2014 Archived Content

Cambridge Healthtech Institute’s Eleventh Annual

Clinical Sequencing

Translating NGS to Practice

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


Day 1 | Day 2 | Day 3 | Download Brochure 

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


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.   


12:20 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


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 Diffuse Large B-Cell Lymphoma

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


 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 Health
NextCODE 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  


4:00 Chairperson’s Remarks

Gabe Rudy, Vice President, Product Development, Golden Helix

4:05 CLIA-Certified Cancer Genome Diagnostic Testing in a Rapidly Changing Environment

David Wheeler, Ph.D., Co-Director, Bioinformatics; Associate Professor, Department of Molecular and Human Genetics, Baylor College of Medicine

A CLIA lab seeks reproducibility and stability in the assays performed. However, the rapidly accumulation of novel and exciting cancer genome discoveries is expanding our view of the genetic landscape of cancer and impacting how diagnostic testing can be performed. Here I will discuss analytical and biological advances that are changing the way we think about diagnostic services, and how we are integrating them into the CLIA lab.

4:35 Implementation of Next-Generation Sequencing in the Clinical Molecular Oncology Laboratory

Eric Duncavage, M.D., Assistant Professor; Director, Molecular Genetic Pathology Training Program, Department of Pathology and Immunology, Division of Clinical and Genomic Medicine, Washington University

This talk will focus on the design, informatics, and validation of clinical grade NGS-based oncology testing based on experience in the Washington University Genomics and Pathology Services Laboratory. Design considerations including enrichment methods and selecting the best genes for an oncology panel will be discussed and an evaluation of clinical-grade variant analysis tools will be provided. Finally, NGS validation practices, regulatory guidelines, and reimbursement issues will be reviewed.

5:05 Interpreting My DTC Exomes Using Public Access Clinical Databases

Gabe Rudy, Vice President, Product Development, Golden Helix

23andMe provided through a limited pilot the delivery of uninterpreted exomes in 2012. In this talk, I use GenomeBrowse and publicly available clinical databases such as ClinVar and OMIM, as well as many other integrative genomic annotations, to interpret the exomes of myself, wife and son. Recent improvements in alignment, variant calling and public annotation sources may be able to take my research grade exome to a clinical grade interpretation.

5:35 Close of Conference Program

Day 1 | Day 2 | Day 3 | Download Brochure 

Japan-Flag Korea-Flag China-Simplified-Flag China-Traditional-Flag  

Premier Sponsors

Beckman Coulter Life Sciences 

Boston Healthcare



Charles River no tagline


Cofactor Genonics


Menarini Silicon Biosystems






View All Sponsors