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Cancer genomics – Course and Conference Office

EMBL Conference

Cancer genomics

Overview

EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that this conference is going virtual and invite you to join us online.

Conference Overview

This conference will provide an opportunity to learn about and keep up to date with the rapidly progressing area of cancer genomics. It will cover presentations from cancer genome projects, the areas of cancer functional genomics, systems biology, cancer immunogenomics and epigenomics, cancer mouse models and the translation and clinical impact of obtained scientific results. The meeting will bring together leading scientists from across these areas for a unique opportunity to interact and stimulate further integration of these efforts.

Session Topics

  • Mutation and clonal selection in normal tissues
  • Genomic instability and mutational processes
  • Cancer evolution and drivers
  • Emerging technologies in cancer genomics
  • Cancer ecosystems, microenvironment and immunogenomics
  • Cancer genome medicine

What past participants say about the conference:

EMBL provided a wonderful opportunity for the exchange and application of new ideas within the OMICs cancer research. A great conference!” – Angelica Boldt, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Argentina

This is the third time I have attended this conference. I keep coming back because of the quality of work presented, the expectation that presenters discuss their latest findings and the meeting having the optimal number of attendees.” – Sean Grimmond, University of Melbourne, Australia

Speakers

Keynote Speaker

Speakers

Holger Heyn

Holger Heyn

Centre for Genomic

Regulation (CNAG-CRG)

Spain

Fran Supek

Fran Supek

Institute for Research

in Biomedicine

Spain

Scientific Organisers

Conference Organiser

Maryann Heck

EMBL Heidelberg

Germany

Chris Stocks

EMBL Heidelberg

Germany

Programme

Got something to say? Tweet it! #EMBLCanGen

  • The virtual conference includes live-streamed invited speaker talks and live-streamed selected short talks with live Q&A sessions after each talk as well as meet the speaker sessions.
  • All digital poster presenters are encouraged to upload a recorded flash talk
    or narration with their digital poster and to schedule video calls during poster session times.
  • Information on the live stream and access to the discussion platform and digital posters will be provided 1 week before the start of the event.

All times in the programme below are shown as the time in Europe/Berlin.

To find out the equivalent time zone in your location, enter Berlin, the programme time and your city into the Time Zone Converter.

Day 1 – Monday 22 November 2021
TimeSpeaker
12:00 – 12:50

Pre-conference webinars:

  • Precision Medicine meets immuno-oncology – innovative biomarkers and beyond by Bristol-Myers Squibb
  • DNA methylation in biofluids: from genome-wide studies to targeted approaches by Diagenode
(abstracts are available in Pre-conference webinars tab)
13:00 – 13:50

Pre-conference webinars:

  • 3D Genome Analysis Identifies Therapeutic Targets in Pediatric Brain Cancer by Arima Genomics
  • Structural and functional heterogeneity in the spatial organization of glioblastoma patient genomes by Dovetail Genomics
(abstracts are available in Pre-conference webinars tab)
14:00 – 14:10Opening remarks
14:10 – 15:25Session 1:
Mutation and clonal selection in normal tissues
14:10 – 14:40The mutational landscape and clonal dynamics of Human Somatic and Germline cells
Raheleh Rahbari – Wellcome Sanger Institute, UK
AVAILABLE ON DEMAND AFTER LIVE STREAM
14:40 – 14:55Somatic Mutations in The Ageing Brain
Luke Harvey – Welcome Trust Sanger Institute, UK
AVAILABLE ON DEMAND AFTER LIVE STREAM
14:55 – 15:25Monogenic and polygenic inheritance become instruments for clonal selection
Po-Ru Loh – Harvard Medical School, USA
AVAILABLE ON DEMAND AFTER LIVE STREAM
15:25 – 15:40Break
15:40 – 16:25Keynote: Talk title to be announced
Peter Campbell – Wellcome Sanger Institute, UK
AVAILABLE ON DEMAND AFTER LIVE STREAM
16:25 – 17:00Meet the speakers from Session 1
17:00 – 18:00Poster Session 1
(live chats and video calls with poster presenters with last names A-L)
18:00 – 18:15Break
18:15 – 20:15Session 2:
Genomic instability and mutational processes
18:15 – 18:45Patterns in local mutation density in cancer genomes
Fran Supek – Institute for Research in Biomedicine, Spain
AVAILABLE ON DEMAND AFTER LIVE STREAM
18:45 – 19:00Re-running cancer evolution in vivo: a high-resolution multi-omics approach
Sarah Aitken – University of Cambridge, UK
AVAILABLE ON DEMAND AFTER LIVE STREAM
19:00 – 19:30In silico saturation mutagenesis of cancer genes
Nuria Lopez-Bigas – Institute for Research in Biomedicine, Spain
AVAILABLE ON DEMAND AFTER LIVE STREAM
19:30 – 19:45Antiviral treatment causes a unique mutational signature in cancers of transplantation recipients
Jurrian de Kanter – Princess Máxima Center for Pediatric Oncology, The Netherlands
AVAILABLE ON DEMAND AFTER LIVE STREAM
19:45 – 20:15Haplotype-aware single-cell multiomics uncovers functional effects of somatic structural variation
Jan Korbel – EMBL Heidelberg, Germany
AVAILABLE ON DEMAND AFTER LIVE STREAM
20:15 – 20:25Break
20:25 – 20:55Meet the speakers from Session 2
20:55 – 21:30Virtual Speed Networking
Day 2 – Tuesday 23 November 2021
Time Speaker
13:30 – 13:50 Industry session
14:00 – 16:30Session 3: Cancer evolution and drivers
14:00 – 14:30Molecular classification and risk stratification of colorectal cancer
Seishi Ogawa – Kyoto University, Japan
AVAILABLE ON DEMAND AFTER LIVE STREAM
14:30 – 14:45Discerning patterns of evolution during progression and metastatic spread in high risk neuroblastoma
Gunes Gundem – Memorial Sloan Kettering Cancer Center, USA
AVAILABLE ON DEMAND AFTER LIVE STREAM
14:45 – 15:00ASCAT.sc: a generic framework for copy-number calling
Maxime Tarabichi – Université Libre de Bruxelles (ULB), Belgium
AVAILABLE ON DEMAND AFTER LIVE STREAM
15:00 – 15:30Genotype to phenotype mapping of tumorigenesis at single cell resolution
Christina Curtis – Stanford University, USA
LIVE STREAM ONLY
15:30 – 15:45Break
15:45 – 16:15Stalled development through altered epigenetic states
at the root of oncohistone pathogenicity
Nada Jabado – McGill University, Canada
AVAILABLE ON DEMAND AFTER LIVE STREAM
16:15 – 16:30Reconstructing Chromothriptic Chromosomes in Oesophageal Adenocarcinomas
Jannat Ijaz – Wellcome Trust Sanger Institute, UK
AVAILABLE ON DEMAND AFTER LIVE STREAM
16:30- 17:05Meet the speakers from Session 3
17:05 – 18:05Poster Session 2
(live chats and video calls with poster presenters with last names M-Z)
18:05 – 18:20Break
18:20 – 19:50Session 4:
Emerging technologies in cancer genomics
18:20 – 18:50Pathognomonic long molecule footprints of backup repair pathways in homologous recombination deficient cancers
Marcin Imilienski – Weill Cornell Medicine, USA
AVAILABLE ON DEMAND AFTER LIVE STREAM
18:50 – 19:05Exploiting immunity of hepatocellular carcinoma (HCC) to improve treatment of patients
Domitille Chalopin-Fillot – Université de Bordeaux, France
AVAILABLE ON DEMAND AFTER LIVE STREAM
19:05 – 19:35Single-cell and spatially-resolved
tumor immune microenvironments
Holger Heyn – Centre for Genomic Regulation (CNAG-CRG), Spain
AVAILABLE ON DEMAND AFTER LIVE STREAM
19:35 – 19:50Modeling human clonal hematopoiesis in vitro
Franziska Briest – Universitäts Medizin Berlin, Germany
LIVE STREAM ONLY
19:50 – 20:00Break
20:00 – 20:30Meet the speakers from Session 4
20:30 – 21:30Bar Mixer
Day 3 – Wednesday 24 November 2021
TimeSpeaker
14:00 – 16:30Session 5:
Cancer ecosystems, microenvironment and

immunogenomics
14:00 – 14:30Understanding of cancer genotype-phenotype association
using organoid technology
Toshiro Sato – Keio University, Japan
AVAILABLE ON DEMAND AFTER LIVE STREAM
14:30 – 14:45The relationship of germline risk to somatic EGFR mutation in lung cancer
Matthew Meyerson – Dana-Farber Cancer Institute, USA
AVAILABLE ON DEMAND AFTER LIVE STREAM
14:45 – 15:00The impact and prevalence of genetic immune escape in primary and metastatic cancer
Francisco Martínez-Jiménez – UMC Utrecht, The Netherlands
AVAILABLE ON DEMAND AFTER LIVE STREAM
15:00 – 15:30Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states
Dan Landau – Weill Cornell Medical College, USA
AVAILABLE ON DEMAND AFTER LIVE STREAM
15:30 – 15:45Break
15:45 – 16:15Germline immune variants influence tumor
immunotherapy outcomes
Hannah Carter – University of California, San Diego, USA
AVAILABLE ON DEMAND AFTER LIVE STREAM
16:15 – 16:30The somatic mutational landscape of normal tissues in chemotherapy-treated cancer patients
Ellie Dunstone – Sanger Institute, UK
AVAILABLE ON DEMAND AFTER LIVE STREAM
16:30 – 17:05Meet the speakers from Session 5
17:05 – 17:20Break
17:20 – 19:20Session 6:
Cancer genome medicine
17:20 – 17:50Talk title to be announced
Elli Papaemanouil – Memorial Sloan Kettering Cancer Center, USA
LIVE STREAM ONLY
17:50 – 18:05A clinical-molecular and personalized risk scoring system for patients with myelodysplastic syndromes
Elsa Bernard – Memorial Sloan Kettering Cancer Center, USA
AVAILABLE ON DEMAND AFTER LIVE STREAM
18:05 – 18:35Spatial genomics maps the structure, character and evolution of cancer clones
Moritz Gerstung – EMBL-EBI Hinxton, UK
AVAILABLE ON DEMAND AFTER LIVE STREAM
18:35 – 18:50Mutagenic effects of chemotherapy in secondary malignancies and normal cells in pediatric cancer patients
Axel Rosendahl Huber – Princess Máxima Center for Pediatric Oncology and Oncode Institute, The Netherlands
AVAILABLE ON DEMAND AFTER LIVE STREAM
18:50 – 19:20Understanding mutational landscapes in metastatic cancer
Edwin Cuppen – UMC Utrecht, The Netherlands
AVAILABLE ON DEMAND AFTER LIVE STREAM
19:20 – 19:30Closing remarks
19:30 – 20:00Meet the speakers from Session 6

Practical Information

Registration Fees and Abstract Submission

Registration Fees (include access to all of the talks, digital poster sessions and online group discussions, and help us cover our costs to run the event. For further information please refer to the FAQ page):

Academia190 Euro
PhD Student140 Euro
Industry240 Euro
EMBL StaffIntranet access

Accredited journalists may be eligible to register for a complimentary registration. Registrants may be required to provide accreditation or equivalent proof of press membership after registration. Please contact Maryann Heck for more information.

Confirmation and Payment

Registration will be on a first-come first-served basis. Your place can only be confirmed after payment of the registration fee.
Types of payments accepted are international bank transfers and credit card payments.

Abstract submission

Only registered participants are eligible to submit an abstract. We only accept online abstract submissions.

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

When submitting your abstract you can also apply for an oral or poster presentation. A selection process will take place with the results announced 2-3 weeks after the abstract submission deadline.

Financial Assistance

Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by the EMBL Advanced Training Centre Corporate Partnership Programme, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. Attendance at the event is required in order to be eligible to receive the reimbursement. In order to apply for this grant, you must be registered by the abstract submission deadline.

Application

Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal. Take a look at the instructions for applying for financial assistance.

Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons 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 some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.

Selection

The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

A list of external funding opportunities can be found here, and information on attending a conference as an event reporter here.

For further information about financial assistance please refer to the FAQ page.

Virtual Participation Guidelines

Guidelines

Please do:

  • Use the event-specific hashtag as communicated during the event for any related tweets
  • Tweet unless the speaker specifically says otherwise
  • Be mindful of unpublished data
  • Be respectful in tone and content

Please don’t:

  • Share Slack, live stream or poster session links with others
  • Broadcast the conference to unregistered participants
  • Capture, transmit or redistribute data presented at the meeting unless presenter gives explicit consent
  • Use offensive language in your posts
  • Engage in rudeness or personal attacks

Additional information can be found in our Code of Conduct.

Health and well-being

It is important to stay healthy and move around, especially when you are attending an event virtually. We have put together a few coffee break stretches and yoga videos in the events Slack workspace for you to enjoy during the event.

How to ask questions

Questions during and after the talks can be asked in live streaming platform. The chair moderates the questions and shares them with the speaker. If time runs out or you think of a question later, you can use Slack to ask your questions in the dedicated session channels or via direct message.

Time zone

The programme is planned based on Central European Summer Time (CEST), unless otherwise stated. As many virtual participants are attending from around the world, we do our best to accomodate as many timezones as possible when creating the programme. Please take your time zone into consideration when planning your attendance.

Virtual event platforms

We are using a virtual event platform for this conference. More information about the platform will be shared ahead of the conference.

Sponsors

 

Gold sponsor

 

Silver sponsors

 

Media Partnership

Molecular Systems Biology, an EMBO Press journal

Molecular Oncology, a FEBSPRESS journal

International Union of Biochemistry and Molecular Biology

Open Biology, a Royal Society journal

 

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 conferences, 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 sponsoring@embl.de.

Pre-conference webinars

Pre-symposium webinars will take place on Monday, 22 November 2021

Participation in this webinar is free of charge for registered conference attendees. The number of available places is limited (first come, first served). All registered conference attendees will receive an email with a registration link.

 

12:00 – 12:50 (Berlin / Germany)

Bristol-Myers Squibb: Precision Medicine meets immuno-oncology – innovative biomarkers and beyond

Speaker: Dr. Christoph Benedikt Westphalen, Comprehensive Cancer Center München

Immunotherapeutic interventions have revolutionised the treatment landscape in various malignancies. 

A more profound understanding of mechanisms underlying response and resistance to this class of agents will help to maximise patients’ benefit.

A range of potentially predictive biomarkers beyond PD-L1 and dMMR/MSI are under investigation to help identify patients qualifying for immune therapy. Furthermore, additional modalities such as digital pathology, artificial intelligence and functional imaging are coming of age. 

This seminar aims to give an overview on emerging biomarkers and technologies supporting personalised approached in immunotherapy. 

Diagenode: DNA methylation in biofluids: from genome-wide studies to targeted approaches

Speaker: Matteo Tosolini, PhD, Business Development Manager, Epigenomic Services Profiling, Diagenode, a Hologic Company

DNA methylation is an epigenetic mechanism characterized by the addition of a methyl group to the DNA, mainly at cytosines. It can occur at different genomic locations, and it can modify gene expression and function. The profile of DNA methylation is tissue-type and cell-type specific. A hallmark of cancer is the presence of an aberrant DNA methylation profile and this modification appears to happen early during carcinogenesis. For these reasons DNA methylation can be used as a cancer specific biomarker.

Circulating cell-free DNA (cfDNA) is composed by fragmented DNA released by different mechanisms into the bloodstream, mainly from apoptotic cells including healthy body cells as well as cancer cells. Analysis of cfDNA is very promising and has a great potential in cancer diagnostics given its noninvasive approach requiring only a blood or plasma sample in a process known as liquid biopsy. Interestingly cfDNA retains the genetic and epigenetic information of the tissue of origin. Circulating tumour DNA (ctDNA), meaning DNA fragments that originate from cancer cells, can thus be used as potential biomarker for early cancer detection and diagnosis. The first proof of concept was published last year by the Circulating Cell-free Genome Atlas consortium (CCGA).

The analysis of methylated cfDNA by bisulfite sequencing does not come without challenges as those samples are in low quantity and poor quality because cfDNA is highly fragmented and the ctDNA is diluted by cfDNA from normal body cells.

In this webinar we will present how Diagenode can help by applying our workflow of DNA methylation biomarker discovery and validation in biofluids. We will start with Whole Genome Bisulfite Sequencing (WGBS) on cfDNA to determine the CpGs and the pattern of DNA methylation by using standard statistics as well as data mining approaches and to discriminate between different groups. We will proceed with the most adapted and fully customized Targeted Bisulfite Sequencing approach on cfDNA to validate the previously identified CpG methylation signature as biomarker and screen a higher number of patients.

 

13:00 – 13:50 (Berlin / Germany)

Arima Genomics: 3D Genome Analysis Identifies Therapeutic Targets in Pediatric Brain Cancer

Speaker: Anthony Schmitt, PhD., SVP of Science, Arima Genomics

Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma occur mainly in young children and frequently recur after treatment.

Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target. Innovative therapeutic approaches are urgently needed. 

Join this webinar to learn how we:

  • Uncovered chromosomal rearrangements and regulatory mechanisms underlying aberrant expression of genes that are essential for ependymoma tumorigenesis.
  • Identified potential novel therapeutic vulnerabilities in ependymoma and validated newly identified therapeutic targets through genetic or pharmacologic inhibition experiments. 
  • Revealed tumor-dependency genes and pathways by oncogenic 3D genome conformations even in tumors that lack known genetic alterations.
Dovetail Genomics: Structural and functional heterogeneity in the spatial organization of glioblastoma patient genomes

Speaker: Argyris Papantonis, Dovetail Genomics

Recent work has established that 3D genome organization is causally linked to gene expression control, also in tumors and cancer. In addition, most cancer genomes are infested with structural variants (SVs) that contribute to oncogenesis and cancer progression via various mechanisms. We performed Hi-C experiments on glioblastoma stem cells (GSCs) from 26 patients to generate a resource of >13 billion contacts. We used this Hi-C data resource to detect and characterize patient-specific SVs, and then build individualized genome references.  We identified >1100 high-confident SVs, which were highly heterogeneously distributed across the 26 patient genomes. Following integration with gene expression data, and despite heterogeneity, we found partially recurrent effects on gene expression misregulation that could be linked to the formation of many hundreds of neo-TADs and neo-loops in these GSC genomes. Together, this is the first such comprehensive approach in leveraging 3D genome heterogeneity to understand regulatory dependencies in glioblastoma.

Date: 22 - 24 Nov 2021

Location: Virtual


Deadline(s):

Abstract submission: Closed

Registration: Closed


Organisers:

  • Jan Korbel
    EMBL Heidelberg, Germany
    • Núria López-Bigas
      Institute for Research in Biomedicine, Spain

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