopsies – Course and Conference Office

EMBL Course

Liquid biopsies

Overview

Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.

Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

Course Overview

There is an increasing interest and need to analyze biomarkers in liquid biopsies, including basic research and clinical applications. Liquid biopsies have several advantages including being minimally invasive, allow repeated sampling and sampling is often a clinical routine. This course will provide an overview of several techniques to detect and analyze liquid biopsy-based analytes such as circulating tumor cells, cell free tumor-DNA (ctDNA), miRNA, extracellular vesicles, mRNA, carbohydrates and proteins. Participants will be introduced to all aspects of liquid biopsies ranging from proper sampling through analyte analysis and final data analysis. Experimentally, we will demonstrate ultrasensitive ctDNA analysis using sequencing and digital PCR, targeted miRNA profiling, flow cytometry and targeted protein expression analysis. We will cover aspects of other analytes by lectures and we will have a strong focus on applications, especially cancer applications. Aspects of biobanking and clinical implementation will also be highlighted.

Audience

This course targets scientists entering the field of liquid biopsy analysis and wanting to learn about the benefits and limitations of different approaches.

Modules/Resources

  • Ultra-sensitive mutation detection using sequencing 
  • Flow cytometry analysis
  • Digital PCR applications in the liquid biopsy workflow 
  • Protein analysis in liquid biopsies 
  • miRNA analysis in liquid biopsies 
  • Hands-on data analysis and interpretations

Learning Outcomes

Participants will receive an overview of various experimental workflows in liquid biopsies, from sample preparation to data analysis. The course provides an overview of current theories, methods and emerging applications. Whereby a strong focus will be on experimental design, best practices, pitfalls as well as dos and don’ts. After the course, participants should be able to assess the best methods for their application as well as design their experiment.

What past participants say about the course

“This was a great course that has helped me understand the basics, as well as gain in-depth knowledge on liquid biopsies. Simply phenomenal.” – M A Bari Siddiqui, All India Institute of Medical Sciences

Speakers

Speakers, trainers, and staff

Michael Pfaffl

Technical University of Munich

Germany

(Virtual speaker)

Scientific organisers

Course organisers

Preliminary programme

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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Monday, 9 October 2023
Time (Europe/Berlin)SessionLocation
08:35Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
08:45 – 09:00RegistrationFlex Lab A & B
09:00 – 09:45Welcome and house notes and course overviewFlex Lab A & B
09:45 – 10:15Background lecture
Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden
Flex Lab A & B
10:15 – 10:30IcebreakerFlex Lab A & B
10:30 – 10:45FlashtalksFlex Lab A & B
10:45 – 11:00Coffee breakFlex Lab A & B
11:00 – 12:00Lecture: Flow Cytometry
Beata Ramasz – EMBL Heidelberg, Germany
Flex Lab A & B
12:00 – 13:00LunchEMBL Canteen
13:00 – 13:30Lecture: SiMSen-Seq workflow
Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden
Flex Lab A & B
13:30 – 15:00Practical session 1: DNA extraction from PlasmaTraining Lab B
15:00 – 15:15Coffee breakFlex Lab A & B
15:15 – 16:30Practical session 2: Library PreparationTraining Lab B
16:30 – 18:30Practical session 3: Clean-Up and quality controlTraining Lab B
18:30 – 19:30DinnerEMBL Canteen
19:30 – 21:00Poster session 1ATC Helix A
21:00Departure to HotelATC Entrance
Day 2 – Tuesday, 10 October 2023
Time (Europe/Berlin)SessionLocation
08:35Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:15Overview of the dayFlex Lab A & B
09:15 – 10:30Practical session 4: Single Cell Sorting
Beata Ramasz – EMBL Heidelberg, Germany
Training lab B
10:30 – 10:45Coffee breakFlex Lab A & B
10:45 – 12:00Practical session 5: TBCTraining lab B
12:00 – 13:00Technology lunchATC Foyer
13:00 – 13:30Practical session 6: Single-cell RT
Bianka Baying – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training lab B
13:30 – 14:30Lecture: Introduction to ddPCR
Francisco Bizouarn – BioRad, USA
Flex Lab A & B
14:30 – 15:00Practical session 7: Single-cell qPCR
Bianka Baying – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training lab B
15:00 – 15:15Coffee breakFlex Lab A & B
15:15 – 17:00Practical session 8: ddPCR
Jörg Bantin – BioRad, USA
Francisco Bizouarn – BioRad, USA
Training lab B
17:00 – 18:00Practical session 9:
Introduction into QuantaSoft
Start reading the experiment

Jörg Bantin – BioRad, USA
Francisco Bizouarn – BioRad, USA
Training lab B
18:00 – 19:00DinnerEMBL Canteen
19:00 – 20:30Poster session IIATC Helix A
20:30Departure to HotelATC Entrance
Day 3 – Wednesday, 11 October 2023
Time (Europe/Berlin)SessionLocation
08:35Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:15Overview of the dayFlex Lab A & B
09:15 – 10:15Practical session 10: Data analysis with QuantaSoft
Jörg Bantin – BioRad, USA
Francisco Bizouarn – BioRad, USA
Training lab B
10:15 – 10:30Coffee breakFlex Lab A & B
10:30 – 11:30Practical session 11: Data analysis with QuantaSoft
Jörg Bantin – BioRad, USA
Francisco Bizouarn – BioRad, USA
Training lab B
11:30 – 12:30Lecture: Role of biobanks in securing process quality in sample retrieval and storage
Romy Kirsten – National Center for Tumor Diseases (NCT) Heidelberg, Germany
Flex Lab A & B
12:30 – 13:30LunchEMBL Canteen
13:30 – 14:30Lecture: Effect of pre-analytical factors on the measurement of Evs in Liquid Biopsies
An Hendrix – Ghent University, Belgium
Flex Lab A & B
14:30 – 16:00Lecture: Single-Cell Analysis: Technologies and Applications
Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden
Flex Lab A & B
16:00 – 16:30Coffee breakFlex Lab A & B
16:30 – 17:30Lecture: Clinical validation of droplet-based procedures in the context of liquid biopsies
Valerie Taly – Paris Descartes University, France
Flex Lab A & B
17:30Free evening
17:40Departure to HotelIn front of ATC entrance
18:15Bus to NeckarmünzplatzBus stop in front of ISG Hotel
18:30Optional: Heidelberg old town tourNeckarmünzplatz
Day 4 – Thursday, 12 October 2023
Time (Europe/Berlin)SessionLocation
08:35Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:15Overview of the dayFlex Lab A & B
09:15 – 10:30Lecture: Exosomal Biomarkers in Liquid Biopsies: How to identify valid and better ‘Biomarker Signatures’ from micro-vesicular small-RNA Sequencing
Michael Pfaffl – Technical University of Munich, Germany
Flex Lab A & B
10:30 – 10:45Group photoTBA
10:45 – 11:00Lecture: Workflow overview: Protein detection
Bianka Baying – EMBL Heidelberg, Germany
Lei Chen – Uppsala University, Sweden
Laura Villacorta – EMBL Heidelberg, Germany
Flex Lab A & B
11:00 – 12:00Practical session 12:
Plasma Protein detection (PEA)
Detection Probe Set-up

Lei Chen – Uppsala University, Sweden
Training lab B
12:00 – 13:00LunchEMBL Canteen
13:00 – 14:30Practical session 13: Plasma Protein detection (PEA) qPCR Set-up
Lei Chen – Uppsala University, Sweden
Training lab B
14:30 – 15:45Lecture: Protein detection in Liquid Biopsies
Ulf Landegren – Uppsala University, Sweden
Flex Lab A & B
15:45 – 18:00Practical session 14:
Plasma Protein detection (PEA)
Demo: Data analysis

Lei Chen – Uppsala University, Sweden
Training lab B
18:00Departure to HotelIn front of ATC entrance
18:40Departure to the restaurant Wirtshaus zum NepomukBus stop in front of ISG Hotel
19:00Course dinnerWirtshaus zum Nepomuk
Day 5 – Friday, 13 October 2023
Time (Europe/Berlin)SessionLocation
08:35Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:15Overview of the dayHelix Seminar Room B
09:15 – 10:30Lecture: Liquid Biopsies in the clinical context, High-fidelity sequencing
Tony E. Godfrey – Boston University School of Medicine, USA
Helix Seminar Room B
10:30 – 10:45Coffee breakComputer Training Lab
10:45 – 11:45Lecture: CTC, Single-Cell, Two-Tailed PCR for microRNA and cfDNA
Mikael Kubista – Institute of Biotechnology and TATAA Biocenter, Czech Republic
Computer Training Lab
11:45 – 12:45LunchEMBL Canteen
12:45 – 14:30Practical session 15: Single-cell analysis
Data analysis
Speaker First name Last name
Computer Training Lab
14:30 – 15:00Q&A sessionComputer Training Lab
15:00 – 15:30Coffee BreakComputer Training Lab
15:30 – 16:30Lecture: Liquid Biopsy: From discovery of metastasis biology to clinical application
Klaus Pantel – University Medical Center Hamburg-Eppendorf, Germany
Helix Seminar Room B
16:30 – 18:00Lecture: Implementing liquid biopsies in routine clinic. What’s the need?
Anders Edsjö – Skåne University Hospital, Sweden
Helix Seminar Room B
18:00Departure to the HotelIn front of ATC entrance
18:30Flammkuchen DinnerISG Hotel
Day 6 – Saturday, 14 October 2023
Time (Europe/Berlin)SessionLocation
08:35Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:15Overview of the dayComputer Training Lab
09:15 – 10:15Practical session 15:
Single-cell analysis, Data analysis

Mikael Kubista – Institute of Biotechnology and TATAA Biocenter, Czech Republic
Computer Training Lab
10:15 – 10:45Coffee breakComputer Training Lab
10:45 – 12:15Practical session 16:
SiMSen-Seq, Data analysis

Gustav Johansson – Sahlgrenska Academy at University of Gothenburg, Sweden
Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden
Computer Training Lab
12:15 – 13:15LunchEMBL Canteen
13:15 – 14:30Practical session 17:
SiMSen-Seq, Data analysis

Gustav Johansson – Sahlgrenska Academy at University of Gothenburg, Sweden
Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden
Computer Training Lab
14:30 – 15:00Wrap upComputer Training Lab
15:15Departure to Hotel & Heidelberg main train stationIn front of ATC entrance

Sponsors

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Warning

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Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
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  • All payments are on invoice.

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Media kit

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Date: 9 - 14 Oct 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre

Organisers:

  • Anders Ståhlberg
    University of Gothenburg, Sweden
    • Karin Sundfeldt
      University of Gothenburg, Sweden

    Contact: Events


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