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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.

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.

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

Daniel Gimenes

EMBL Heidelberg

Germany

Mikael Kubista

Institute of Biotechnology of the Czech Academy of Sciences

Czech Republic

Scientific organisers

Course organisers

Sophie Dutzi

Course and Conference Officer

EMBL Heidelberg

Germany

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)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
08:45 – 09:00RegistrationFlex Lab A & B
09:00 – 09:30Welcome and house notes and course overviewFlex Lab A & B
09:30 – 10:30Background/SimSen-protocol lecture
Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, Sweden
Karin Sundfeldt – University of Gothenburg, Sweden
Flex Lab A & B
Flexible Coffee BreakIn front of Training Lab Area
10:30 – 12:00Practical session 1: DNA extraction
Manuel Marceliano Luna Santa-María – Sahlgrenska Academy at University of Gothenburg, Sweden
Hilal Ozgur – EMBL Heidelberg, Germany
Jessica Sutter – EMBL Heidelberg, Germany
Training Lab B
12:00 – 13:00LunchEMBL Canteen
13:00 – 14:30Practical session 2: SiMSen-Seq – library preparation
Manuel Marceliano Luna Santa-María – Sahlgrenska Academy at University of Gothenburg, Sweden
Hilal Ozgur – EMBL Heidelberg, Germany
Jessica Sutter – EMBL Heidelberg, Germany
Training Lab B
14:30 – 15:00Coffee breakIn front of Training Lab Area
15:00 – 16:30Ice breaker & Flash talks
Flex Lab A & B
16:30 – 17:00Q&A session to pre-recorded lectures Anders Ståhlberg – Sahlgrenska Academy at University of Gothenburg, SwedenFlex Lab A & B
17:00 – 18:30Practical session 3: SiMSen-Seq Clean-Up and quality control
Manuel Marceliano Luna Santa-María – Sahlgrenska Academy at University of Gothenburg, Sweden
Hilal Ozgur – EMBL Heidelberg, Germany
Jessica Sutter – EMBL Heidelberg, Germany
Training Lab B
18:30 – 20:30Pizza and Poster Session 1ATC Helix B
20:30Departure to HotelATC Entrance
Day 2 – Tuesday, 10 October 2023
Time (Europe/Berlin)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:05Overview of the dayFlex Lab A & B
09:05 – 10:00Lecture: Single Cell Sorting
Beata Ramasz – EMBL Heidelberg, Germany
FACS Facility / GeneCore Facility
Flexible Coffee BreakIn front of Training Lab Area
10:00 – 12:00Practical session 4: Single Cell Sorting
Beata Ramasz – EMBL Heidelberg, Germany
Daniel Gimenes – EMBL Heidelberg, Germany / GeneCore tour
FACS Facility / GeneCore Facility
12:00 – 12:30Practical 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
12:30 – 13:30LunchCanteen
13:30 – 14:30Lecture: 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
14:30 – 15:00Practical session 6: Single-cell RT
Manuel Marceliano Luna Santa-María – Sahlgrenska Academy at University of Gothenburg, Sweden
Hilal Ozgur – EMBL Heidelberg, Germany
Jessica Sutter – EMBL Heidelberg, Germany
Training lab B
15:00 – 16:00Lecture: Introduction to ddPCR
Jörg Bantin – Bio-Rad, Germany
Flex Lab A & B
16:00 – 16:30Practical session 7: Single-cell qPCR
Manuel Marceliano Luna Santa-María – Sahlgrenska Academy at University of Gothenburg, Sweden
Hilal Ozgur – EMBL Heidelberg, Germany
Jessica Sutter – EMBL Heidelberg, Germany
Training lab B
16:30 – 16:45Coffee breakIn front of Training Lab Area
16:45 – 18:30Practical session 8: ddPCR
Jörg Bantin – BioRad, Germany
Pia Scheu – Bio-Rad, Germany
Training lab B
18:30 – 19:30Practical session 9:
PCR setup, droplet generation and cycling
Start reading the experiment

Jörg Bantin – BioRad, Germany
Pia Scheu – Bio-Rad, Germany
Training lab B
19:30 – 21:30Poster session 2 – tapasATC Helix B
21:30Departure to HotelATC Entrance
Day 3 – Wednesday, 11 October 2023
Time (Europe/Berlin)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:15Overview of the dayFlex Lab A & B
09:15 – 11:15Practical session 10: Data analysis with QX Manager
Jörg Bantin – BioRad, Germany
Pia Scheu – Bio-Rad, Germany
Flex Lab A & B
11:15 – 11:30Coffee breakIn front of Training Lab Area
11:30 – 12:30Lecture: Role of biobanks in securing process quality in sample retrieval and storage
Romy Kirsten – University Hospital Mannheim, Germany
Flex Lab A & B
12:30 – 13:30Technology lunchRooftop Lounge
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 – 15:30Title to be confirmed
Nayara Azevedo – Roche, Germany
Flex Lab A & B
15:30 – 16:00Coffee break and Course PictureIn front of Training Lab Area
16:00 – 17:00Lecture: Clinical validation of droplet-based procedures in the context of liquid biopsies
Valerie Taly – Paris Descartes University, France
Flex Lab A & B
17:00Free evening
17:00Departure to HotelIn front of ATC entrance
17:30Bus to NeckarmünzplatzBus stop in front of ISG Hotel
Day 4 – Thursday, 12 October 2023
Time (Europe/Berlin)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:15Overview of the dayFlex Lab A & B
09:15 – 10:15Lecture: Europium nanoparticle based test concept for glycovariants of traditional and novel biomarkers to provide enhanced cancer specificty
Kim Pettersson – University of Turku, Finland
Flex Lab A & B
10:15 – 10:45Coffee breakIn front of Training Lab Area
10:45 – 11:45Lecture: Protein detection in Liquid Biopsies
Ulf Landegren – Uppsala University, Sweden
Flex Lab A & B
11:45 – 12:45Poster group discussionFlex Lab A & B
12:45 – 13:45LunchEMBL Canteen
13:45 – 14:45Lecture: Diagnostic potential of tumor DNA in proximal fluids in gynecologic cancer.
Karin Sundfeldt – Sahlgrenska Academy at University of Gothenburg, Sweden
Flex Lab A & B
14:45 – 16:00Lecture two tailed PCR
Mikael Kubista – Institute of Biotechnology and TATAA Biocenter, Czech Republic
Computer Training Lab
16:00 – 16:30Coffee break
In front of Training Lab Area
16:30 – 18:00Practical session 11: Single-cell analysis Data analysis and compliance
Mikael Kubista – Institute of Biotechnology of the Czech Academy of Sciences, Czech Republic
Computer Training Lab
18:00 – 18:30Departure to Hotel and DowntownIn front of ATC entrance
18:30 – 19:30Free Time in the City Centre
19:30 – 22:00Course dinner downtown
Day 5 – Friday, 13 October 2023
Time (Europe/Berlin)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:15Overview of the dayFlex Lab A & B
09:15 – 10:15Lecture: Liquid Biopsies in the clinical context
High-fidelity sequencing

Tony E. Godfrey – Boston University School of Medicine, USA
Flex Lab A & B
10:15 – 10:30Coffee breakComputer Training Lab
10:30 – 12:00Practical session 12: multivariate analysis
Mikael Kubista – Institute of Biotechnology and TATAA Biocenter, Czech Republic
Computer Training Lab
12:00 – 13:00LunchEMBL Canteen
13:00 – 16:00Practical session 13: SiMSen-Seq Data analysis
Tobias Österlund and Manuel Marceliano Luna Santa-María – Sahlgrenska Academy at University of Gothenburg, Sweden
Computer Training Lab
16:00 – 16:30Coffee BreakComputer Training Lab
16:30 – 17:30Lecture: Implementing liquid biopsies in the clinic – needs, obstacles and possibilities
Anders Edsjö – Skåne University Hospital, Sweden
Flex Lab A & B
17:30 – 18:00Course wrap upFlex Lab A & B
18:00Departure to the HotelIn front of ATC entrance
18:30DinnerISG 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

  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. 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.

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.

Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course

– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance 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 Hotel. 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.

Sponsors

Course partners

Course 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

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

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.

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Date: 9 - 13 Oct 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:


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