Edit

Liquid biopsies – Course and Conference Office

EMBL Course

Liquid biopsies

Overview
Speakers
Preliminary programme
Practical information
Sponsors
Media kit

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

Course Overview

There is an increasing interest and need to analyse biomarkers in liquid biopsies, including basic research and clinical applications. Liquid biopsies have several advantages including being minimally invasive, allowing repeated sampling and sampling is often clinical routine.

This course will provide an overview of the several techniques to detect and analyse liquid biopsy-based analytes such as circulating tumour cells, cell-free tumor-DNA (ctDNA), miRNA, extracellular vesicles, mRNA, carbohydrates and proteins. Participants will be introduced to all aspects ranging from proper sampling through analyte analysis and final data analysis. Experimentally, we will demonstrate ultrasensitive ctDNA analysis using sequencing and digital PCR. In addition, targeted miRNA profiling and flow cytometry with single-cell analysis will be highlighted. 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 and single-cell analysis
Digital PCR applications in the liquid biopsy workflow
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.

Valérie Taly

Paris Descartes University

France

Scientific organisers

Anders Ståhlberg

University of Gothenburg

Sweden

Karin Sundfeldt

University of Gothenburg

Sweden

Course organisers

Sophie Dutzi

Course and Conference Officer

EMBL Heidelberg

Germany

Irena Provaznikova

Training Lab Technician

EMBL Heidelberg

Germany

Preliminary programme

Got something to say? Tweet it! #EMBLLiquidBiopsies

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)	Programme	Location
08:40 – 09:00	Bus from hotel to EMBL ATC Entrance	Bus stop in front of ISG Hotel
08:45 – 09:00	Registration	Flex Lab A & B
09:00 – 09:30	Welcome and house notes and course overview	Flex Lab A & B
09:30 – 10:30	Background lecture Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden Karin Sundfeldt – University of Gothenburg, Sweden	Flex Lab A & B
10:30 – 10:45	Coffee break	Flex Lab A & B
10:45 – 11:30	Icebreaker	Flex Lab A & B
11:30 – 12:15	Flash talks	Flex Lab A & B
12:15 – 13:15	Lunch	EMBL Canteen
13:15 – 13:45	Lecture: SiMSen-Seq workflow Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden	Flex Lab A & B
13:45 – 15:15	Practical session 1: DNA extraction from Plasma Hilal Ozgur – EMBL Heidelberg, Germany Jessica Sutter – EMBL Heidelberg, Germany	Training Lab B
15:15 – 15:45	Coffee break	Flex Lab A & B
15:45 – 17:00	Practical session 2: Library Preparation Hilal Ozgur – EMBL Heidelberg, Germany Jessica Sutter – EMBL Heidelberg, Germany	Training Lab B
17:00 – 19:00	Practical session 3: Clean-Up and quality control Hilal Ozgur – EMBL Heidelberg, Germany Jessica Sutter – EMBL Heidelberg, Germany	Training Lab B
19:00 – 21:00	Pizza and Poster Session 1	ATC Helix A
21:00	Departure to Hotel	ATC Entrance

Day 2 – Tuesday, 10 October 2023

Time (Europe/Berlin)	Programme	Location
08:40 – 09:00	Bus from hotel to EMBL ATC Entrance	Bus stop in front of ISG Hotel
09:00 – 09:15	Overview of the day	Flex Lab A & B
09:15 – 10:30	Practical session 4: Single Cell Sorting Beata Ramasz – EMBL Heidelberg, Germany	Training lab B
10:30 – 10:45	Coffee break	Flex Lab A & B
10:45 – 12:00	Practical session 5: SiMSen-Seq QC Library pooling Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden Hilal Ozgur – EMBL Heidelberg, Germany Jessica Sutter – EMBL Heidelberg, Germany	Training lab B
12:00 – 12:30	GeneCore tour	GeneCore Facility
12:30 – 13:30	Lunch	Canteen
13:30 – 14:30	Lecture: 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
14:30 – 15:00	Practical session 6: Single-cell RT Hilal Ozgur – EMBL Heidelberg, Germany Jessica Sutter – EMBL Heidelberg, Germany	Training lab B
15:00 – 16:00	Lecture: Introduction to ddPCR Jörg Bantin – Bio-Rad, Germany	Flex Lab A & B
16:00 – 16:30	Practical session 7: Single-cell qPCR Hilal Ozgur – EMBL Heidelberg, Germany Jessica Sutter – EMBL Heidelberg, Germany	Training lab B
16:30 – 16:45	Coffee break	Flex Lab A & B
16:45 – 18:30	Practical session 8: ddPCR Jörg Bantin – BioRad, Germany Pia Scheu – Bio-Rad, Germany	Training lab B
18:30 – 19:30	Practical session 9: Introduction into QuantaSoft Start reading the experiment Jörg Bantin – BioRad, Germany Pia Scheu – Bio-Rad, Germany	Training lab B
19:30 – 21:30	Poster session 2 – tapas	EMBL Canteen
21:30	Departure to Hotel	ATC Entrance

Day 3 – Wednesday, 11 October 2023

Time (Europe/Berlin)	Programme	Location
08:40 – 09:00	Bus from hotel to EMBL ATC Entrance	Bus stop in front of ISG Hotel
09:00 – 09:15	Overview of the day	Flex Lab A & B
09:15 – 10:15	Practical session 10: Data analysis with QuantaSoft Jörg Bantin – BioRad, Germany Pia Scheu – Bio-Rad, Germany	Training lab B
10:15 – 10:30	Coffee break	Flex Lab A & B
10:30 – 11:30	Practical session 11: Data analysis with QuantaSoft Jörg Bantin – BioRad, Germany Pia Scheu – Bio-Rad, Germany	Training lab B
11:30 – 12:30	Lecture: 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 – 13:30	Technology lunch	Rooftop Lounge
13:30 – 14:30	Lecture: Effect of pre-analytical factors on the measurement of Evs in Liquid Biopsies An Hendrix – Ghent University, Belgium	Flex Lab A & B
14:30 – 15:30	Title to be confirmed Nayara Azevedo – Roche, Germany	Flex Lab A & B
15:30 – 16:00	Coffee break	Flex Lab A & B
16:00 – 17:00	Lecture: Clinical validation of droplet-based procedures in the context of liquid biopsies Valerie Taly – Paris Descartes University, France	Flex Lab A & B
17:00	Free evening
17:40	Departure to Hotel	In front of ATC entrance
18:15	Bus to Neckarmünzplatz	Bus stop in front of ISG Hotel

Day 4 – Thursday, 12 October 2023

Time (Europe/Berlin)	Programme	Location
08:40 – 09:00	Bus from hotel to EMBL ATC Entrance	Bus stop in front of ISG Hotel
09:00 – 09:15	Overview of the day	Flex Lab A & B
09:15 – 10:15	Lecture: Title to be confirmed Kim Pettersson – University of Turku, Finland	Flex Lab A & B
10:15 – 10:45	Coffee break	TBA
10:45 – 11:45	Lecture: Protein detection in Liquid Biopsies Ulf Landegren – Uppsala University, Sweden	Flex Lab A & B
11:45 – 12:45	Poster group discussion	Flex Lab A & B
12:45 – 13:45	Lunch	EMBL Canteen
13:45 – 14:45	Lecture: Title to be confirmed Karin Sundfeldt – Sahlgrenska Academy at University of Gothenburg, Sweden	Flex Lab A & B
14:45 – 17:00	Interactive practical session: CTC, Single-Cell, Two tailed PCR for microRNA and cfDNA? Mikael Kubista – Institute of Biotechnology and TATAA Biocenter, Czech Republic	Computer Training Lab
17:00 – 17:30	Coffee break	Flex Lab A & B
17:30 – 18:30	Practical session 15: Single-cell analysis Data analysis Mikael Kubista – Institute of Biotechnology and TATAA Biocenter, Czech Republic	Computer Training Lab
18:30 – 19:15	Departure to Hotel and Dowtown
19:15 – 21:15	Course dinner downtown

Day 5 – Friday, 13 October 2023

Time (Europe/Berlin)	Programme	Location
08:40 – 09:00	Bus from hotel to EMBL ATC Entrance	Bus stop in front of ISG Hotel
09:00 – 09:15	Overview of the day	Flex Lab A & B
09:15 – 10:15	Lecture: Liquid Biopsies in the clinical context High-fidelity sequencing Tony E. Godfrey – Boston University School of Medicine, USA	Flex Lab A & B
10:15 – 10:30	Coffee break	Computer Training Lab
10:30 – 12:00	Practical session 16: SiMSen-Seq Data analysis Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden	Computer Training Lab
12:00 – 13:00	Lunch	EMBL Canteen
13:00 – 14:45	Practical session 15: Single-cell analysis Data analysis Mikael Kubista – Institute of Biotechnology and TATAA Biocenter, Czech Republic	Computer Training Lab
14:45 – 16:00	Practical session 17: SiMSen-Seq Data analysis Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden	Computer Training Lab
16:00 – 16:30	Coffee Break	Computer Training Lab
16:30 – 17:30	Lecture: Implementing liquid biopsies in the clinic – needs, obstacles and possibilities Anders Edsjö – Skåne University Hospital, Sweden	Flex Lab A & B
17:30 – 18:00	Course wrap up	Flex Lab A & B
18:00	Departure to the Hotel	In front of ATC entrance
18:30	Dinner	ISG Hotel

Practical information

Registration fees and motivation letter

The course is limited to 16 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks.

Academia	€790
PhD Student	€790
Industry	€1200

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed.

We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively, you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Accommodation and shuttles

Hotel

Single rooms have been reserved for 5 nights (9 – 14 October 2023) at the ISG Hote l. After the selection process, selected participants should contact the hotel directly to make a booking (booking code LIQ23-01). We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page .

Technical requirements and event software

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus.

Additional information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.