Programmes are published as submitted by the organisers.

Chairs: D. Donnai, J. Clayton-Smith

The Organisers of the Dysmorphology Workshop invite clinicians to submit rare known and unknown cases with dysmorphic syndromes before the workshop.
Please bring a short case presentation on a USB stick from 12.30 - 13.00 hrs to the lecture room. Maximum time for presentation: 5 minutes.

Chairs: T. Clancy, A. Tibben

15.15-15.30
Predictive genetic tests in adolescence: a review of the counselling issues
Aad Tibben

15.30-15.45
Predictive genetic tests in adolescence: a review of the ethical issues
Tara Clancy

15.45-16.45
Discussion of cases

We welcome any cases on predictive testing in adolescence that you would find it helpful to discuss. Please email a short summary of your case to tara.clancy(at)cmft.nhs.uk by Friday May 20th.

Chair: R. Kuhn

Attendees are requested to bring your own laptop for this workshop.

The UCSC Genome Browser (http://genome.ucsc.edu) integrates information from a wide variety of genomic resources, including, but not limited to gene predictions; disease associates, including OMIM and locus-specific databases; gene-expression data; copy-number
variation; comparative genomics; SNPs; HapMap data; gene-chip mappings; and histone- and DNA- modification data.

The large number of genome-wide datasets available allows users to pursue inquiries requiring multiple lines of evidence all in one location.  By allowing users the flexibilty to select only those data relevant to making a particular scientific argument, the Browser allows the pursuit of inquiry-driven data analysis by displaying all pertinent information in one graphical view.

This session will introduce participants to the basic functions of the Genome Browser (http://genome.ucsc.edu), including interface conventions, navigation and search strategies for effective use of the Browser.  The Session tool for sharing the results of inquiries with colleagues will be presented, as will export of camera-ready pdf files for publication.

The Table Browser, a powerful tool for direct mining of the underlying data tables will be demonstrated.  Brief mention of the Galaxy toolkit will set the stage for its introduction in the Intermediate session.

Chairs: Martina Cornel and Milan Macek Jr.

Theme: From bench to health care

15:15
Prof. Inge Liebaers
Medical Genetics, University Hospital Brussels, Belgium
Recommendation CM/Rec(2010)11 of the committee of Ministers to member states on the impact of genetics on the organisation of health care services and training of health professionals

15:30
Dr. Carla van El on behalf of the Public and Professional Policy Committee of ESHG
Clinical Genetics/EMGO Institute for Health & Care Research,
VU University Medical Centre, Amsterdam
Genetic testing and common diseases: the challenge of implementing genetic tests with clinical utility while avoiding unsound applications

15:45
Prof. Martina Cornel on behalf of the Tender NBS Team
Clinical Genetics/EMGO Institute for Health & Care Research,
VU University Medical Centre, Amsterdam
The Governance of the European newborn screening systems. What framework for future EU newborn screening policies?

16:00
Prof. Bartha Maria Knoppers
Netherlands Genomics Initiative distinguished Visiting Scientist
Canada Research Chair in Law and Medicine
Director, Centre of Genomics and Policy
The Governance of Newborn screening in North America: Lessons Learned

16:15
Dr. Laurence Lwoff
Head of Bioethics Division
Health and Bioethics Department
Council of Europe
Update on relevant activities of the Council of Europe

16:30-16:45
Forum discussion: the challenge of implementing genetic tests with clinical utility while avoiding unsound applications
Prof. Pascal Borry
Prof. Jörg Schmidtke


16:45 End of the workshop

Chair: J. Veltman

In this interactive workshop we will discuss practicalities, possibilities and challenges of whole genome/exome based approaches. How are groups setting this up? For what diseases? What hurdles have to be taken? What is possible in the near future? New to us all, so please participate and contribute to the discussion!

15.15 - 15.20     Introduction by Joris Veltman (Nijmegen)
15.20 - 15.35    Developing an exome sequencing workflow in diagnostics. Marcel Nelen (Nijmegen)
15.35 - 15.50    Whole genome/exome sequencing - What more do we want to know except the diagnosis? Martijn Breuning     (Leiden)
15.50 - 16.05     Questions and challenges related to whole genome/exome sequencing. Helena Kääriäinen (Helsinki)
16.05 - 16.45    Interactive discussion with all participants

Chair: N. Hoogerbrugge

15.15 - 15.45 Presentations for discussion

1. BRCA1/2 mutation testing in breast cancer patients prior to genetic counselling
Nicoline Hoogerbrugge

2. Ending ovarian cancer surveillance
Gareth Evans

15.45 - 16.45   Discussion of oncogenetic cases together with an expert panel

Cases selected in advance, presented by the sender, using 2 slides. Submit your case before Friday May 13th to: hereditarycancer(at)umcn.nl

The expert panel consists of:

• Gareth Evans, MD, PhD, Clinical Geneticist and Professor of Medical Genetics, with a focus in Hereditary Breast Cancer, Regional Genetic Service St Mary's Hospital Manchester, United Kingdom.
  
  
• Thierry Frebourg, MD, PhD, Clinical Geneticist, and Professor in Genetics with a focus on cancer genetics, University Hospital, Rouen, Head of the department of Human Genetics University Hospital of Rouen, France.
   
• Elke Holinski-Feder, MD, PhD, is Managing Director of the Medical Genetics Center, with a focus on colorectal cancer. She is affiliated as an Adjunct Professor in Human Genetics at the University of Munich, Germany.
   
• Marjolijn Ligtenberg, PhD, Clinical Molecular Geneticist specialized in oncogenetics and molecular pathology, Head of the Laboratory of Tumor Genetics, Radboud University Nijmegen Medical Centre, The Netherlands.
   
• Rolf Sijmons, MD, PhD, Associate professor in Clinical Genetics, at the University Medical Center of Groningen, Netherlands. He is especially experienced in the clinical relevance of Unclassified Variants and differential diagnosis of familial cancer (www.facd. Info)
   
• Nicoline Hoogerbrugge, MD, PhD, Professor in Hereditary Cancer, head of the hereditary cancer clinic, Radboud University Medical centre Nijmegen, The Netherlands

HOW TO SUBMIT A CASE

We kindly invite you to send us cancer genetic cases for the ESHG workshop: “Oncogenetics case discussion” at Sunday May 29th. Cases that you would like to discuss with the expert panel, or those with particular educational value are welcome.

The expert panel will select 6-8 cases that will be presented at the workshop by the sender using 2 slides, after which the audience and expert panel will be asked for comments. A third slide may be used for the clue. We will let you know 1 week in advance whether or not your case has been selected for presentation.

Please send us the following information in PowerPoint format before Friday May 13th to:  hereditarycancer(at)umcn.nl.

1. First slide: Question and summary of the background information.
2. Second slide: Pedigree including  data on molecular genetics and  pathology whenever appropriate.

The case discussions will be preceded by two presentations of 10 minutes each both ending in two statements for discussion that starts by voting for answer by the audience using hand hold coloured cards.

1. DNA testing for BRCA1/2 in breast cancer patients prior to genetic counselling by Nicoline Hoogerbrugge
2. Ending ovarian cancer surveillance by Gareth Evans

We hope that everybody interested in oncogenetics will take the opportunity to participate in this interactive session.

Chair: J. Barrett, C. Wijmenga

While GWAS have identified hundreds of loci contributing to complex diseases, the work of identifying causal variants and understanding their consequences has just begun. This workshop will include presentations from experts, worked examples, and discussion sessions focused on translating GWAS findings into biological knowledge.

15.15 - 15.25: Intro & Goals: identifying causal variants and understanding their functional consequences, Cisca Wijmenga

15:25 - 15:40: Approach 1 - coding variation, Ben Voight

15:40 - 15:55: Approach 2 - eQTLs, Lude Franke

15:55 - 16:10: Worked example, Jeff Barrett

16:10 - 16:25: Approach 3 - detailed public functional annotation, Ewan Birney

16:25 - 16:45: Discussion, Led by Cisca Wijmenga

• What are the relative values of the different techniques?
• In what circumstances are different datasets most appropriate?
• Can we think about universal frameworks or does every disease require a different strategy?

5

Chairs: D. Donnai, J. Clayton-Smith

The Organisers of the Dysmorphology Workshop invite clinicians to submit rare known and unknown cases with dysmorphic syndromes before the workshop.
Please bring a short case presentation on a USB stick from 12.30 - 13.00 hrs to the lecture room. Maximum time for presentation: 5 minutes.

Chairs: Jörg Schmidtke, Hannover (Germany), Ulf Kristoffersson, Lund (Sweden)

Genetic tests can have implications in many individual and social settings, including care and prevention of disease, making reproductive decisions, taking insurances, and making provisions for one's personal life including housing and retirement. In health care systems with elements of both solidarity and individual responsibilities, who should carry the financial burdens imposed by genetic risks and their assessment? Where should we draw the lines?

Part 1: Setting the stage
Chair: U. Kristoffersson

15:15-15:25 - Jörg Schmidtke: Definitions and the providers' perspective
15:25-15:30 - Alastair Kent: The patients' perspective
15:30-15:35 - Robert Kneepkens: The payers' perspective
15:35-15:40 - Gerry Evers-Kiebooms: The societal perspective

Part 2: Group discussions (parallel)
15:45-16:15

Each participant is assigned to one case and is expected to take part in discussing it under the aspects of clinical, personal, public health and social utility. Each group selects a rapporteur who will summarize the discussion in Part 3.

Case 1: A Factor V Leiden test done on a young woman, without a personal or familial history for venous thrombosis, wishing to take oral contraceptives.

Case 2: A couple without a personal or family history of genetic disease wishing to take a universal heterozygote carrier test for recessive conditions.

Case 3: A 40-year-old man with a family history of early onset Alzheimer's disease wishing to be tested.

Case 4: A newborn with meconium ileus and a positive sweat test - should a genetic test follow?

Part 3: Reports from the discussion groups and summing-up
Chair: J. Schmidtke
16:20-16:45

Professor Gerry Evers-Kiebooms, Department of Human Genetics, K. U. Leuven (Belgium)
Gerry.kiebooms(at)med.kuleuven.be
Head of the Psychosocial Genetics Unit, Center for Human Genetics of the University of  Leuven, Belgium till 2010. The main objectives of her group: (1) Research on the psychological aspects of genetic counseling and genetic testing, with particular attention paid to predictive testing for late onset disease; (2) Psychological counseling and support in the context of a multidisciplinary approach for predictive testing; (3) Integrated genetic education for the population at large and for specific target groups. Since 1.1.2011 she is Special Emeritus Professor in the Department of Human Genetics. Since 1996 she is a member of the Belgian Advisory Committee on Bioethics. She was a member of the PPPC of the ESHG for more than 10 years and is member of the Board of the ESHG.

Alastair Kent, Genetic Interest Group, Cambridge, UK
alastair(at)gig.org.uk
Director of Genetic Alliance UK. This is an alliance of 150 patient support groups for those affected by or at risk for all forms of genetic condition. GA-UK provides strategic advocacy from a patient and family perspective on health and science policy issues and on the development of services and support for those at risk based on needs and which incorporate best clinical practice and current scientific possibility. Genetic Alliance UK works at local, national, European and international level to advance understanding of the needs of patients and families and to promote effective responses to these.

Dr. Robert Kneepkens, M.D., Achmea Leven/Eureko, Tilburg, The Netherlands
RFJM.Kneepkens(at)interpolis.nl
Graduation at the Faculty of Medicine, State University of Utrecht. Since 1991 he worked for a number of life insurance companies as Medical Officer. Since 2009 he is the Chief medical officer of Achmea Life, the leading Dutch insurance company of the European insurance provider Eureko. Dr. Kneepkens is excutive member of the International Committee for Insurance Medicine (ICLAM) and participates in a number of actuarial and medical life insurance committees, including the Medical & Ethical Affairs Committee, the Working Group Genetics, and the Working Group HIV of the Dutch Association of Insurers. Dr. Kneepkens published and presented a number of Opinion Articles on medical underwriting and insurability of people with hereditary traits, HIV, or other chronic disease.

Professor Ulf Kristoffersson, M.D., Department of Medical Genetics, University of Lund (Sweden)
Ulf.kristoffersson(at)med.lu.se
Head of the Department of Clinical Genetics at the University and Regional Laboratories, University Hospital Lund. His research focus was from the beginning on cancer cytogenetics, but since the early 1990-ies his focus has shifted towards service provision and development in clinical genetics, this includes drafting national and international guidelines such as the National Professional Guidelines for Hereditary Breast Cancer and the OECD Guidelines for Quality Assessment in Molecular Genetics. He has been a member of the ESHG board 1997-2002, and PPPC-member 1997-2008. He has participated in several EU funded projects such as EUCROMIC; CAGSE, GenEd, Capability and EuroGentest and EuroGentest2. He was also editor, together with Jörg Schmidtke and Jean-Jacques Cassiman, of the book “Quality Issues in Clinical Genetics Services” published in 2010.

Professor Jörg Schmidtke, M.D., Department of Human Genetics, Hannover Medical School (Germany)
schmidtke.joerg(at)mh-hannover.de
Director of the Institute for Human Genetics at Hannover Medical School, Germany. He runs diagnostic and research labs and a genetic dysmorpholgy and counselling unit. One service and research focus is on Marfan Syndrome and related disorders, another one deals with TSPY and TSPY-related genes. Over the last years he has been active in genetic health care research and participated in several EU-funded projects devoted to this field including CAGSE, GenEd, Capability, Orphanet, and Eurogentest. He is editor-in-chief of the “Journal of Community Genetics”, and section editor for the “Clinical Utility Gene Cards” in the European Journal of Human Genetics. He chairs the guidelines commission at the Robert-Koch-Institute, Berlin, established by the German federal law on genetic testing. He is President of ESHG from 2011-2012.

Chairs: R. Kuhn, D. Clements

Attendees are requested to bring your own laptop for this workshop.

Part 1: UCSC Genome Browser - Intermediate Tools: Custom Tracks and Table Browser  (Kuhn)

This session will present Custom Tracks, a utility enabling researchers to upload and view their own data in the context of the public data hosted on the UCSC Genome Browser.  Datasets can be any data mappable to genomic coordinates, including deletion/duplication data from comparative genomic hybridization studies in a clinical setting.

The very large datasets that result from next-generation sequencing (NGS) data may also be visualized in the browser using a user-hosted model that will be demonstrated.

Also featured will be advanced queries with the Table Browser, a full-featured data-mining tool for genome-wide analysis of the Browser annotation database.  The latter will include examples of integrating mutliple datasets.  For example, histone marks and gene mappings may be superimposed to determine biologically relevant features, and the knownGene table may be intersected with the snp131 table to find the rs numbers and functional relevance of all SNPs assocatiated with a gene.

Part 2: Large Scale Analysis of UCSC data in your web browser using the Galaxy toolit

Galaxy (http://usegalaxy.org) makes it easy to perform analysis interactively through the web, on arbitrarily large datasets. With hundreds of tools there are few limits on what can be done. Combined with UCSC data, you can do more in the Cloud.

The goal of this session is to highlight the latest features of Galaxy framework with a particular emphasis on NGS data analysis. The topics will include:

• The hitchhiker's guide to Galaxy architecture (What is Galaxy anyway?)
• Pipelines for analysis of Illumina, SOLiD, and 454 datasets (How do I do mapping, SNP calling, ChIP-seq, and RNA-seq entirely through Galaxy and visualize results at UCSC)
• Galaxy as the platform for reproducible genomics (How do I share, publish, and collaborate through Galaxy?)
• Deployment of private Galaxy instances on local resources and on the Cloud (How do I install my own Galaxy on the Cloud or on local IT resources?)
• Management of large datasets with the Galaxy Library System (How do I manage my lab/facility/institution data?)

Chairs: R. Hastings, C. van Ravenswaaij-Arts

Short talk:
What are the essential elements of a diagnostic array report from a clinicians perspective.
Conny van Ravenswaaij-Arts

Short talk:
What was essentially missing from laboratory diagnostic array report submissions in recent microarray EQAs.
Ros Hastings

Workshop (1 hour):
Discussion of four interesting case scenarios involving arrays which exemplify some of the issues.

Exemplary reports will be made available for attendees.

Chair: M. Dermitzakis

The workshop will focus on the interpretation of whole genome sequencing
data for purposes of population genetic analysis, functional genomics
and the clinic. Three short presentations (15 mins) by Carlos Bustamante
(Stanford), Manolis Dermitzakis (Geneva) and Joris Veltman (Nijmegen)
will be given followed by a panel and audience discussion on the various
topics raised by the speakers and questions from the audience.

Chairs:E. Dequeker, M. Morris

Quality assurance and quality improvement considerations are critical for genetic testing. This workshop provides practical examples and information for diagnostic professionals and researchers, addressing wide-ranging elements of quality assurance for genetic testing including EQA, clinical validation, evaluation and improvement of testing technologies and novel ways to evaluate diagnostic workload.

15:15 Introduction: Why should we implement a quality system and go for accreditation?
E Dequeker (Belgium)

15:25 Discrepancies in reporting the CAG repeat lengths for Huntington's disease
O. W. Quarrell (U.K)

15:40 External quality assessment schemes for molecular testing on blood spots
A. Wittner (U.K)

15:55 EuroGentest Clinical Utility Gene Cards - guidelines for the clinically validated use of genetic testing
A. Dierking (Germany)

16:10 Automated melting analysis for quality assessment of high resolution scanning data of multi-exon genes
M. Erali (U.S)

16:25 A robust measure of workload for molecular diagnostic laboratories S. Stenhouse (U.K)

16:40  Conclusion
M Morris (Switzerland)

Chairs:P. Farndon, T. Öczelik