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Clinical Genomics for Cancer Diagnostics
Clinical Genomics for
Cancer Diagnostics
2013 Brochure


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Day 1 | Day 2


7:30 am Morning Coffee


8:00 Chairperson's Remarks

Seth D. Crosby, M.D., Director, Alliances and Partnerships, Department of Genetics, Washington University School of Medicine

8:05 Clinical Molecular Cytogenetics: The Past, the Present, and the Future

Marilyn M. Li, M.D., Professor & Director, Cancer Genetics Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine

Geneticists have long recognized the role of genomic alterations, such as deletion, duplication, or translocation of chromosomal material, in the pathogenesis of human disorders. Different technologies have been developed to detect genomic alterations since the discovery of the correct chromosome number in human cells in 1956. This presentation discusses the most advanced molecular cytogenetics technologies, their strengths and limitations, and their impact on medical practice.

8:35 Juxtaposing Genomic Insights of Cancer for Patient Care

Michael E. Berens, Ph.D., Deputy Director, TGen Research Resources; Director, Cancer & Cell Biology Division; Professor, Brain Tumor Unit, TGen

"Big data" on cancer patient specimens offers expanding insights to disease mechanisms; confidently translating this into knowledge that informs actionable therapeutic guidance is a tractable pursuit. Careful alignment of the elements of an effective, evolving "genomics tumor board", as implemented at TGen, serves the research, regulatory, and clinical communities.

9:05 Clinical Cancer Genotyping: Snapshot

John Iafrate, M.D., Ph.D., Assistant Professor, Pathology, Harvard Medical School; Assistant Pathologist, Massachusetts General Hospital

This presentation will discuss a broad cancer genotyping platform, termed SNAPSHOT, which detects recurrent mutations in DNA from archived pathology specimens. This platform is allowing for a molecular stratification of cancer patients, and in some cases allowing for placement of patients into trials of novel agents that target specific mutated gene products.

9:35 A Novel, Automated Post-Genomic Prostate Cancer Biopsy Test Predictive of Aggressiveness

Peter Blume-Jensen, M.D., Ph.D., CSO, Metamark Genetics, Inc.

The ability to accurately predict the aggressiveness of early stage prostate cancer based on prostate biopsies is one of the biggest unmet clinical needs in disease management. At Metamark we have pioneered a novel, automated platform based on quantitative multiplex immunofluorescence measurement of proteins in intact, defined tissue regions of interest. This is accomplished through integration with advanced object recognition which renders our test highly accurate and reproducible, independent of pathologist interpretation. We will present the development of our novel prostate cancer biopsy test based on this approach.

10:05 Coffee Break with Exhibit and Poster Viewing


Appistry10:45 Clinical Best Practices for Cancer Genetic Analysis Pipelines

Richard Mazzarella, Ph.D., CSO, Appistry, Inc.

For NGS to inform precision medicine initiatives, genetic analysis must become production-ready and capable of delivering results reliably and efficiently. Proven pipelines based on best practices for standard genetic analysis tasks can free labs to focus on more challenging analysis issues. This presentation  overviews the key functionality required to build, run, and validate complete pipelines for clinical somatic studies, with a focus on the pros and cons offered by different analysis methods. 

11:15 My Cancer Genome - Cancer Genomics Knowledge Resource

Christine Micheel, Ph.D., Research Assistant Professor, Medicine, Vanderbilt-Ingram Cancer Center; Managing Editor,

Evidence regarding the clinical significance of tumor gene mutations for predicting response to cancer treatments is evolving at a rate that outpaces traditional approaches to knowledge dissemination. My Cancer Genome addresses this challenge by providing up-to-date information on mutation-specific treatments and clinical trials. Current content covers 293 mutations across 18 cancer types.

11:45 Applying Multiscale Network Modeling to Enable Personalized Cancer Therapy

Joel Dudley, Ph.D., Assistant Professor, Genetics and Genomic Sciences; Director, Biomedical Informatics, Mount Sinai School of Medicine

This presentation will discuss a new Mount Sinai program that is leveraging next-generation sequencing and predictive network models to drive personalized cancer therapy. We are performing patient-specific mutational analyses, applying those results to inform screens using patient-specific mutant fly models, among other model systems and in silico approaches. We are then weaving all of the resulting DNA, RNA, CNV, and mutation information together to generate probabilistic causal networks in the hopes of identifying the perturbations that drive cancer.

12:15 pm Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own


1:15 Chairperson's Remarks

Scott M. Kahn, Ph.D., Adjunct Associate Research Scientist, Department of Urology; Member, Herbert Irving Comprehensive Cancer Center, Columbia University; Chairman, Biomarkers Council, International Cancer Advocacy Network (ICAN)

1:20 Clinical Next-Generation Sequencing: From Genomic Data to Clinical Action

Seth D. Crosby, M.D., Director, Alliances and Partnerships, Department of Genetics, Washington University School of Medicine

Genomics and Pathology Services at Washington University develops and clinically validates NGS tests that deliver actionable information for patient care. We describe our experience reporting somatic mutations across 40 actionable cancer genes in a reimbursed test, highlighting our use of the custom developed Clinical Genomicist Workstation for rapid analysis and interpretation of clinical genomic data to guide treatment decisions in oncology as well as cardiac, renal, and other constitutional disease.

1:50 Cancer Pharmacogenomic Testing, Clinician Adoption and Patient Benefit

Lynn Dressler, Ph.D., Director, Personalized Medicine, Fullerton Genetics Center, Mission Health

Cancer pharmacogenomics (caPGx) evaluates the genomic profiles of individuals and their tumors to predict response to treatment, including the potential to select which treatment or dose may be more effective with the least adverse side effects. Understanding the factors that influence clinician adoption of caPGx tests is important to promote timely and equitable patient benefit.

2:20 The Promise and Challenges of Personalized Medicine in Cancer Drug Development: An Industry Perspective

Joseph Pearlberg, M.D., Ph.D., Senior Medical Director, Oncology, Sanofi

This talk will highlight not only the promise of clinical genomics and personalized medicine in cancer drug development but will also highlight the challenges, such as ability to obtain biopsy material for analysis (especially repeat biopsies), tumor heterogeneity, assay robustness and availability, cost, privacy, and development of resistance. For each challenge a proposed path forward will be articulated.

2:50 Sponsored Presentations (Opportunities Available)

3:20 Refreshment Break with Exhibit and Poster Viewing


4:00 Return of Sequencing Results to Physicians & Patients

Cinnamon S. Bloss, Ph.D., Director, Social Sciences & Bioethics, Assistant Professor, Scripps Translational Science Institute

There has been considerable debate in the scientific and clinical communities regarding the return of genetic findings from clinical genome sequencing to patients. Questions surrounding which health care professional(s) should deliver this information, as well as what types of results should be returned loom large. Empirical data on patient and provider preferences for results, as well as perceptions of the return-of-results communication itself can inform this debate and will be presented.

Delivering Genomic Information to Patients: Harmful or Helpful?

with Dr. Cinnamon Bloss

4:30 The Patient Perspective

Kim Ryan, Director, Patient Information Services, Fight Colorectal Cancer

"Personalized Medicine" means different things to different patients. Understanding the role that gene expression can play in the choices of a patient's cancer treatment options is important. What do patients know about this? How will it affect their treatment choices? Gain a better understanding of how patients think, and how patients process information. Their understanding of test results and how to interpret them is crucial.

5:00 Close of Conference

Day 1 | Day 2

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