2014 Archived Content

Cambridge Healthtech Institute’s Fifth Annual

Personalized Diagnostics

Best Practices for Clinical Implementation

February 10-12, 2014 | Moscone North Convention Center | San Francisco, CA  

 

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Wednesday, February 12 

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee 


8:00 Plenary Keynote Session (Click Here For More Details) 

9:45 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall 


DIFFERENT APPROACHES TO DIAGNOSING USING NGS 

10:35 Chairperson's Remarks 

Karl Voelkerding, M.D., Associate Professor, Pathology, University of Utah; Medical Director, Advanced Technology & Bioinformatics, ARUP Laboratories

10:40 Use of Exome Sequencing for Genetic Diagnosis: Clinical Experience and Case Examples 

Wayne W. Grody, M.D., Ph.D., Professor, Medical Genetics and Molecular Pathology, Pathology & Lab Medicine, Pediatrics, and Human Genetics; Director, Molecular Diagnostic Laboratories and Clinical Genomics Center, UCLA School of Medicine

The advent of massively parallel or next-generation DNA sequencing has finally brought into reach the long-anticipated "Thousand Dollar Genome", or the ability to sequence an individual's entire genome at reasonable cost. This presentation will review such aspects as clinical utility, challenges in test interpretation and genetic counseling, return of incidental findings and reimbursement, all within the context of our own experience performing clinical whole-exome sequencing at an academic medical center.

11:10 The Art of Interpreting and Reporting Results from a Multi-Gene, NGS-Based Panel for Solid Tumor Mutation Testing 

Allie Grossmann, M.D., Ph.D., Staff Pathologist, Surgical Pathology and Oncology, ARUP Laboratories

With the advent of clinical testing of tumors with NGS technology, the breadth of sequence coverage has expanded beyond the scope of well-characterized mutations. This presents a challenge to both interpreting variants and to meeting reasonable clinical turn-around times for reporting. These challenges will be discussed within the context of clinical case examples with an emphasis on "lessons learned" in the adoption of NGS for solid tumor mutation testing.

11:40 Providing More Comprehensive Genetic Diagnostics by Next-Generation Sequencing-Based Multi-Gene Panels 

Karl Voelkerding, M.D., Associate Professor, Pathology, University of Utah; Medical Director, Advanced Technology & Bioinformatics, ARUP Laboratories

For many genetic disorders, heterogeneity is the rule and NGS has provided a new avenue by which to overcome the limitations of Sanger sequencing-based diagnostic approaches. This presentation will highlight how NGS is transforming the diagnostic evaluation of genetic disorders through more comprehensive multi-gene panel-based methods. Technical options and bioinformatics considerations will be discussed along with how Sanger sequencing and NGS are being used in an integrative fashion.

 12:10 pm Pertinence Metric Enables Hypothesis-Independent Genome-Phenome Analysis in Seconds 
Michael M. Segal, M.D., Ph.D., Chief Scientist, SimulConsult 
Genome-phenome analysis uses a genomic variant table and compares patient’s findings to those of known diseases (“phenome”).  Accuracy was 100% with trios with family-aware calling, and close to that with only probands.  The gene pertinence metric calculated in the analysis was 99.9% for the causal genes, and the analysis took seconds and was hypothesis-independent. 

12:25 Luncheon Presentation: Sequencer-Ready Target Enrichment for Clinical Next Generation Sequencing: A Massively Parallel Singleplex PCR Approach

Xun Xu, Ph.D., Deputy Director, BGI Research, WaferGen BioSystems

Advances in NGS technology have resulted in dramatic improvements in sequencing throughput and turnaround time, yet a critical bottle neck in NGS workflows exists at the library preparation stage. We present a technology that dramatically reduces process time by generating sequencer-ready amplicon libraries in a single step. This coupled with the ability to simultaneously process multiple samples enables a high fidelity, scalable and cost effective high throughput solution for NGS targeted resequencing.

1:00 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing 


INSIGHTS INTO BIOLOGY OF CANCER FROM NGS 

1:40 Chairperson's Remarks 

German Pihan, M.D., Director, Hematopathology Lab, Pathology, Beth Israel Deaconess Medical Center & Harvard Medical School

1:45 The Spectrum of Mutations and Mutated Cancer Genes Across Many Tumor Types 

Michael Lawrence, Ph.D., Computational Biologist, Cancer Genome Computational Analysis, Broad Institute of MIT and Harvard University

Comprehensive knowledge of the genes underlying human cancers is a critical foundation for cancer diagnostics, therapeutics, clinical trial design and selection of rational combination therapies. While some cancer genes are mutated at very high frequency (20% of patients), the vast majority are found at intermediate frequencies (2-20%) and sometimes even lower frequencies.

2:15 The Evolving Genome of Glioblastoma 

Siyuan Zheng, Ph.D., Postdoctoral Fellow, Bioinformatics & Computational Biology, MD Anderson Cancer Center, University of Texas

Glioblastoma (GBM) rates amongst the most deadly of adult tumors. We have performed extensive genomic profiling to characterize the landscape of somatic alterations of GBM. Analysis of matched pre- and post-treatment GBM showed that the GBM genome evolves under the selective pressures from cytotoxic therapy and cytoreductive surgery. We provide new insights into the heterogeneity of this disease, and the factors contributing to it.

2:45 Mutational Heterogeneity and Evolution in Diffuse Large B-Cell Lymphoma 

Ryan D. Morin, Ph.D., Assistant Professor, Bioinformatics, Molecular Biology and Biochemistry, Simon Fraser University

Diffuse large B-cell lymphoma is the most common aggressive non-Hodgkin lymphoma. Whole genome and transcriptome sequencing in this tumor type has uncovered a plethora of common mutation targets and a long tail of infrequently mutated genes with potential relevance. We have also computationally dissected individual DLBCL tumors to identify multiple sub clones and evidence for ongoing acquisition of driver mutations in this disease. 

3:15 Clinician-Friendly Tools and Efficient Database Architecture to Accelerate Genetic Diagnoses of Challenging Patients
Jeff Gulcher, M.D., Ph.D.,President, CSO, NextCODE HealthNextCODE offers informatics systems originally developed at deCODE Geneticsalong with a curated knowledge base for end-to-end analysis of whole exome and whole genome data for patients, families, and large cohorts.  Clinical Sequence Analyzer (CSA) is a clinician-friendly web-based interface for sequence-based diagnostics. NextCODE‘s GOR database infrastructure allows for more efficient storage,  query, and display of large scale sequence and coverage data.  Our de novo mutation detector improves accuracy of de novo mutation calls.        

3:45 Refreshment Break 


EVALUATING CANCER MOLECULAR MARKERS 

4:00 Chairperson's Remarks 

Daniel W. Chan, Ph.D., DABCC, FACB, Professor, Pathology, Oncology, Radiology and Urology; Director, Center for Biomarker Discovery and Translation & Clinical Chemistry, Johns Hopkins University


4:05 KEYNOTE PRESENTATION:

Key to Success in Translating Cancer Biomarkers to the Clinical Laboratory 

Daniel W. Chan, Ph.D., DABCC, FACB, Professor, Pathology, Oncology, Radiology and Urology; Director, Center for Biomarker Discovery and Translation & Clinical Chemistry, Johns Hopkins University

Specific examples will be shown to demonstrate the opportunities and challenges for the development of clinical proteomic diagnostics. The successful translation of these biomarkers into clinical practice will require close collaboration between researcher, industry, regulatory agency and clinician.


4:35 Advanced Machine Learning Techniques Reveal Molecular Correlates of Tumor Histopathology in GBM and Low Grade Glioma 

Bahram Parvin, Ph.D., Principal Scientist, Life Sciences, Lawrence Berkeley National Laboratory

The case study includes Glioblastoma Multiform from The Cancer Genome Atlas (TCGA), where four subtypes were identified from computed morphometric indices, and a subset of these subtypes are shown to be predictive of the outcome. In each case, molecular correlates are able to provide hypotheses for therapeutic targeting.

5:05 Clinical Evaluation of Exosomes as Oncology Biomarkers 

Shidong Jia, Ph.D., Scientist, Oncology Biomarker Development, Genentech, Inc.

Dr. Jia's lab has developed working procedures to evaluate exosomal RNA signature as novel biomarkers for cancer prognosis, prediction and patient stratification. In particular, their work has refreshed current practice and demonstrated a new approach for studying RNA signature in patient blood samples.

5:35 Close of Conference Program 



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2015 MMTC Final Agenda 

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