Bio-IT World and Cambridge Healthtech Institute’s Second Annual
Genome Informatics
Deciphering Disease through Sequencing Data

5-6 December 2013 | Sheraton Lisbon Hotel & Spa | Lisbon, Portugal

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All agree genomic technologies hold the potential to improve diagnosis and treatment of inherited and complex diseases--including cancer--and facilitate the move towards personalized predictive medicine. However, the higher throughput and rapidly falling costs of next-gen sequencing have resulted in voluminous genomic data and downstream computational challenges. Thus, the shift from discovery research to clinical implementation can only be accomplished through stringent data management, analysis, interpretation and quantification. Bio-IT World and Cambridge Healthtech Institute’s Clinical Genomics and Informatics Europe is pleased to host the Second Annual Genome Informatics conference. Ultimately, putting genomic data analysis tools into the hands of biomedical experts will ensure that patients receive the correct diagnosis and treatment. 

Thursday, 5 DECEMBER

11:30 Conference Registration

12:35 Enjoy Lunch on Your Own

ANALYTICAL TOOLS 

14:00 Chairperson’s Opening Remarks

Simone Sharma, Application Specialist, Data Analytics, Perkin Elmer Informatics

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 Cloud e-Genome: NGS Workflows on the Cloud Using e-Science Central

Paolo Missier, Ph.D., Lecturer, Information and Knowledge Management, School of Computing Science, Newcastle University, United Kingdom

"Cloud e-Genome" is a two-year pilot project, only recently started, funded by the U.K.’s National Institute for Health Research (NIHR). Its aim is to facilitate the adoption of systematic genetic testing in clinical practice, by providing large-scale cloud-based deployment of 2nd-Gen Sequencing analysis pipelines for exome variant analysis and interpretation. The project provides an ideal test bed for e-Science Central, a cloud-based workflow management system developed at Newcastle as a research prototype. In this talk, I will first provide a brief overview of the project’s aims and goals, and then focus on the functionality offered by e-Science Central, specifically on support for provenance and its importance for the project.

15:35 Interpreting Genomic Variation in the Research and Clinical Context Using OmicsOffice on the Spotfire Analytics Platform

Eduardo Gonzalez Couto, Ph.D., CSO, Integromics, Spain

Genomic variants studies require a subtle combination of enrichment, with diverse biological and clinical annotations, followed by filtering and ranking of the annotated variants. The OmicsOffice intelligence suite clinical workflow is designed to enable researchers and clinicians to easily explore variants, pinpoint known facts as well as discover novel associations.

 16:05 Refreshment Break in the Exhibit Hall with Poster Viewing  

EXOME SEQUENCING 

16:50 Big Science & Biomedicine at Petascale

Andrew McCabe, CTO, EMEA Healthcare, EMC

The exponential decline in the cost of next generation sequencing is making it possible to discover rare genetic variants that explain uncommon childhood diseases and cancer. To detect these rare variants requires the aggregation and analysis of genomics and clinical data at scale.  Consequently the need to manage and to compute biomedical data at scale is driving the dramatic rethinking and re-architecting of IT infrastructures. We will explore best practices for managing data at petabyte scale.

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 Whole-Exome Sequencing in Heterogeneous Neurodegenerative Diseases

Conceição Bettencourt, Ph.D., Research Associate, Molecular Neuroscience, Institute of Neurology, University College London, United Kingdom

Hereditary spastic paraplegias (HSPs) constitute a group of clinically and genetically heterogeneous neurodegenerative diseases. More than 50 loci and 30 genes have already been identified and, therefore, a gene-by-gene diagnostic approach is becoming unpractical. This talk will focus on the utility of whole-exome sequencing making easier the identification of mutations, and further extending the clinical spectrum of these heterogeneous diseases.

18:20 Close of Day

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