Workshop outlines are published as submitted by the organisers. Note that the content of the workshop is under the sole responsibility of the respective workshop organisers.

Organiser: Vincenzo Nigro, Gijs Santen
Plenary Hall

NGS is rapidly taking over as standard sequencing tool in genetic diagnostic services. Meanwhile NGS continuous to be further developed making it important to share knowledge and insights. Therefore this workshop will cover several topics related to NGS. We have selected topics relevant to those working with NGS technology as a diagnostic tool, but also to those using NGS results in their clinical work.
Each topic (listed below) will be shortly introduced by the workshop organizers, followed by several short presentations from submitted abstracts. After the presentations, there will be an interactive discussion with the audience. Questions may be asked to the presenters, and if time permits statements can be discussed.
We would also like to launch a pilot this year: one of the most frequently occurring issues in NGS application is the occurrence of Variants of Uncertain Significance (VUS), and discussions whether these VUS cause the phenotype. We welcome any cases highlighting these discussions. Because a thorough discussion will require preparation and consultation with clinical and molecular experts, we ask cases to be submitted no later than May 10^th, by email to the workshop organizers (vinnigro(at)gmail.com, santen(at)lumc.nl). 

Topics

1. Sanger confirmation: time to stop?

There are generally two reasons to perform Sanger confirmation: confirming NGS findings and ruling out sample swaps. However, Sanger confirmation is laborious and therefore costly. Until recently all diagnostic laboratories would confirm any NGS findings by Sanger sequencing, but several laboratories have already stopped.

2. Large gene panels, WES or WGS?

Many laboratories are making choices between WGS, WES or large gene panels. We have asked several submitters of abstracts who either focus on multiple techniques, or who have endeavoured on a cost-effectiveness analysis to enlighten the audience with their insight on this choice. 

3. CNV detection in targeted data

Although targeted NGS is not the optimal technology to detect CNVs, there have been many attempts to perform CNV calling and new programs are being developed continuously. In this part we will try and help the audience to make informed choices in this regard.

4. Variant interpretation: a continuous challenge!

One of the most difficult challenges in NGS implementation is the interpretation of the wealth of variants that are detected. We would like to discuss these issues and also a small number of submitted cases in the Discussion.

Organisers: Jill Clayton Smith, Sofia Douzgou
Room 112

The workshops will discuss complex undiagnosed cases with distinctive features and patients with known diagnoses which are particularly educational and demonstrate new clinical information or genomic mechanisms. 

Cases for presentation should be brought to the auditorium in the 30mins before the workshop starts. Places for presentation are allocated on a first come, first serve basis. Each presenter is asked to give a concise outline of their case and demonstrate the relevant features in a short (approximately 6 slides) PowerPoint presentation. The discussion of the case will then be facilitated by the workshop chairs with comments invited from experts in the audience. No photographs of slides should be taken in the session.

Organisers: Eva Klopocki, Nicole de Leeuw
Room 117

The aim of this workshop is to focus on various aspects of copy number variant (CNV) interpretation and classification in a diagnostic setting. We will talk about multi-, intra- and intergenic CNVs detected by genome wide array analysis, but also CNV detection in Whole Exome Sequencing data will be included. We will use illustrative cases from our own diagnostic laboratories to have an interactive discussion on the more challenging findings, including low-penetrant, recurrent Copy Number Variants (CNVs) and structurally rearranged chromosomal imbalances as well as patients with compound heterozygous variants in a recessive disease gene.

We will have an app-based feedback system available for this interactive session, so please bring your smart phone, tablet or laptop.

Participants are invited to send questions, comments or suggestions related to this topic by e-mail to Nicole.deLeeuw(at)radboudumc.nl before May 21, 2016.

Organisers: Lidewij Henneman, Borut Peterlin
Room 113+114

Preconception carrier testing is the detection of carrier status for recessive disorders in order to facilitate informed reproductive decision-making by identifying individuals or couples at risk of having an affected child. Carrier screening at a population level detects carrier status in persons who do not have an a priori increased risk of having a child with a certain disease based on their, or their partners’ personal or family history.
New genetic testing technologies enable the expansion of carrier screening to multiple conditions, genes or variants with almost no extra cost or effort. What are the challenges for introducing expanded carrier screening? In clinical diagnostics (whole exome/genome sequencing) carrier status is increasingly identified as an ‘incidental finding’, including in children. Should this information be explicitly sought and reported back to patients when testing is already taking place?

New technologies have the potential to change the screening landscape but also raise new ethical and societal issues. The European Society of Human Genetics recently published recommendations for responsible implementation of expanded carrier screening (EJHG, 2016).
This workshop will discuss experiences with carrier screening and testing and challenges associated with the introduction of expanded screening panels.

Programme
US experiences with expanded carrier screening panels
Gabriel Lazarin, Counsyl, USA

Learning from screening multiple disorders in a Dutch founder population
Inge Mathijssen, Amsterdam, Netherlands

Optimal timing of carrier testing? Parents' and genetic health professionals’ perspectives on testing children
Danya Vears, Leuven, Belgium & Melbourne, Australia

The 100,000 Genomes Project: Consenting for optional feedback of reproductive additional findings (carrier testing)
Caroline Benjamin, Liverpool & Preston, United Kingdom

Interactive discussion with speakers and audience

Organisers: GertJan van Ommen, Nickie Roake
Room 115+116

50' Talks and interactive discussion featuring:

• Tiago Faial, Editor Nature Genetics
• Bettina Meiser, Section Editor EJHG
• Christina Patch, Section Editor EJHG
• Alberto Piazza, Section Editor EJHG
• Inga Prokopenko, Section Editor EJHG
• Nickie Roake, Nature Publishing Group
• Alessandra Renieri, Section Editor EJHG
• GertJan van Ommen, Editor in Chief, European Journal of Human Genetics
• Denise Waldon, Editor Nature Reviews Genetics

40' General Discussion, Q&A

Organiser: Robert Kuhn
Room 111

The UCSC Genome Browser is a widely used platform for access to genomic data provided by laboratories around the world and for display of user data alongside it.  New tools are constantly being developed by our team, and this workshop will demonstrate the latest offerings.  The new Data Integrator allows the intersection of up to five tables by genomic coordinates and can be used, for example, to export a list of the genes in an uploaded region(s), all the SNPs in dbSNP associated with those genes and the biochemical consequences of the variants.

The newest Browser feature is a display mode tailored to whole-exome sequencing, allowing the display of only the exons, and all their associated annotations.  An alternate use of this mode is the ability to juxtapose regions of the genome of different chromosomes on the same screen, including the vizualization of the many alt sequences that are part of the latest human genome assembly, hg38 (GRCh38), in their genomic context.

Finally, participants will learn about the Genome Browser-in-a-Box, a virtual-machine version of the Browser that runs on the desktop and provides enhanced data security and privacy by operating within an institutional firewall.  Users can view their own data locally with full Genome Browser capability, without having to upload anything to UCSC.  Previous familiarity with the Genome Browser is recommended, but not required.  Laptops strongly encouraged.

Organisers: Sergi Beltran, Alexandre Reymond
Room 118+119 

Summary

In this workshop, selected speakers will present their work on gene regulation using a variety of approaches. The studies that will be discussed have been done on humans or on model organisms, in vivo or in silico, focusing on a single gene, the whole genome or even on the mitochondrial epigenome.

Programme

Long-range gene regulation during craniofacial development (Dr. Catia Attanasio)

Identification of p53-target genes in Danio rerio (Dr. Barbara Mandriani)

A transcription factor binding site-driven approach to identify cis-regulatory variants (Dr. Sunil Kumar)

Distinct trends of DNA methylation patterning in the innate and adaptive immune systems (Dr. Ronald P. Schuyler)

New insights into mitochondrial regulation: the first epigenome-wide investigation into mitochondrial methylation (Mr. Matthew A. Devall)