Clinical Genomics & Informatics Europe - Program

Organized by Cambridge Healthtech Institute
Clinical Exome Sequencing
RNA-Seq and Transcriptome Analysis
ClinicalGenomicsInformatics.com
High-Scale Computing
Genome Informatics
Sequencing Informatics
Europe
Clinical Genomics
&Informatics
Bio-IT World & Cambridge Healthtech Institute’s Fifth International
4-6 December 2013 • Sheraton Hotel & Spa • Lisbon, Portugal
Pre-Conference Symposia:
Clinical Epigenetics Digital Detection
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Register by 16 August and Save Up to €350!Final Agenda
Anne Cambon-Thomsen, M.D.,
Centre National de la Recherche
Scientifique (CNRS)
Niklas Blomberg, Ph.D.,
ELIXIR
Timothy Hubbard, Ph.D.,
Wellcome Trust Sanger
Institute
Hans-Hilger Ropers, M. D.,
Humboldt University and
Max Planck Institute for
Molecular Genetics
Keynote Speakers:

2
Tuesday, 3 December Wednesday, 4 December Thursday, 5 December Friday, 6 December
AM
Clinical Epigenetics
Symposium
Sequencing Stream:
Sequencing Stream:
Sequencing Stream: RNA-Seq
and Transcriptome Analysis
PM
Sequencing Stream:
AM Quantitative
Digital Detection
Technologies
Symposium
Informatics Stream:
Informatics Stream:
Informatics Stream: Genome Informatics
PM
Informatics Stream:
Informatics Stream: Genome Informatics Informatics Stream: Genome Informatics
Conference-at-a-Glance
About the Event
Bio-IT World and Cambridge Healthtech Institute are proud to announce the Fifth International Clinical Genomics & Informatics Europe
conference. This year’s meeting will be held 4-6 December 2013 in Lisbon, Portugal. The conference will feature four main tracks on
Clinical Exome Sequencing, High-Scale Computing, Genome Informatics, and RNA-Seq and Transcriptome Analysis. In addition, we will be
featuring two pre-conference Symposia on Tuesday, 3 December on Clinical Epigenetics and Quantitative Digital Detection Technologies.
The conference will tackle the huge amounts of sequencing data produced by new technologies that have introduced significant challenges
for bioinformatics, both in terms of the analysis and interpretation of data and clinical implementation of novel variants. Members of the
international community will come together to look at the science and informatics required to utilize next-generation sequencing for the
molecular diagnosis of complex diseases.
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Exhibitors will enjoy facilitated networking opportunities with highly-targeted
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Hotel & Travel Information
Conference Venue & Hotel:
Sheraton Lisboa Hotel & Spa
Rua Latino Coelho No 1
1069-025 Lisboa, Portugal
+351-21-312-0000
Please visit www.ClinicalGenomicsInformatics.com to reserve your sleeping
accommodations or call the Hotel directly.You will need to identify yourself as
a Cambridge Healthtech conference attendee to receive the discounted room
rate with the Host Hotel. Reservations made after the cut-off date or after the
group room block has been filled (whichever comes first) will be accepted on a
space- and rate-availability basis. Rooms are limited, so please book early.
Flights: If you need help booking airfare please contact our dedicated travel
agent, Rona Meizler, at +1 617-559-3735 or
rona.meizler@protravelinc.com.
Discounted Room Rate:
€120 Single/€140 Double
**Includes Breakfast**
Discounted Room Rate Cut-off
Date: 5 November 2013
Top Reasons to book at the
Sheraton Hotel & Spa
• Breakfast is included in the room rate.
• No commute! The conference is taking place in the hotel.
• Ultra modern Spirito Spa & Fitness Center, outdoor heated pool &
Mediterranean spa services.
• Located just minutes from the city’s downtown Baxia, where you can
admire Augusta Street, Russio and Commercio Square (shopping,
galleries & theaters).
• 15 minutes from Lisbon’s Portela International Airport.
• Minutes from local attractions like Avenida da Liberdade,
Praca do Comercio (magnificent Square by the River),
Estrelas Basilicia, and Belem Tower to name a few.

4
Pre-Conference Symposium: Clinical Epigenetics
08:30 Registration and Morning Coffee
09:00 Chairperson’s Opening Remarks
UNDERLYING MECHANISMS LEADING TO DISEASE
09:10 The Molecular Basis of CpG Island Methylator Phenotype
Manon van Engeland, Ph.D., Professor, Department of Pathology, School for Oncology and
Developmental Biology, Maastricht University Medical Center, The Netherlands
09:40 DNA Methylation and Demethylation in Health and Disease
François Fuks, Ph.D., Director, Laboratory of Cancer Epigenetics, Faculty of Medicine, Free
University of Brussels, Belgium
A host of new actors and novel cytosine modifications and the ten eleven
translocation (TET) enzymes have appeared on the scene, sparking great
interest. The challenge is now to uncover the roles they play and how they
relate to DNA demethylation. Knowledge is accumulating linking these
new players to essential biological processes (e.g. cell pluripotency and
development) and also to cancerogenesis. We will present data highlighting
new modes of action of TETs and their roles in diseases.
10:10 Long Noncoding RNAs and the Specification of Epigenetic
Modifications in Development and Disease
Marcel Dinger, Ph.D., Head, Clinical Genomics, Centre for Clinical Genomics, Garvan Institute of
Medical Research, Australia
Although the mechanisms and protein complexes that enact such epigenetic
modifications are known, it remains a mystery how these chromatin-
modifying factors, which seldom possess any sequence-specificity per se, are
directed with such remarkable specificity to particular sites of the genome.
In this presentation, I will present evidence to support the case that long
non-coding RNAs may fulfill a fundamental role in directing generic chromatin-
modifying machinery to particular sites in the genome.
10:40 Coffee Break
UTILIZATION OF EPIGENETIC BIOMARKERS IN
CLINICAL MANAGEMENT
11:10 DNA Methylation Biomarkers for Early Detection and Monitoring
of Cancer
Guro Elisabeth Lind, Ph.D., Head, Epigenetics, Department of Cancer Prevention, Institute for
Cancer Research, Oslo University Hospital, Norway
A panel of methylated biomarkers suitable for detecting colorectal cancer at an
early stage will be presented. In tissue samples, this panel outperforms several
previously published epi-markers, including VIM and SEPT9 which are included
in current non-invasive colorectal cancer tests. We are also working with
urological cancers, lymphomas and cholangiocarcinomas and some of our latest
data for early detection and/or monitoring of these diseases will be presented.
11:40 The Epigenetic and Genetic Context of MGMT Promoter
Methylation and Its Impact on the Predictive versus Prognostic
Value as a Biomarker for Glioma
Monika E. Hegi, Ph.D., Head, Laboratory of Tumor Biology & Genetics, Department of
Neurosurgery, Centre Hospitalier Universitaire Vaudois (CHUV), Switzerland
The presentation will review the predictive value of MGMT promoter methylation
in glioblastoma (glioma, WHO grade IV) for benefit from alkylating agent therapy.
This is a mechanistically plausible relationship due to the DNA repair function of
MGMT that removes the most cytotoxic lesion introduced by alkylating agents.
Surprisingly, a strong prognostic effect was observed for MGMT methylation
in clinical trials with grade III glioma.The genetic and epigenetic context of this
surprising, and clinically relevant difference will be discussed.
12:10 Sponsored Presentation (Sponsorship Opportunity Available)
12:40 Luncheon Presentation (Sponsorship Opportunity Available) or
Lunch on Your Own
13:10 Session Break
DISCOVERY OF EPIGENETIC MARKERS FOR
DIAGNOSTIC & PROGNOSTIC UTILITY
14:05 Dynamic Changes in 5-Hydroxymethylation (5hmC) Signatures
Underpin Early and Late Events in Drug Exposed Liver
Richard Meehan, Ph.D., Senior Scientist, Chromosomes and Gene Expression, Medical Research
Council, The Human Genetics Unit (HGU), Western General Hospital, United Kingdom
Combined epigenomic and transcriptomic approaches can identify sets of
potential biomarkers for disease progression, including cancer. Our work
demonstrates that 5hmC profiling can be used as a unique indicator of cell
states during organ maturation and drug-induced responses. 5hmC profiling
provides novel epigenetic signatures for integrated pathway analysis and is
the foundation for the epigenetics of identity.
14:35 Genome-Wide Methylation Analysis on Neuroendocrine Tumors
Christina Thirwell, Ph.D., Senior Lecturer & Medical Oncologist, University College London,
United Kingdom
My group has undertaken the first large scale integrated genomic analysis of
pancreatic and intestinal NETs including exome sequencing, genome-wide
DNA methylation analysis, RNA expression and copy number analysis. DNA
methylation biomarkers have been identified which differentiate between
normal tissue and NETs and also between histological grade of NET. Most
recently we have isolated and sequenced DNA from single NET circulating
tumor cells (CTCs). Analysis of this “liquid biopsy” will in the future enable us
to truly personalize cancer therapy for NET patients.
15:35 Refreshment Break
16:10 DNA Methylation in Childhood Cancer
Keith Brown, Ph.D., Reader, Molecular Pathology, School of Cellular & Molecular Medicine,
University of Bristol, United Kingdom
We have used genome-wide DNA methylation analysis to identify epigenetic
alterations in clinically important childhood cancers, specifically Wilms’ tumor
of the kidney and neuroblastoma, a cancer of the sympathetic nervous
system. We have identified the first example of long-range epigenetic
silencing in childhood cancer, as well as novel single genes that are silenced
by DNA methylation. Analyzes of clinically annotated patient cohorts are being
used to test the diagnostic and prognostic utility of these markers.
16:35 DNA Methylation Signatures for Prediction of Biochemical
Recurrence after Radical Prostatectomy of Clinically Localized
Prostate Cancer
Christa Haldrup, Ph.D., Research Scientist, Department of Molecular Medicine, Aarhus
University Hospital, Denmark
Through screening of prostate cancer samples and samples of adjacent
normal prostate tissue, we here identify six genes (AOX1, C1orf114, GAS6,
HAPLN3, KLF8, and MOB3B) which are hypermethylated in prostate cancer.
Furthermore, DNA methylation of C1orf114 is significantly associated with
time to PSA recurrence in multivariate cox regression analysis encompassing
standard histopathological parameters in two international radical
prostatectomy cohorts. Additionally we develop a dichotomized three gene
DNA methylation signature which also predicts time to PSA recurrence in
multivariate analysis significantly in two cohorts.
17:10 Single-Cell Genomics to Study DNA-Mutation, Genetic
Heterogeneity and Disease
Thierry Voet, Ph.D., Head, Laboratory of Reproductive Genomics, KU Leuven, Belgium; Associate
Faculty Member, Wellcome Trust Sanger Institute
We have developed various wet-lab and computational methods that allow
analyzing a solitary cell. We apply these genome-wide methods to study
DNA-mutation, genetic heterogeneity and cancer. Furthermore, we developed
novel generic single-cell methods for preimplantation genetic diagnosis (PGD)
of human cleavage stage embryos in the clinic.
17:35 Close of Symposium
16:00-18:00 Main Conference Registration
3 December 2013

5
Pre-Conference Symposium: Quantitative Digital Detection Technologies
DIGITAL PCR TECHNOLOGIES AND TECHNIQUES
09:10 Clinical Implementation of ddPCR in the Diagnosis, and
Management of Myeloproliferative Neoplasms (MPNs)
Christopher Campbell, West Midlands Regional Genetics Laboratory, Birmingham Women’s
Hospital, United Kingdom
09:40 Value Assignment of Certified Reference Material by
dPCR Technologies
Philippe Corbisier, Ph.D., Scientific and Technical Project Manager, Standards for Innovation and
Sustainable Development, European Commission - JRC - IRMM, Belgium
dPCR technologies allow us to quantify nucleic acids without the use of
standard curve and are therefore particularly suited to characterize nucleic
acids standards used as calibrants in quantitative PCR experiments. A number
of parameters that affect the accuracy of the measurements will be discussed
and results using commercially available microfluidic chamber based PCR and
droplet digital PCR will be discussed.
10:10 Global Detection of BRAF V600 Mutations Using a Wild-Type
Negative LNA Probe-Based Droplet Digital PCR Assay
Curtis Hughesman, Ph.D., Post-Doctoral Research Fellow, Michael Smith Laboratories,
University of British Columbia, Canada
Here we report a reliable method to collectively detect all known BRAF V600
mutations in a single assay using two LNA probes applied in a droplet digital
PCR format. We have used this assay to successful screen cell lines and
plasmids bearing 8 unique nucleotide mutations at codon 600 of BRAF with
an analytical specificity of <0.05%.
10:40 Coffee Break
11:10 Plasma DNA Digital PCR as a Noninvasive Tool for Detection of
Genomic Alterations in Metastatic Breast Cancer
Gaia Schiavon, M.D., Ph.D., Cridlan Fellow in Medical Oncology – Breast Unit, The Royal
Marsden NHS Foundation Trust, United Kingdom
Proof of the concept exists that circulating cell-free DNA (cfDNA) carrying
tumor-specific alterations is detectable in plasma of these patients and
represents a sensitive biomarker of tumor burden. Performing analysis of
cfDNA with digital PCR, we screened for the acquisition of HER2 amplification
in metastatic breast cancers and this approach could potentially be adapted to
the analysis of any locus amplified in cancer.
11:40 The Use of dPCR to Measure Her-2 in Borderline-Amplified
Breast Cancer Research Samples
Gabriele Zoppoli, M.D., Ph.D., Internal Medicine Resident, University of Genova & IRCCS AOU
San Martino IST, Italy
Here, we describe the use of dPCR in a set of ERBB2 “equivocal status” BC
patients. We also assess TOP2A copy number, and both TOP2A and ERBB2
gene expression intensity, on the described sample set. We discuss dPCR
results compared to those obtained by qRT-PCR, IHC, and aCGH methods.
Lunch on Your Own
13:10 Session Break
IMPROVEMENTS TO TRADITIONAL PCR
AND MICROFLUIDICS
N. Reginald Beer, Ph.D., Medical Diagnostics Initiative Leader, Center for Micro and
Nanotechnologies, Lawrence Livermore National Laboratory, United States
14:05 Preparative Microarrays & Laser Induced Dehybridization: The
Intersection of Microarrays, PCR, and Sequencing
N. Reginald Beer, Ph.D., Medical Diagnostics Initiative Leader, Center for Micro and
Nanotechnologies, Lawrence Livermore National Laboratory, United States
This talk will describe a novel approach using a focused IR laser to dehybridize
bound oligos from individual microarray spots. The bound oligos can be
200 bp or longer, providing much more information than just the bases
complementary to the short probe sequences. This method has the potential
to improve detection and downstream analysis for rare or highly divergent
targets in genotyping or microbial discovery applications.
14:35 A Novel Platform for Digital Isothermal Nucleic Acid
Amplifications Using BART
Guy Kiddle, Ph.D., Senior Molecular Biologist, IVD Technologies, Lumora Ltd., United Kingdom
Lumora Ltd. has demonstrated that BART technology (a bioluminescent
reporter system for isothermal amplification) in conjunction with loop
mediated isothermal amplification (LAMP) represent a novel, highly scalable
and low-cost platform for digital amplifications based on CCD camera image
capture. The LAMP-BART platform has been demonstrated on two applied
challenges. This presentation will highlight the potential of dBART, as a
commercial alternative to conventional digital PCR.
15:35 Refreshment Break
SINGLE-CELL ANALYSIS METHODS
16:10 Cell Heterogeneity and Single Cell Analysis: A New Paradigm for
Translational Medicine
Ferdinando Mannello, Ph.D., Assistant Professor, Cell Biology, Department of Biomolecular
Sciences, Section of Clinical Biochemistry and Cell Biology, University “Carlo Bo” of
Urbino, Italy
Cellular heterogeneity forms the fundamental principle of cell biology,
but the new generation technology of single-cell analysis is able to better
characterize cells population, identifying and differentiating outlier cells, and
driving beyond the capability of conventional technology. Single-cell analysis
is the new frontier in “OMICS”-era, which will become a diffuse and efficient
investigational strategy for translational medicine.
16:35 Quantitative High-Resolution Genomic Analysis of Single
Cancer Cells
Burkhard Brandt, Ph.D., Department of Tumor Biology, University Medical Center
Hamburg-Eppendorf, Germany
We present a method for quantitative high-resolution genomic analysis
of single cells. Cells were isolated under permanent microscopic control
followed by high-fidelity whole genome amplification and subsequent
analyzes by fine tiling array-CGH and qPCR. The assay was applied to single
breast cancer cells to analyze the chromosomal region centered by the
therapeutically relevant EGFR gene. This method allows precise quantitative
analysis of copy number variations in single cell diagnostics.
17:10 Single-Cell Genomics to Study DNA-Mutation, Genetic
Heterogeneity and Disease
Thierry Voet, Ph.D., Head, Laboratory of Reproductive Genomics, KU Leuven, Belgium; Associate
Faculty Member, Wellcome Trust Sanger Institute
We have developed various wet-lab and computational methods that allow
analyzing a solitary cell. We apply these genome-wide methods to study
DNA-mutation, genetic heterogeneity and cancer. Furthermore, we developed
novel generic single-cell methods for preimplantation genetic diagnosis (PGD)
of human cleavage stage embryos in the clinic.
17:35 Close of Symposium
16:00-18:00 Main Conference Registration
3 December 2013

6
WEDNESDAY, 4 DECEMBER
TARGETED SEQUENCING
»» KEYNOTE presentation
08:40 New Sequencing Techniques: Why They are Indispensable for Health
Care, and What We Can Do to Speed Up Their Clinical Implementation
Hans-Hilger Ropers, M. D., Board Certified Clinical Geneticist, Professor of Human Genetics,
Humboldt University and Director, Max Planck Institute for Molecular Genetics, Berlin, Germany
09:10 External Quality Assessment for NGS
David E. Barton, Ph.D., Chief Scientist, National Centre for Medical Genetics, Our Lady’s
Children’s Hospital, Crumlin, Ireland, United Kingdom
The European Molecular Genetics Quality Network (EMQN) provides external
quality assessment to genetic testing laboratories world-wide. Experience
shows that the introduction of new technologies into clinical diagnostics
carries risks. Thorough validation and quality assessment are essential.
EMQN, in collaboration with UK NEQAS, ran a pilot EQA for Next-Gen DNA
sequencing in 2013. Results of this pilot study will be reported.
09:40 Targeted Next-Generation Sequencing Can Replace Sanger
Sequencing in Clinical Diagnostics
Jan D. H. Jongbloed, Ph.D., Department of Genetics, University of Groningen, University
Medical Centre Groningen, The Netherlands
This talk will include results of the manuscript on targeted NGS such as recent
results of the use of our method in routine clinical diagnostics; a comparison of
results in these patients obtained with both targeted and exome sequencing
(we have quite some patients that were analyzed with both methods); a study
concerning the effect of over dispersion in both methods.
10:10 Coffee Break in the Exhibit Hall with Poster Viewing
COMPARING EXOME AND WHOLE
GENOME SEQUENCING
10:45 Comparing Exome vs. Genome Sequencing for Genetic
Component of Diseases
Han G. Brunner, Ph.D., Medical Geneticist, Radboud University Nijmegen Medical Centre,
The Netherlands
Given that a considerable proportion of rare diseases are based in genetics,
patients with complex clinical presentation may soon be included in a program
for undiagnosed diseases where the first step is exome sequencing. Such a
strategy would provide many accurate diagnoses, thereby reducing doctor’s
delay, unnecessary invasive, costly and burdensome procedures.
11:15 Comparing Clinical v. Whole Exome Sequencing for Monogenic
Diseases and Undiagnosed Patients
Pascal Joset, Ph.D., Research Associate, Institute of Medical Genetics, University of
Zurich, Switzerland
The advent of NGS techniques is paving the way for novel large scale
approaches with an unforeseen diagnostic power. While whole exome
sequencing may provide theoretically the highest cost-efficient power, it may
miss mutations due to incomplete coverage. We therefore evaluated the
power of a “clinical exome” limited to about 2700 genes with currently known
monogenic mutations.
Lunch on Your Own
13:15 Session Break
14:00 Chairperson’s Remarks
14:05 Increasing Accuracy for Exome and Whole Genome Sequencing
Gholson J. Lyon, M.D., Ph.D., Assistant Professor of Human Genetics, Cold Spring Harbor
Laboratory and Research Scientist, Utah Foundation for Biomedical Research, United States
Our recent results suggest that more caution should be exercised in genomic
medicine settings when analyzing individual exomes and genomes, including
interpreting positive and negative findings with scrutiny, especially for indels.
We advocate for renewed collection and sequencing of multi-generational
families to increase the overall accuracy of whole genomes.
14:35 Changing the Clinical Genetic Testing Paradigm: Reducing Cost
and Increasing Utility
Steve Lincoln, Senior Vice President, Scientific Applications, InVitae, United States
15:05 Experiences from our Integrated Genomics Clinic; Rapid Identification
and Clinical Reporting of Causative Mutations throughWGS andWES
Elizabeth Worthey, Ph.D., Human and Molecular Genetics Center, The Medical College of
Wisconsin, United States
MCW’s Genomic Medicine Clinic has been operational for more than 18 months.
As the first genomics based integrated genetics clinic of its kind its development
required definition of appropriate: patient counseling, analysis, interpretation, and
reporting. I will discuss how to incorporate genomic data to support diagnosis
with a particular focus on the informatics as well as providing discussion of the
discoveries, challenges and lessons learned applying NGS in the clinic.
16:05 Refreshment Break in the Exhibit Hall with Poster Viewing
16:45 Exome Sequencing in Complex Disease: Data Quality and
Clinical Heterogeneity
Sarah Ennis, Ph.D., Associate Professor, Head, Genomic Informatics, Genomic Informatics,
University of Southampton Human Genetics & Genomic Medicine, United Kingdom
This talk will present key aspects in the exome analysis of a cohort of
paediatric patients diagnosed with severe inflammatory bowel disease. The
talk will outline some key issues with regard to data management and quality
and go on to present approaches to pathway analysis in complex disease and
present key findings that underpin disease in individual patients.
17:15 Panel Discussion with Day’s Speakers
17:45 Welcome Reception in the Exhibit Hall with Poster Viewing
19:15 Close of Day
THURSDAY, 5 DECEMBER
08:00 Morning Coffee
DEVELOPING TECHNOLOGIES AND INTERFACE FOR
INTERPRETING GENOMES
08:35 Strategies for Disease-Gene Identification in Exome Sequencing
Peter N. Robinson, Institute for Medical Genetics and Human Genetics, Charité-
Universitätsmedizin Berlin, Germany
Whole exome sequencing (WES) is revolutionizing many areas of diagnostics
and research in human genetics, but the sheer number of candidate
genes revealed by typical WES studies represents a challenge to medical
and biological interpretation. We will present new algorithms for utilizing
phenotypic analysis and protein interaction networks to effectively prioritize
candidates in exome sequencing studies.
Clinical Exome SequencingInaugural
Sequencing4-5 December 2013
Changing the Nature of Genetic Diagnosis

7
09:05 The Post-WGS Cancer Genome: Alphabet Soup, Syllabus
or Cyclopaedia?
German Pihan, M.D., Staff Pathologist and Director, Hematopathology Service, Department of
Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, United States
Review of how the WGS cancer genome data deluge is changing our views
of the pathogenesis and biology of cancer as well as how the new knowledge
may be harnessed to combat the “Emperor of all maladies.”
11:15 Integrated Exome Sequencing and Copy Number Analysis of
Pancreatic Cancer Reveals a HER2-Amplified Subtype
Mark Cowley, Ph.D., Senior Bioinformatics Research Officer, Genome Informatics & Clinical
Genomics, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, New Zealand
We have recently performed WES and copy number analysis from 99 pancreatic
ductal adenocarcinoma tumors within the ICGC. By copy number analysis, and
supported by WGS, microarray analysis, IHC and FISH, we identified a case with
HER2-amplification. Our results have potentially defined the first targeted
therapy for pancreatic cancer, which we are taking to an adaptive clinical trial.
»» PLENARY KEYNOTE
11:45 From Genome Annotation to Genome Medicine
Timothy Hubbard, Ph.D., Senior Group Leader, Wellcome Trust Sanger Institute, United Kingdom
12:35 Close of Conference
thursday, 5 DECEMBER
11:30 Conference Registration
I will describe the status of the human genome sequence and its annotation,
in particular the generation of the GENCODE geneset as part of the ENCODE
project and the impact of RNA-seq. I’ll also discuss the latest human genome
assembly from the Genome Reference Consortium (GRC). As the UK plans
to sequence 100,000 human genomes in the National Health Service (NHS),
I’ll discuss requirements for integrating genomics into healthcare systems
and summarize progress towards genomic medicine in UK.
12:35 Enjoy Lunch on Your Own
ADVANCES IN RNA-SEQ DATA ANALYSIS
14:05 De Novo Full-Length Transcriptome Analysis by a Hybrid
Sequencing Analysis by a Hybrid Sequencing Approach
Wei Chen, Ph.D., Senior Scientist & Group Leader, Max Delbruck Center for Molecular
Medicine, Germany
I will present a hybrid sequencing approach based transcriptome analysis
pipeline that reports high quality transcripts in their full length independent of
reference genome sequences. Using full-length cDNA libraries in conjunction
with Single Molecule Read-Time (SMRT) DNA sequencing technology, we can
directly capture the full-length transcripts, but with low sequencing accuracy.
To report high quality transcriptome, we then developed a novel computational
tool, IPEC, which utilizes the high quality Illumina sequencing data to correct
random errors generated.
14:35 Detecting Differential Splicing Employing Splicing Compass on
RNA Sequencing Data
Rainer König, Ph.D., Group Head, Divisions of Theoretical Bioinformatics, Heidelberg
University, Germany
The emergence of next-generation RNA sequencing (RNA-seq) provides an
exciting new technology to analyze alternative splicing on a large scale. We
present a new method and software to predict genes that are differentially
spliced between two different conditions using RNA-seq data. Our method
employs geometric angles between the high dimensional vectors of exon read
counts. With this, differential splicing can be detected even if the splicing events
comprise of higher complexity and involve previously unknown splicing patterns.
15:05 A Hybrid Approach to Comprehensive Transcriptome
Reconstruction Using Genome-Guided and de novo RNA-Seq Assembly
Leveraging Trinity and PASA2
Brian Haas, Manager, Genome Annotation, Outreach, Bioinformatics and Analysis, The Broad
Institute, United States
Existing reference genomes or draft genome assemblies may yield a limited
view of the transcript content of a sample due genome misassembly,
sequencing gaps, or genuine sequence variation between sequenced
samples and available reference genomes. Here we present a hybrid
approach that combines genome-guided and de novo RNA-Seq assembly to
annotate gene structures and capture those transcripts missing or otherwise
insufficiently represented by genome assemblies. We demonstrate our
approach to be highly effective across diverse eukaryotes and to the
restructured genomes of human breast cancer cell lines.
EXPLORING THE COMPLEXITY OF THE TRANSCRIPTOME
17:20 Profiling microRNAs and Circular RNAs in Brain – Implication for
Disease and Development
Jørgen Kjems, Ph.D., Professor & Director, Department of Molecular Biology and Genetics,
Aarhus University, Denmark
Circular RNA (circRNA) has recently been established as significant regulator
of miRNA activity and evidence suggest that differential expression of circRNA
may play a role in tissue development end progression of disease. In particular
microRNA-7 appear to be tightly controlled by a circular RNA sponge for miR-7
(ciRS-7) in a dynamic fashion in brains from placental animals. We have profiled
mRNA, miRNA and ciRS expression in fetal pig brains and uncovered novel
non-coding RNA controlled pathways involved in brain development.
RNA-Seq and Transcriptome AnalysisInaugural
Unraveling Layers of Expression

8
17:50 Regulation of Transcriptional Heterogeneity by Chromatin and
Transcription Machinery
Vicente Jose Pelechano, Ph.D., Senior Scientist, Steinmetz Group, Genome Biology,
EMBL, Germany
We have recently revealed an extensive layer of isoform diversity previously
hidden among overlapping RNA molecules. Given the existence of
overlapping, variable transcript isoforms, determining the functional impact
of the transcriptome requires identification of full-length transcripts, rather
than just the genomic regions that are transcribed. By systematically applying
TIF-Seq, we will present new insights in how this extensive transcript diversity
can be generated by a relatively simple eukaryotic genome with limited
splicing, and within a genetically homogeneous population of cells.
18:35 Close of Day
FRIDAY, 6 DECEMBER
CLINICAL APPLICATIONS OF RNA-SEQ
08:35 Lighting Up the Dark Matter: Targeted RNA Sequencing
Reveals Novel Non-coding RNAs Transcribed from Intergenic
Disease-Associated Regions
Marcel Dinger, Ph.D., Head, Clinical Genomics, Garvan Institute of Medical Research, Australia
The relatively recent discovery of widespread transcription of potentially
functional long noncoding RNAs (lncRNAs) from the mammalian genome led
us to investigate whether or not GWAS hits in noncoding regions could be
reconciled by the transcription of regulatory RNAs from these loci.To detect
such specifically expressed transcripts, we used capture arrays targeting 350
noncoding regions of the genome associated with disease and sequenced the
captured RNA transcribed from these regions. We have identified >1,500 new
lncRNAs whose expression appears to be specifically associated with disease.
09:05 The Identification of Long Stress-Induced Non-Coding Transcripts
David I. Smith, Ph.D., Professor, Department of Laboratory Medicine and Pathology, Mayo Clinic,
United States
In an attempt to identify important regulatory transcripts we previously utilized
whole genome tiling arrays to examine the entire genomes response to the
cellular stress of the tobacco carcinogen NNK. I will describe some of the work
that we have done to characterize these interesting transcripts. A number of
transcripts identified from the RNA- seq head and neck data correspond to the
LSINCTs that were identified from the original tiling array experiment.
10:45 Alternative Protein-Coding Transcripts in Prostate Cancer
Melanie Lehman, Ph.D., Research Fellow, Australian Prostate Cancer Research Centre,
Queensland University of Technology, Australia
We have applied de novo transcriptome assembly methods to RNA-seq data to
profile RNA expression in prostate cancer cells. We have identified alternative
protein-coding RNAs that are missing canonical functional domains as well
as long coding RNAs (lncRNAs) that are overlapping—and often mistaken
for—protein-coding RNAs. I will present the implications of these alternative
transcripts to pathway and functional analysis in the context of our research in
late stage prostate cancer.
11:15 RNA-Seq to Identify and Characterize Cancer-Specific
Transcript Variants
Rolf I. Skotheim, Ph.D., Group Leader, Genome Biology, Department of Cancer Prevention, Oslo
University Hospital, Norway
11:45 Deciphering the Neuroblastoma Transcriptome by RNA-Seq, qPCR
and Exon-Level Resolution Array Analyzes
Alexander Schramm, Ph.D., Lab Head, Oncology Research, Children’s Hospital, University
Hospital Essen, Germany
During my presentation, I will report on integration of technologies required to
understand which coding and non-coding RNAs are transcribed in a cancer cell.
Results from array-based technologies, qPCR and next-generation RNA seq will
be compared using the embryonal tumor, neuroblastoma, as a model system. An
automated workflow for the analyzes of RNA-seq data will be presented. Finally, I
will discuss some ideas for integrating NGS data into clinical decision making.
Lunch on Your Own
13:15 Session Break
REFINING EXPRESSION ANALYSIS
14:05 Standards in RNA-Seq Data Analysis
Stuart Brown, Ph.D., Associate Professor, Cell Biology; Director, Sequencing Informatics Group
of Center for Health Informatics & Bioinformatics, NYU School of Medicine, United States
14:35 RNA-Seq and Microarray Gene Expression Vie for Superiority
within a Comprehensive Study Design
Weida Tong, Ph.D., Division Director, Division of Bioinformatics and Biostatistics, National
Center for Toxicological Research, FDA, United States
The 3rd phase of the FDA-led community wide Microarray Quality Control
(MAQC-III) project investigated the reliability and utility of RNA-Seq. All the
samples in this project were profiled by both RNA-Seq and microarrays, which
produced unprecedented opportunity to comprehensively compare RNA-seq
with microarrays. RNA-Seq seems to provide comparable or better transcriptomic
profiling as compared with the standard microarray technology for the elucidation
of biological responses.This project involves ~200 participants from >80
organizations with comprehensive results that will impact FDA policy.
15:05 Multi-Platform and Cross-Methodological Reproducibility of
Transcriptome Profiling by RNA-Seq in the ABRF Next-Generation
Sequencing Study (ABRF-NGS)
Christopher Mason, Ph.D., Assistant Professor, Computational Biomedicine, Weill Cornell
Medical College, United States
We use standard reference samples to evaluate RNA-Seq across a range of
sample quality levels, sample preparation methods and bioinformatics analysis
approaches, with results that have the potential to improve the utility and
comparability of these various methods and five NGS platforms (Illumina,
PacBio, 454, PGM, Proton). Importantly, we demonstrate that even severely
degraded RNA, when prepared and analyzed with appropriate methods, can
be as useful as intact RNA for sequencing-based quantitative profiling.
15:35 Functional Dysregulation in Inflammatory Diseases
Carsten O. Daub, Ph.D., Assistant Professor, Biosciences and Nutrition & Science for Life
Laboratory, Karolinska Institutet, Sweden
Employing genome-wide expression profiling for contrasting disease and
control patients allows not only identification of differentially regulated
protein or non-coding transcripts but also inference of the underlying
regulatory events.
Inaugural
RNA-Seq and Transcriptome Analysis Unraveling Layers of Expression

9
4-5 December 2013 Informatics
High-Scale Computing Turning Big Genomics Data into Smart DataFifth Annual
Wednesday, 4 DECEMBER
SUPPORTING GENOMICS WITH IT INFRASTRUCTURE
»» KEYNOTE PRESENTATION
08:40 ELIXIR: The European Research Infrastructure for Life
Science Data
Niklas Blomberg, Ph.D., Founding Director, ELIXIR, United Kingdom
The mission of ELIXIR is to construct and operate a sustainable infrastructure
for the sharing of biological information throughout Europe, to support life
science research and drive its translation to medicine and the environment,
the bio industries and society.The challenges in storing, integrating and
analyzing the data from modern biological experiments are real; ELIXIR
meets this challenge through a distributed e-infrastructure of bioinformatics
services built around established European centres of excellence.
09:10 Scalability, Reproducibility and Traceability in Large-Scale
NGS Facilities
Gianmauro Cuccuru, Ph.D., Researcher, CRS4 Bioinformatics Laboratory, Italy
As the rate of samples to process increases, manually performing and
tracking operations becomes increasingly difficult, costly and error-
prone, while processing the massive amounts of data poses significant
computational challenges. We will present how combining scientific
workflow applications (Galaxy) with state-of-the-art processing technologies
like Hadoop, OMERO and iRODS can help address these challenges, thus,
empowering more complex life science studies while providing scalability, full
reproducibility and traceability.
09:40 Providing the Clinical Genomics Platform: A How-To Guide for
Flexible and Extensible Services for Clinical Big Data
Brent Richter, Executive Director, Enterprise Research Infrastructure & Services, Information
Systems & Academic Programs, Partners HealthCare & Massachusetts General Hospital/
Brigham & Women’s Hospital, United States
Managing NGS data and reporting results require secure but extensible
infrastructures. Continuing to adopt these platforms to additional clinical areas
such as pathology and microbiotics is the current challenge, but the future
brings the promise of network medicine that incorporates all information
about a patient, from genomics to real-time imaging. What will be the
information technology architectures required that places storage, networks
and analytics together in a secure and available environment? What services
need to be developed?
10:45 1000 Genomes/UK10K Projects: Data Management and
Data Sharing
Thomas Keane, Ph.D., Senior Scientific Manager, Vertebrate Resequencing Informatics,
Wellcome Trust Sanger Institute, United Kingdom
We have now reached the point where large-scale human disease
association studies are carried out primarily using next-generation sequencing
technologies. These studies can generate many hundreds of terabases of
sequencing data. One of the key challenges is to devise scalable and robust
data management and data sharing solutions. In this talk, I will cover how we
have addressed these challenges at the Wellcome Trust Sanger Institute.
11:15 Implementation of the CDC Translational Informatics Platform: From
Genetic Variants to the National Swedish Rheumatology Quality Register
Jesper Tegnér, Ph.D., Professor, Strategic Chair, Computational Medicine and Head, Unit for
Computational Medicine, Center for Molecular Medicine, Medicine, Karolinska Institutet and
Karolinska University Hospital, Sweden
11:45 Sponsored Presentation Sponsored by
Speaker to be Announced
Lunch on Your Own
13:15 Session Break
CLOUD AS A COMPUTING RESOURCE
14:05 Cloud4Science: Using Public Clouds in NGS Pipelines
Ignacio Blanquer, Ph.D., Associate Professor/Researcher, Computer Systems/Institute of
Instrumentation for Molecular Imaging, Universitat Politècnica de València, Spain
Cloud4Science is an initiative funded by Microsoft to boost the use of clouds
in science. The first prototype focuses on genomics on the cloud (www.
cloud4science.eu) and integrates a complete pipeline for mutation detection
analysis running on Windows Azure cloud, which users can easily deploy and
run using their Azure credentials. Cloud4Science has focused on the issues in
data transfer, provenance and massive processing from a user-friendly portal
that transparently deploys the needed resources.
14:35 Cost-Effective GPU-Grid for Genome-Wide Epistasis Calculations
Benno Pütz, Ph.D., Statistical Genetics, Max Planck Institute of Psychiatry, Germany
With local restrictions on handing out clinical data to external computer
centers, the cloud, we were forced to establish appropriate computing
resources in-house as an alternative solution. From a price/performance point
of view, low-cost systems based on consumer graphics cards turned out to be
our best option. The system setup as well as some of the work performed on
epistasis will be presented.
15:05 CloudMC: A Cloud Computing Platform for Radiation Calculations
Hector Miras, Medical Physicist, Department of Medical Physics, Virgen Macarena University
Hospital, Spain
Rubén Jiménez, Chief Software Architect, R&D Division, Icinetic, Spain
Monte Carlo (MC) algorithms are considered the gold standard for radiation
calculations, but they are computationally expensive. That is why they are
not used in routine clinical practice. CloudMC is a platform developed on
Windows Azure intended for parallelization of radiation calculations using MC
algorithms. This platform allows any user to have access to a big computing
power to perform MC simulations paying only for the resources used.
Speaker to be announced
16:45 Bioinformatics Use Cases for Cloud Computing
Mohamed M. El-Kalioby, Research Scientist, Bioinformatics Group, Center for Informatics
Science, Nile University, Egypt
Bioinformatics data is getting larger and larger every day, especially after NGS.
Computation infrastructure required to handle this is getting harder and is
expensive to build. How can we utilize the scalability and availability of cloud
computing for such activities?
17:15 The EUDAT Project and Cloud Storage
Wolfgang Gentzsch, Ph.D., Co-Founder, The UberCloud HPC Experiment; Executive Consultant,
HPC, Grid and Cloud; Advisor, EUDAT; Chairman, ISC Cloud Conferences, Germany
EUDAT aims to develop and support a Collaborative Data Infrastructure
allowing researchers to share data across communities and carry out research
effectively. EUDAT’s data services, like persistent storage, identification,
authenticity, workflow execution and mining, can leverage cloud storage. But
copyright or national law might not allow the data to leave the country or even
the data centre in which they are curated. EUDAT takes a long-term view of
the data it holds and is considering “trust marks” for digital archiving.
17:45 Welcome Reception in the Exhibit Hall with Poster Viewing
19:15 Close of Day

10
NGS DATA MANAGEMENT AND ANALYTICS
08:35 Preprocessing of High-Throughput Sequencing Data Speeds Up
Targeted Research
Tomasz Konopka, Ph.D., Research Scientist, Sebastian Nijman Laboratory, Informatics and Synthetic
Biology, CeMM, Research Center for Molecular Medicine, Austrian Academy of Sciences, Austria
Information encoded in high-throughput sequencing reads can be valuable for
targeted hypothesis-driven research questions. It is thus worthwhile to access
relevant portions of large datasets in fastq format without costly processing
of the remainder. The TriageTools suite available on SourceForge provides fast
utilities for preprocessing fastq data. It includes a method for extracting reads
likely to map onto predefined regions of interest and extracting data on a few
DNA- or RNA-seq samples’ target genes with speedup factors up to ~90.
09:05 Compression Models for DNA Sequences
Armando J. Pinho, Ph.D., Director, Instituto de Engenharia Electrónica e Telemática de Aveiro
(IEETA) and Associate Professor, Departamento de Electrónica, Telecomunicações e Informática
(DETI), Universidade de Aveiro, Portugal
Research in the genomic sciences is confronted with the volume of
sequencing and resequencing data increasing at a higher pace than that
of data storage and communication resources, shifting a significant part
of research budgets from the sequencing component of a project to the
computational one. Hence, being able to efficiently store sequencing and
resequencing data is a problem of paramount importance. In this talk, we will
present and discuss DNA sequence compression models that we have been
developing during the past years.
09:35 An Integrated High Performance Computing Sponsored by
Platform for Genomics and Translational Research
Janis E. Landry-Lane, Program Director, World Wide High Performance Technical Computing,
Life Sciences/Higher Education Segments, IBM
Tzy-Hwa (Kathy) Tzeng, Ph.D., Senior Technical Staff Member, IBM Life Science and NGS Solution
High-performance computing and storage are required to efficiently process data
generated by NGS.The applications used to map reads and detect variants are
typically CPU and I/O intensive. IBM has characterized this workload and developed
optimal genomics platform to address the demand.The goal of any sequencing
project is to gain insight into diverse range of biological processes by integrating
genome data with corresponding phenotypes. Large computational capacity and
sophisticate algorithms are mandatory in the translational platform.We will illustrate
how IBM seamlessly integrates genomics and translational platforms.
11:15 Management of Genomic Big Data in a Country-Wide
Collaborative Initiative for Rare Disease Gene Finding
Joaquin Dopazo, Ph.D., Head, Computational Genomics, Centro de Investigacion Principe
Felipe, Spain
About 1000 exomes were analyzed in a nationwide initiative to find disease genes
in many inherited diseases.This flood of DNA and RNA-seq data led to pipeline
optimization for NGS data analysis, including accelerating runtimes and increasing
sensitivity in mapping and variant calling processes, the development of new
visualization tools and the development of new systems-biology-based candidate gene
prioritization methods.The Medical Genome Project and the Spanish network for Rare
Diseases constitute an example of a collaborative nationwide genome project.
11:30 Conference Registration
12:35 Enjoy Lunch on Your Own
ANALYTICAL TOOLS
14:05 Annotate-it and eXtasy: Interpretation and Prioritization of
Single-Nucleotide Variation in Clinical Genomics
Alejandro Sifrim, Ph.D., Research Scientist, Yves Moreau Laboratory, Bioinformatics, Electrical
Engineering, Katholieke Universiteit Leuven, Belgium
The human genome harbors a plethora of neutral, common and rare
variations. In order to find the cause of genetic disease, one must be able
to distinguish these neutral variants from the disease-causing variants. Here
we present Annotate-it and eXtasy, two software tools which aid the clinical
geneticist in discovering disease-causing SNVs.
14:35 TAG (Tumor Analysis in Galaxy): A Web Server Application for
the Detection of Somatic Mutations in the Absence of Associated
Healthy Control
Andrew Stubbs, Ph.D., Assistant Professor, Bioinformatics, Erasmus University Medical Center,
The Netherlands
The first step in tumor analysis is typically a correction with a normal sample,
taken from the individual’s healthy tissue for which 80%-95% of variations in a
tumor sample present in the healthy tissue. We have developed a web-based,
control-free tumor analysis and reporting application with a “virtual normal”
as reference to determine somatic mutations. It removed up to 97% of the
variants detected by the standard tumor/normal approach. We will present our
analysis, available in a public Galaxy/CLOUD.
15:05 Harnessing e-Science Central for NGS
Simon Woodman, Ph.D., Senior Research Associate, Systems Research Group, Newcastle
University, United Kingdom
The talk will be about how we use e-Science Central for analyzing NGS data
within the Cloud4Science project. This will include the pipelines we have
implemented and challenges faced by storing and analyzing very large data
sets. I will also examine the importance of provenance capture and analysis in
this environment.
4-5 December 2013
5-6 December 2013
Informatics
Informatics
Genome Informatics
Turning Big Genomics Data into Smart Data
Deciphering Disease through Sequencing Data
Fifth Annual
Second Annual

11
15:50 Sponsored Presentation (Opportunity Available)
EXOME SEQUENCING
17:20 Sequenza – A Bayesian Analytical Framework to Provide
Comprehensive Characterization of Tumor Samples Based on
Exome Sequencing
Zoltan Szallasi, M.D., Senior Research Scientist, Children’s Hospital Informatics Program,
Harvard Medical School, United States and Professor, Systems Biology, Danish Technical
University, Denmark
We are presenting here a powerful bayesian statistics-based analytical
framework to analyze exome sequence data from tumor biopsies. Sequenze
produces accurate estimates on normal tissue contamination and ploidy levels.
It produces highly accurate mutational calls and also enables to extract loss of
heterozygosity and copy number variations as accurately as SNP array profiles.
We will also present several clinical case studies where Sequenza-based
analysis of tumor exome sequences produced valuable clinical information.
17:50 EVA-Suite (Exome Variation Analyzer): A User-Friendly Web
Solution for Annotating, Filtering and Prioritizing Candidate Variants in
Medical Genomics
Hélène Dauchel, Ph.D., Assistant Professor, Genomics and Applied Bioinformatics, University of
Rouen, France
To provide clinicians and human geneticists with user-friendly assistant
software to help them deal with variation analysis in medical NGS projects,
we have partnered with medical geneticists and developed EVA-Suite (Exome
Variation Analyzer), a user-friendly web interface and free solution. It allows
non-programming biomedical experts to manage variation data by themselves,
from annotation to functional effect analysis of candidate variants through
efficient versatile filtering strategies. Demonstrative examples for germline
mutations in genetic disorders and somatic cancer mutations will be exposed.
18:20 Close of Day
FRIDAY, 6 DECEMBER
THERAPEUTIC TARGETS
08:35 Clinical Genome Architecture Circuitry and Next-Generation
Cancer Drug Targets
Dimitrios H. Roukos, M.D., Ph.D., Founding Director, Centre for BioSystems & Genomic
Network Medicine, CBS.GenNetMed and Department of Surgery, Ioannina University School of
Medicine, Greece
The ENCODE data change the “central dogma” of one-gene/protein-
one phenotype which continues to represent the foundation of all drugs
developed and currently used in clinical practice. Latest advances in clinical
genomics and dynamic signaling networks are presented revealing the
exciting perspectives and challenges in targeting individual cancer patient
and discovering the next-generation transcriptional circuitry-based drugs.
Challenges and perspectives of genomic network medicine are discussed.
09:05 Big Data in Drug Discovery – Challenges and Perspectives
Philip Groth, Ph.D., IT Business Partner, CoE Research, Bayer HealthCare
Pharmaceuticals, Germany
After the discovery that mutations influence cancer initiation and
development, targeted drugs like Crizotinib or Imatinib have shown dramatic
effects on treatment of some cancers. To deepen understanding of the role
of mutations in cancer, NGS has been employed to generate large-scale
genomic mutation data. These “Big Data” must be stored, processed and
analyzed to develop innovative cancer treatments. We present perspectives
on cancer sequencing efforts, insights into the manifold technical, ethical,
legal and scientific challenges and some solutions.
TRANSLATION INTO THE CLINIC
10:45 The Ethical Introduction of Genome-Based Information and
Technologies into Public Health
Heidi Howard, Ph.D., Senior Research Fellow, Département d’épidémiologie et de Santé
Publique, Faculté de Médecine, Université Toulouse, France
11:15 Challenges of Translation of Next-Generation Sequencing to
Clinical Practice
Ángel Carracedo, Ph.D., Director, Fundación Galega de Medicine Xenómica (FPGMX), Hospital
Clínico Universitario, Spain
We will discuss some of challenges of the use of NGS for the diagnosis of
Mendelian diseases and pharmacogenomics. Some of the main problems
need advanced bioinformatics tools and are related to the amount of the data
generated and the interpretation of variants of uncertain significance. We will
show our approaches to face these problems.
»» KEYNOTE PRESENTATION
11:45The Ethical Dimensions of Data Sharing and the Maze of Identifiability
Anne Cambon-Thomsen, M.D., Director, Research, Centre National de la Recherche
Scientifique (CNRS), France
Lunch on Your Own
13:15 Session Break
RNA-Seq
14:05 Standards in RNA-Seq Data Analysis
Stuart Brown, Ph.D., Associate Professor, Cell Biology; Director, Sequencing Informatics Group
of Center for Health Informatics & Bioinformatics, NYU School of Medicine, United States
14:35 RNA-Seq and Microarray Gene Expression Vie for Superiority
within a Comprehensive Study Design
Weida Tong, Ph.D., Division Director, Division of Bioinformatics and Biostatistics, National
Center for Toxicological Research, FDA, United States
The 3rd phase of the FDA-led community-wide Microarray Quality Control
(MAQC-III) project investigated the reliability and utility of RNA-Seq. All the
samples in this project were profiled by both RNA-Seq and microarrays,
which produced unprecedented opportunity to comprehensively compare
RNA-seq with microarrays. RNA-Seq seems to provide comparable or better
transcriptomic profiling as compared with the standard microarray technology for
the elucidation of biological responses.This project involves ~200 participants
from >80 organizations with comprehensive results that will impact FDA policy.
15:05 Multi-Platform and Cross-Methodological Reproducibility of
Transcriptome Profiling by RNA-Seq in the ABRF Next-Generation
Sequencing Study (ABRF-NGS)
Christopher Mason, Ph.D., Assistant Professor, Computational Biomedicine, Weill Cornell
Medical College, United States
We use standard reference samples to evaluate RNA-Seq across a range of
sample quality levels, sample preparation methods and bioinformatics analysis
approaches, with results that have the potential to improve the utility and
comparability of these various methods and five NGS platforms (Illumina,
PacBio, 454, PGM, Proton). Importantly, we demonstrate that even severely
degraded RNA, when prepared and analyzed with appropriate methods, can
be as useful as intact RNA for sequencing-based quantitative profiling.
15:35 Functional Dysregulation in Inflammatory Diseases
Carsten O. Daub, Ph.D., Assistant Professor, Biosciences and Nutrition & Science for Life
Laboratory, Karolinska Institutet, Sweden
Employing genome-wide expression profiling for contrasting disease and
control patients allows not only identification of differentially regulated
protein or non-coding transcripts but also inference of the underlying
regulatory events.

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