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TUESDAY, 5 OCTOBER

9:00 Conference Registration and Morning Coffee

9:30 Chairperson’s Opening Remarks

9:35 Next-Generation Sequencing in the Analysis of Polymicrobial Infections: Some Essential Considerations

Geraint Rogers, Ph.D., Pharmaceutical Science, King’s College London, United Kingdom

The development of next-generation sequencing presents an unparalleled opportunity to investigate the highly complex microbial interactions that are involved in many clinical infections; however, without due consideration of factors such as appropriate sample acquisition and handling, exclusion of non-viable microbial cells, and downstream data processing, the insight provided by its application is greatly diminished. Areas of experimental design key to successful infection analysis will be discussed.

10:05 Comparative Genomics to Understand the Population Structure and Evolution of the Major Human Pathogen Mycobacterium Tuberculosis

Stefan Niemann, Ph.D., Head, Molecular Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Germany

Whole genome sequencing using “next-generation” technologies allows the cost-effective re-sequencing of larger collections of major human pathogens, e.g. clinical isolates of the Mycobacterium tuberculosis complex (MTBC). This process allows deciphering a much more accurate picture of the global population structure and evolution of the MTBC. It will shed light on the micro evolutionary processes occurring in M. tuberculosis strains during spread, especially in the context of multidrug resistance.

10:35 Coffee Break

11:00 The Human Intestinal Metagenome

S. Dusko Ehrlich, Ph.D., Research Director and MetaHIT Coordinator, Department of Microbiology and Food Chain (MICA), INRA, France

We have established an extensive catalog of the gut microbial genes within the MetaHIT consortium, using metagenomic sequencing. Some 0.6 Tb sequence of the DNA prepared from fecal samples of 124 individuals of the European origin was generated, assembled and analyzed. The catalog contains 3.3 million non-redundant microbial genes, 150 times more than the human gene complement, contains an overwhelming majority of the prevalent microbial genes present in the cohort and likely includes a large proportion of the prevalent human intestinal microbial genes. This catalog opens avenues towards new diagnostic and prognostic tools, based on associations of bacterial genes and human disease.

11:30 Novel Diagnostic Opportunities for Oral Health through Application of NGS

Bart Keijser, Ph.D., Principal Investigator, Microbial Genomics, TNO, The Netherlands

TNO and the Academic Centre for Dentistry Amsterdam (ACTA) have joined forces in the aim to a full fundamental insight in biological processes and etiological factors that underlie conservation of oral health and to develop of novel, integrated approaches for diagnostics and prevention in oral care. Data generated on the temporal and spatial dynamics of the oral ecosystem, interaction with the host, and in relation to oral health status will be presented. This combined approach has proven to be a powerful strategy to elucidate fundamental interactions between the oral microbiota and the host in relation to maintenance of oral health status.

Sponsored by
12:00 Sponsored Presentation
To Be Announced

12:30 Lunch for Purchase in the Exhibit Hall

13:45 Dedicated Poster Viewing in the Exhibit Hall

14:30 Chairperson’s Remarks

14:35 Systems Medicine Perspective towards Bionetworks-Based Discovery of Biomarkers and Biologic Agents in Cancer

Dimitrios Roukos, M.D., Ph.D., Associate Professor, Department of Surgery, Ioannina University School of Medicine, Greece

Emerging evidence suggests that cancer initiation, progression and metastases are driven by interacting genes, signaling pathways and cancer cell interactions within an individual tumor. The cancerous process is further complicated by the impact of environmental factors, lifestyle, genetic ancestry and susceptibility to cancer. These bionetworks are modestly considered by the current R&D for drug discovery. This presentation will describe how systems medicine and biology approaches may lead to biomarkers and biologic drugs in cancer prevention and treatment. Challenges and expectations to understand the complex genotype-phenotype map towards personalized medicine will be discussed.

15:05 Highly Sensitive Detection of Genome Instability Using Next-Generation Sequencing

Francesca Ciccarelli, Ph.D., Principal Investigator, IEO, European Institute of Oncology, Italy

We have developed a highly sensitive procedure to measure genomic instability that is based on the re-sequencing of a cancer genomic region using next-generation sequencing technology. Using this approach, we detect genomic instability even in nonneoplastic tissues of cancer patients, thus showing that our procedure is more sensitive of currently used methods. This constitutes the proof of principle for the development of a more sensitive molecular assay of genomic instability.

15:35 Refreshment Break

Sponsored by
16:00 Understanding Genomic Variations in NGS Data
Frank Schacherer, Ph.D., COO, BIOBASE GmbH
Next generation genome sequencing yields thousands of SNPs, but which of these have functional impact, and which are just noise? In this presentation you will learn how you can use the new NGS offering from BIOBASE, Genome TraxTM, in combination with both public and commercial tools, to quickly identify functional genomic elements in sequence data from NGS. You will be able to map SNPs to mutations that are associated with disease, and to gene regulation sites, adding value to the sequence data you generate.

16:15 Sponsored Presentation (Opportunity Available)

16:30 Use of Cancer-Specific Genomic Rearrangements to Quantify Disease Burden in Plasma from Patients with Solid Tumors

Phil Stephens, Ph.D., Sr. Scientist, Cancer Genome Project, Sanger Institute, United Kingdom

Next-generation sequencing allows rapid and cost effective identification of patient-specific rearrangements in cancer samples. We mapped genomic rearrangements in over 100 solid tumors and identified at least one somatically acquired rearrangement in each sample. We developed PCR assays for tumor specific rearrangements which were able to detect a single copy of the tumor genome in plasma from the patient without false positives. In the future, this strategy could be readily established in diagnostic laboratories, with major impact on monitoring of disease status and personalizing treatment of solid tumors.

17:00 Genetic Diagnosis of Familial Breast Cancer Using Clonal Sequencing

Graham Taylor, Ph.D., Professor, University of Leeds Institute of Molecular Medicine, St. James’s University Hospital, United Kingdom

Clonal “next-generation” sequencing is cheap and dirty. Bombastic claims about cheap access to genome sequences need to be balanced with the risk that low quality data could generate false negative and false positive results. In the case of germline mutations, the low quality can often be compensated by read depth. This may not be an option for tumor samples containing mixed populations. This presentation will explore the cost, risks and benefits of deploying clonal sequencing in a diagnostic setting with examples in familial cancers and in tumor analysis.

17:30 Deep Clonal Sequencing of Archival Tumor Samples Increases Mutation Detection Success

Neil Gibson, Ph.D., Team Leader, Research and Genetics, AstraZeneca, United Kingdom
AZD7762 has been shown to potentiate response in several different settings where inhibition of checkpoint kinase results in the abrogation of DNA damage-induced cell cycle arrest. To determine whether tp53 mutation is predictive of clinical response to AZD7762, it is necessary to sequence the gene at high sensitivity in clinical tumor samples. We describe a method for the next-generation clonal sequencing of the tp53 gene in formalin fixed tumors that enables mutation detection down to an estimated clonal frequency of 5% combined with high data generation success. We also discuss the practical requirements of a sequence-based diagnostic assay for highly polymorphic genes such as tp53.

18:15 Interactive Breakout Discussion Groups

Join a facilitated discussion group focused around specific scientific and technology related topics. This unique session allows conference participants to exchange ideas, experiences, and develop future collaborations around a focused topic. Current discussion groups include:

NGS and Data Quality for Diagnostic Applications

Graham Taylor, Ph.D., Professor, University of Leeds Institute of Molecular Medicine, St. James’s University Hospital, United Kingdom

Discussion topics include:

Sources of error and methods to address them
Run quality
Platform specific errors
Amplification
Alignment errors and artifacts
Detection of low abundance variants
Contamination

Sequencing Cancer Genomes: Potential Healthcare Applications

Phil Stephens, Ph.D., Senior Scientist, Cancer Genome Project, Sanger Institute, United Kingdom

Discussion topics include:

Identification of novel therapeutic targets
Characterisation of mechanisms of resistance to targeted therapeutics
Surrogate marker of cell kill in early phase clinical trials
Monitoring tumor response to therapy in real-time – Reducing toxicity, preventing drug waste
Identifying disease relapse before clinically evident (pre-emptive therapy)
Choosing intensity of adjuvant therapy based on risk stratification
Personal medicine

Circulating Tumor Cells and Cell Free Nucleic Acids: A Real Time Access to the Cancer Genome

Tim Ward, Ph.D., Staff Scientist, Clinical and Experimental Pharmacology, Paterson Institute for Cancer Research, University of Manchester, United Kingdom

Discussion topics include:

Can we use circulating DNA as a surrogate for tumor DNA?
Does circulating DNA represent the cancer genome?
Will micro RNA be more informative?
Can we undertake molecular characterisation of low numbers of circulating cancer cells?

What Does Success Look Like for an Infectious Disease Molecular Diagnostics Test, and Which of the Following Factors Drive This?

Vanya Gant, M.D., Ph.D., Head of Departments of Microbiology and Infectious Diseases, University College Hospitals, NHS Foundation Trust, United Kingdom

Discussion topics include:

Ease of use?
Robustness?
Ease of implementation?
Price?
Speed?
Performance?
Gap in existing market?

High-Throughput Protein Detection Technologies in Molecular Diagnostics of Cancer
Cristiana Tanase M.D., Ph.D., Head, Biochemistry Proteomics, Victor Babes National Institute of Pathology, Romania
Discussion topics include:

Multiplex analysis for biomarkers in cancer
Early detection of biomarker by serum samples analysis
Proteomic profiling biomarker discovery by SELDI-ToF-MS, MALDI-ToF-MS, 2DGE and others

NGS: Opportunities for Improving Oral Care Diagnostics. Translating Research to Practice.
Bart Keijser, Ph.D., Principal Investigator, Microbial Genomics, TNO, The Netherlands
Discussion topics include:

How can the oral care patient benefit from NGS technology?
What are the potential hurdles to bring NGS from and R&D setting into routine diagnostics setting?
What do we need to translate NGS data and technology to the oral care practice?
Could diagnostic NGS data sets be used for data mining?