Day One

5 December 2012

8.00 Registration, Coffee and Networking

8.50 Chair’s Opening Remarks

How Advances in NGS are Increasing our Understanding of the Cancer Genome

9.00 Facilitating Preclinical to Clincal Translation by Optimizing Models and Processes

Methods for optimizing translation from preclinical to clinical
Using ‘genomic decision trees’ to better categorize cancers into specific subtypes
Matching omic features of the TCGA to treatment regimes to improve patient treatment choices

Joe Gray, Director, Division of Life Sciences, Lawrence Berkeley National Laboratory

9.30 Case Study: The Broad Institute TCGA Analysis Pipeline

How the TCGA analysis pipeline can coordinate the flow of terabyte-scale genome datasets through quantitative algorithms
A practical guide to using this software for analysis of NGS cancer genome data

Michael Noble, GDAC Pipeline Manager, Broad Institute

10.00 Speed Networking & Morning Refreshments

Translating the Cancer Genome into Clinically Actionable Biomarkers

11.30 Interpreting the Cancer Genome and Identifying the Driver Events

Review analysis methods to derive mutation calls, copy number changes and gene fusions from exome sequencing of patients
Leverage gene expression data to identify tumor driving genomic events
Genomic and transcript integration for biomarkers discovery

Yair Benita, Senior Computational Biologist, Merck

12.00 Rapid and Sensitive Detection and Confirmation of Clinically Actionable Mutations in FFPE and FNA Tumor Biopsies using Orthogonal NGS Technologies

Diane Ilsley, Marketing Manager, Asuragen

12.30 Lunch & Networking

1.45 Case Study: AVEO’s Pathway-Based Biomarker Discovery Approach Using Microarray Data from Next-Generation Mouse Models

An introduction to the pathway-based microarray analysis bioinformatics tools used by AVEO Pharmaceuticals
The use of this tool to identify differentially expressed pathways/modules based on microarray profiles of efficacy tested mice, and validating the biomarker in the Phase 2 study

Bin Feng, Director, Bioinformatics, AVEO Pharmaceuticals

2.15 From Lab to Clinic - Cancer Genomics Moves Towards Patient Care

An introduction to knoSYS™100
Applications of the technology to let clinics install a smart, robust whole genome interpretation pipeline, to generate clinically decisive insights in sporadic and familial cancer cases, and integrate them seamlessly into patient care

Nathan Pearson, Director of Research, Knome

2.30 How is Sequencing Technology Evolving and What Does This Mean for the Future of Drug Development?

How can the cancer genome influence drug development
Which approaches and applications will bear fruit
How can industry work more closely with sequencing providers to improve technology development
In-house or outsource – where will the future lie

Elena Izmailova, Director, Translational Medicine, Millennium

Jiye Shi, Director, Computational Structural Biology, UCB Pharma

Jason Ting, Research Scientist, Eli Lilly

Yaron Turpaz, Vice President, Informatics & Information Sciences, AstraZeneca

Jim Watters, Director, Applied Genomics, Oncology, Sanofi

3.45 Afternoon Refreshments & Networking

4.15 Optimizing Biomarker Discovery using Targeted DNA Sequencing of Clinical Tumor Specimens

How molecular analysis of various sub-types of cancer have revealed genetic biomarkers that predict whether a patient will benefit from a particular treatment
The use of parallel sequencing to identify mutations that predict response to targeted therapies in patients at Memorial Sloan-Kettering Cancer Center

Michael Berger, Assistant Professor, Pathology, Memorial Sloan-Kettering Cancer Center

4.45 Developing Genomic Signatures into Clinically Actionable Markers: Lessons from Glioblastoma

Applying information from characterization of genetic alterations and patterns of signal transduction in brain tumors
Introduction to the novel computational approaches for integrated genomic analysis
How this genomic data is being incorporated into TCGA and the applications of this data

Cameron Brennan, Surgeon and Laboratory Investigator, Memorial Sloan-Kettering Cancer Center