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


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Tuesday, February 11

7:00 am Registration and Morning Coffee

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

9:15 Refreshment Break in the Exhibit Hall with Poster Viewing


10:25 Chairperson’s Remarks

Martin Siaw, Ph.D., Associate Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute 

10:30 NGS-Based Clinical Assays: Building Castles in the Air

Jamie L. Platt, Ph.D., Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute

While applying NGS in the clinical setting may seem like “building castles in the air” to some, the utility of NGS assays can be enormous when built on a strong foundation. The foundation of sample prep will readily prove the validity of “garbage in, garbage out”. Examples of sample prep issues from commercially available NGS tests will be introduced.

11:00 Optimized Sample Handling and Target Enrichment Strategies for Challenging Clinical Samples

Bill Biggs, Ph.D., Director, Clinical Sequencing, Broad Institute of MIT and Harvard

The desire to access valuable clinical FFPE samples using advanced molecular techniques such as next-generation sequencing methods in an efficient and productive manner represents an ongoing challenge for most clinical laboratories. At the Clinical Research Sequencing Platform (CRSP) within the Broad Institute methods have been developed, optimized and implemented which allow for the ready and routine access of FFPE samples for such NGS-based analyses as Whole Exome Sequencing and Targeted Re-sequencing. These processes and methods allow for exceptional data to be obtained from even the most challenging of FFPE samples where low yield (≤ 100ng) or age (> 5 yrs) can confound analytical processes.

11:30 Automation of Sample Preparation for Clinical NGS: The Requirements and the Challenges Presented by the Various Clinical Sample Types

Martin Siaw, Ph.D., Staff Scientist and Associate Director, Advanced Sequencing Core, Advanced Sequencing, Quest Diagnostics Nichols Institute

Sample preparation is an important component of any molecular testing that is being done in clinical laboratories. With the increasing use of NGS for clinical testing comes the need to process increasingly larger numbers of patient samples. Automation of sample preparation should be considered to be critical to the workflow of diagnostic tests involving the use of NGS. My presentation will focus on the requirements and challenges for CLIA-certified clinical laboratories.

12:00 pm Better Annotation Needed at Various Points in the Sequencing Process to Avoid Reporting Errors due to Pseudogenes and High Repeat Genomic Regions

Patricia Mueller, Ph.D., Chief, Molecular Risk Assessment Laboratory, Newborn Screening and Molecular Biology Branch, DLS, Centers for Disease Control and Prevention (CDC)

Outside of clinical genomic sequencing centers, there is a general lack of awareness of the problems in NGS caused by the large number of pseudogenes in the human genome. Current estimates exceed 19,000 pseudogenes. Current standard enrichment methods do not reliably distinguish between highly homologous functional and pseudogenes. Better annotation is needed at different points in the sequencing process, including reference sequences, hybrid-capture arrays, PCR primer design software, and data-analysis software to help those designing tests and analyzing data to avoid reporting errors.

12:30 Session Break

12:40 Luncheon Presentation I: Seven Steps to the Sample Life: Best Practices for Clinical Trial Sample Management

Mark. A Collins, Ph.D, Director, Marketing, BioFortis, Inc.

The increased interest in biomarker-based studies necessitates a new rigor and sophistication in sample and sample related data management within the clinical trial context. In addition many trials occur across geographies, are increasingly externalized with multiple stakeholders and generate large amounts of data, which is putting existing software systems, infrastructures and processes under considerable pressure. Using case studies, attendees will learn emerging best practices for clinical trial sample and data management.

1:10 Luncheon Presentation II

(Sponsorship Opportunity Available)

1:40 Refreshment Break in the Exhibit Hall with Poster Viewing


2:15 Chairperson’s Remarks
Dave Anstey, Global Head, Life Sciences, YarcData 

2:20 Implementing Big Data Analysis and Archival Solutions for NGS Data

Zhiyan Fu, Ph.D., Chief Scientific Computing Officer, Genome Institute of Singapore (A*STAR)

This presentation shows the latest development in big data analysis, compression and storage management. It provides a practical case to implement the big data technologies to a mid-size genome center. Attendees will understand the challenges of big data life-cycle management in a genome center and see how the latest big data technologies are implemented, and the pros and cons of some of the techniques, including Hadoop, HDF5, and different NGS compression algorithms evaluated by GIS.

2:50 Annotation of a Massive Dataset of Whole Genome Sequences Using a Hybrid Approach

Gerry Higgins, M.D., Ph.D., Vice President, Pharmacogenomic Science, AssureRx Health, Inc.

A collection of 17,131 whole genome sequences generated by 2nd generation sequencing using Illumina, Complete Genomics, Inc. and SOliD have been analyzed using a hybrid approach. Annotation was performed using comparative genomics modeling; sequence context; functional predictions using bioinformatics tools; epigenomic alterations; gene modeling; coding disruptions; and a supervised learning machine trained on surrogate phenotypes. Using a hybrid annotation approach lead to the discovery of novel pharmacogenomic variants that could be of value for clinical pharmacogenomics.

3:20 Semantic Technologies Offer Great Promise – with Constraints. We will Discuss a New Approach for Accelerating Research: Graph Analytics at Scale

Dave Anstey, Global Head, Life Sciences, YarcData

Our platform for real-time data discovery is enabling leading research hospitals and life sciences organizations to analyze ALL their diverse data sets together, without sampling to rapidly validate more hypotheses, identify unknown relationships and get more value from their data.

3:50 Speaker to be Announced

4:20 Valentine’s Day Celebration in the Exhibit Hall with Poster Viewing

5:20 Breakout Discussions in the Exhibit Hall

These interactive discussion groups are open to all attendees, speakers, sponsors, & exhibitors. Participants choose a specific breakout discussion group to join. Each group has a moderator to ensure focused discussions around key issues within the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not meant to be a corporate or specific product discussion.

The Future of Prenatal Genomic Testing

Christopher Robinson, M.D., MSCR, Associate Professor, Maternal Fetal Medicine, Obstetrics and Gynecology, University of Virginia 

•Transitioning from high risk patients to global screening with NIPT
•Is there potential for NIPT to achieve diagnostic capability in prenatal testing?
•Cost effectiveness and outcomes following implementation of NIPT

Extracting Biological Information from WGS/WES

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

•Searching for pearls in rough seas: Finding cancer genome sequence variants with predictable clinical impact.
•Imagining cancer biology: In silico prediction and modeling of the biological impact of cancer genome variants.
•Quo vadis cancer genome: What's next in the analysis of cancer genomes?

6:30 Close of Day

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