Agenda - Genome-wide Partnering & Deal-making

For an additional $495 industry or $295 academic, you can register for the pre-summit workshop:
Clinical Sequencing Workshop

Clinical Sequencing Workshop - May 29th, 2012 Moderator: Gary Schroth, Senior Director, Expression Application R&D, Illumina

12:00	Registration

12:55	Welcome & Opening Remarks

1:00	Emerging Next-Generation Sequencing Technologies and its Clinical Applications
	Thomas Scholl, Vice President, Research & Development, Integrated Genetics / LabCorp
	Next-generation sequencing is undergoing accelerating translation into the clinical realm. Several clinical diagnostic tests are available that employ next-generation sequencing and many companies/laboratories have announced launch dates and development plans for additional tests. Some of these products afford improvements on existing themes by harnessing the capacity of next-generation sequencers to increase clinical sensitivity by analyzing disease loci more comprehensively than previously possible. Other products exploit unique characteristics of next-generation sequencing methods to enable entirely new diagnostic assays. An overview of these product categories focusing upon product profiles and technical underpinnings will be presented.
1:30	The Implementation of Next-Generation Sequencing in a CLIA Laboratory - Issues and Challenges
	Matthew Ferber, Assistant Professor of Laboratory Medicine & Pathology, Mayo Clinic
	Recently there has been much discussion regarding how “massively parallel” or “Next Generation” DNA sequencing (NGS) will impact clinical care. While the technology promises to reduce the cost of sequencing an entire human genome to less than $1,000, one must question the diagnostic utility of complete genome sequencing for routine clinical testing, given the many interpretive challenges posed by this approach. In this presentation we will discuss the promise and pitfalls associated with the clinical application of NGS.

2:00	Afternoon Break

2:30	Translation of Next-Gen Sequencing from Research Applications to a Standardized Lab Developed Test in a CLIA Environment
	Andrew Grupe, Senior Director, Pharmacogenomics, Celera
	Next generation sequencing (NGS) has transformed the research sequencing landscape. These technologies have enabled a plethora of new discoveries by allowing us to answer questions more cost-effectively than in past and ask questions that were impossible to address by capillary electrophoresis sequencing or high density chip platforms. Translating NGS applications from a research environment to a standardized test offering in a clinical reference laboratory presents multiple challenges. These range from identifying NGS tests that provide clinical value beyond existing tests on traditional platforms, increased needs for a bioinformatics infrastructure to interpret and report results, genome sequence versioning and subscription access to permit revisiting a prior sequence because of the identification of new indications, to consequences of updates to the technology hardware and software as well as reagents of the rapidly changing NGS field. Changes in the regulatory landscape that may impact the use of these technologies are also being contemplated. This presentation will offer a users perspective of these issues.

3:00	Measuring and Ensuring Quality in NGS
	Tina Hambuch, Scientific Liaison, Clinical and Professional Services, Illumina
	Genetic testing for clinical applications requires many components, such as physician and patient support, informed consent, secure data management, and many others. One of the most critical is an understanding of the analytical quality of the data that is being used to make clinical interpretations. As we move to an era of genomic testing, the importance of analytical validity increases because of the substantially increased potential for what can be learned from the same data. Illumina Clinical Services Laboratory has been performing whole genome sequencing in a CLIA certified, CAP accredited setting for nearly three years. This clinical test provides a comprehensive catalogue of variation across the genome, yielding >90% of the NCBI reportable reference genome and representing >96% of the exome. The quality of the calls is measured and monitored using a variety of metrics. Additionally, every genome is also analyzed on the Human 1M duo array, which genotypes over 1 million variants distributed across the genome, and the concordance to the sequencing results are compared. We have compared the sequence data from multiple genomes, so that we are able to characterize regions and loci of particularly high quality as well as flag what may be unreliable. The quantitative nature of Next Generation Sequencing technologies allows us to evaluate the accuracy, sensitivity and specificity at the single base pair level, thus we report on the quality of every base that is called. As the scope of NGS applications expands in the clinical setting, robust and ongoing evaluations of quality are critical to ensure that NGS will realize its potential for improving patient care.

3:30	[Interactive Q&A Panel]

4:00	Workshop Concludes


Day 1	Day 2

Day 1 - Wednesday, May 30th, 2012

8:00

Registration