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May 20-23, 2012 -
May 20-23, 2012
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TIDES: Oligonucleotide and Peptide® Research, Technology and Product Development
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Nucleic Acids Technologies for Molecular Diagnostics
- Agenda overview: Go to the agenda overview to view the detailed agenda for each day, topic or course.
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Nucleic Acids Technologies for Molecular Diagnostics
Accelerating Product Development through Cutting Edge Regulatory, Business and Technology Strategies
Courses: Sunday | Plenary Sessions: Monday | Main Conference: Tuesday | Wednesday
8:30
Chairperson's Remarks
Sam Rua, VP, Regulatory Affairs and Quality Systems, HTG Molecular Diagnostics, Inc.
Sam Rua, VP, Regulatory Affairs and Quality Systems, HTG Molecular Diagnostics, Inc.
Regulatory Pathways and Quality Strategies
Keynote Presentation
8:45
Update on Commercialization of RUO and IUO Products and Oversight of Lab-Developed TestsThe US FDA has released a number of guidance documents regarding commercialization of Research Use Only (RUO) and Investigational Use Only (IUO) products, and companion diagnostics. It is also their intent to release their framework for Laboratory-developed tests (LDTs) in 2012. This session will provide an update on the guidance documents and communicated FDA perspective regarding oversight of molecular tests and any additional updates.
Sam Rua, VP, Regulatory Affairs and Quality Systems, HTG Molecular Diagnostics, Inc.
Featured Presentation
9:15
Regulatory Considerations: Partnering for Success in Companion Device Product Development
Karen Swatkowski, Director of Regulatory Affairs, Abbott Molecular
Karen Swatkowski, Director of Regulatory Affairs, Abbott Molecular
10:00
Case
Study
Co-Development of a Companion Diagnostic for a Targeted BRAF Kinase InhibitorStudy
The approval of vemurafenib, a first-in-class inhibitor of oncogenic BRAF kinase, and its companion diagnostic, the cobas® 4800 BRAF V600 Mutation Test, represents a successful collaboration between drug and diagnostic development teams. This integrated process resulted in the first personalized medicine for treatment of metastatic melanoma within 5 years of the IND filing, a remarkably short time.
Suzanne Cheng, Ph.D., Director, Research, Genomics and Oncology, Roche Molecular Systems, Inc.
10:30
Networking Refreshment Break in Poster and Exhibit Hall
11:15
Regulatory Challenges and Strategies for Molecular Diagnostics
The attendee will learn how to navigate FDA's evolving regulatory requirements to successfully achieve market approval or clearance for novel molecular technologies. FDA's current thinking on highly multiplexed tests and next generation sequencing technologies will be discussed as well as future changes to EU regulation of IVDs.
Bradford M. Spring, Director of Regulatory Affairs, BD Diagnostics
The attendee will learn how to navigate FDA's evolving regulatory requirements to successfully achieve market approval or clearance for novel molecular technologies. FDA's current thinking on highly multiplexed tests and next generation sequencing technologies will be discussed as well as future changes to EU regulation of IVDs.
Bradford M. Spring, Director of Regulatory Affairs, BD Diagnostics
11:45
The Regulatory Evolution of Genetic Research
With the rapid advancement of genetic testing, research and diagnostics, how do we allow research progression without additional regulatory burden and restriction while still protecting human subjects involved in research? By examining closely 3 timely events, such as the Havasupai Tribe Incident, the Newborn Blood Spot Testing case in Texas and the Henrietta Lacks case, we can see what preventative measures can be taken to promote advancement of genetic research without losing public trust.
Bertha D. deLanda, CIP, IRB Training Specialist, Research Compliance Office, Stanford University
With the rapid advancement of genetic testing, research and diagnostics, how do we allow research progression without additional regulatory burden and restriction while still protecting human subjects involved in research? By examining closely 3 timely events, such as the Havasupai Tribe Incident, the Newborn Blood Spot Testing case in Texas and the Henrietta Lacks case, we can see what preventative measures can be taken to promote advancement of genetic research without losing public trust.
Bertha D. deLanda, CIP, IRB Training Specialist, Research Compliance Office, Stanford University
Audience Interactive Panel Discussion
12:15
Regulatory Support of Innovation: How to Balance FDA's Public Health Charter and Access to Novel Technologies
Moderator:
B. Melina Cimler, Ph.D., Vice President, Quality and Regulatory Affairs, Illumina, Inc.
Panelists: Morning Speakers
Moderator:
B. Melina Cimler, Ph.D., Vice President, Quality and Regulatory Affairs, Illumina, Inc.
Panelists: Morning Speakers
12:45
Networking Luncheon in Poster and Exhibit Hall
Sponsored by
Analytical Methods and Validation
1:50
Chairperson's Remarks
TBA
TBA
2:00
Utility of Ultra HPLC in Oligonucleotide Analysis
A rapid RP Ultra HPLC analytical method using the ACQUITY OST column was developed for the analyses of oligonucleotides. The result was compared against a 30 minute AE HPLC method. The comparison study shows that the RP method is comparable with the conventional AE analysis. Statistical results will be presented.
Robert S. Wu, Ph.D., Principal Scientist, Roche Molecular Systems
Co-authors:, Shu Huang, Roche Molecular Systems, Daniel Fletcher, Roche Molecular Systems, Jeff Cicchino, Roche Molecular Systems, Wen-Jian Fung, Roche Molecular Systems, Concordio Anacleto, Roche Molecular Systems, Nancy Schoenbrunner, Roche Molecular Systems, Dennis Brown, Roche Molecular Systems
A rapid RP Ultra HPLC analytical method using the ACQUITY OST column was developed for the analyses of oligonucleotides. The result was compared against a 30 minute AE HPLC method. The comparison study shows that the RP method is comparable with the conventional AE analysis. Statistical results will be presented.
Robert S. Wu, Ph.D., Principal Scientist, Roche Molecular Systems
Co-authors:, Shu Huang, Roche Molecular Systems, Daniel Fletcher, Roche Molecular Systems, Jeff Cicchino, Roche Molecular Systems, Wen-Jian Fung, Roche Molecular Systems, Concordio Anacleto, Roche Molecular Systems, Nancy Schoenbrunner, Roche Molecular Systems, Dennis Brown, Roche Molecular Systems
2:30
Strategies and Methodologies for Analysis of Oligonucleotides at Various Scales at Merck
siRNA as a proven tool for gene regulation holds great therapeutic potential. Great efforts and progress have been made at Merck on oligonucleotide chemistry as well as in formulation development. Analytical characterizations of oligonucleotide at different scales have been developed to support drug development process. This presentation focuses on strategies and methodologies for oligonucleotide analysis developed at Merck, including various purity analytical methods for different stages of siRNA drug development process.
Huimin Yuan, Senior Investigator, Process Chemistry, Merck & Co., Inc.
siRNA as a proven tool for gene regulation holds great therapeutic potential. Great efforts and progress have been made at Merck on oligonucleotide chemistry as well as in formulation development. Analytical characterizations of oligonucleotide at different scales have been developed to support drug development process. This presentation focuses on strategies and methodologies for oligonucleotide analysis developed at Merck, including various purity analytical methods for different stages of siRNA drug development process.
Huimin Yuan, Senior Investigator, Process Chemistry, Merck & Co., Inc.
3:00
Fully Automated KRAS Assay on Rheonix CARD - From FFPE Tissue to Gene Variants without User Intervention
The Rheonix CARD® molecular diagnostic platform allows fully automated "sample-to-results" molecular analysis of a variety of clinical specimens, including FFPE. Without any user intervention, FFPE samples can be processed through deparaffinization, extraction, PCR of DNA and detection of KRAS markers, even when the tumor DNA represents as little as 0.01% of the total DNA in the sample.
Richard A. Montagna, Ph.D., Senior Vice President for Corporate Business Development, Rheonix, Inc.
The Rheonix CARD® molecular diagnostic platform allows fully automated "sample-to-results" molecular analysis of a variety of clinical specimens, including FFPE. Without any user intervention, FFPE samples can be processed through deparaffinization, extraction, PCR of DNA and detection of KRAS markers, even when the tumor DNA represents as little as 0.01% of the total DNA in the sample.
Richard A. Montagna, Ph.D., Senior Vice President for Corporate Business Development, Rheonix, Inc.
3:30
Networking Refreshment Break in Poster and Exhibit Hall
4:00
Ion Mobility and Tandem Mass Spectrometry for the Identification of Branched Oligonucleotide Sequence and Purity
Branched oligonucleotides offer new opportunities for applications in drug therapy or drug delivery. While conventional methods, such as PAGE or HPLC, can be used to assess full-length products, they fail to completely characterize branching junctions and lack the ability to define synthesis side-products. In this presentation, methods developed for the LC-MS/MS and LC-IMS-MS characterization of branched oligonucleotides will be discussed.
Patrick A. Limbach, Ph.D., Professor, Chemistry, University of Cincinnati
Branched oligonucleotides offer new opportunities for applications in drug therapy or drug delivery. While conventional methods, such as PAGE or HPLC, can be used to assess full-length products, they fail to completely characterize branching junctions and lack the ability to define synthesis side-products. In this presentation, methods developed for the LC-MS/MS and LC-IMS-MS characterization of branched oligonucleotides will be discussed.
Patrick A. Limbach, Ph.D., Professor, Chemistry, University of Cincinnati
4:30
Fully Automated Nucleic Acid Isolation from Formalin-Fixed Paraffin-Embedded Tissue - A Step Forward in Standardizing Molecular Pathology
Siemens has recently launched the Tissue Preparation System, the first fully automated IVD system for the isolation of both RNA and DNA from FFPE tissues. It uses silica-coated nano-particles and provides full automation including deparaffinization and lysis. Data will be presented demonstrating the robustness, reproducibility, and flexibility in research and routine molecular applications including sequencing, genotyping, and expression profiling analysis.
Guido Hennig, Ph.D., Senior Global Scientific Affairs Manager, Molecular Diagnostics, Siemens Healthcare Diagnostics, Germany
Siemens has recently launched the Tissue Preparation System, the first fully automated IVD system for the isolation of both RNA and DNA from FFPE tissues. It uses silica-coated nano-particles and provides full automation including deparaffinization and lysis. Data will be presented demonstrating the robustness, reproducibility, and flexibility in research and routine molecular applications including sequencing, genotyping, and expression profiling analysis.
Guido Hennig, Ph.D., Senior Global Scientific Affairs Manager, Molecular Diagnostics, Siemens Healthcare Diagnostics, Germany
5:00
Democratizing Sequencing
Ion Torrent Semiconductor Sequencing™ delivers DNA sequencing at an unprecedented speed, scalability and low cost. To fully utilize the advantages of Ion sequencing new library creation methods have been invented. One such method, Ion AmpliSeq™, is a simple, efficient and rapid process for enriching hundreds to thousands of genomic targets for Ion sequencing from as little as 10 ng of FFPE or genomic DNA. The flexible nature of this technology scales to meet the demands of both basic and translational research.
John H. Leamon, Ph.D., Director, Technology Innovation, Molecular Biology, Ion Torrent Systems
Ion Torrent Semiconductor Sequencing™ delivers DNA sequencing at an unprecedented speed, scalability and low cost. To fully utilize the advantages of Ion sequencing new library creation methods have been invented. One such method, Ion AmpliSeq™, is a simple, efficient and rapid process for enriching hundreds to thousands of genomic targets for Ion sequencing from as little as 10 ng of FFPE or genomic DNA. The flexible nature of this technology scales to meet the demands of both basic and translational research.
John H. Leamon, Ph.D., Director, Technology Innovation, Molecular Biology, Ion Torrent Systems
5:30
Networking Reception and Booth Crawl in Poster and Exhibit Hall with Dedicated Poster Viewing
Poster presenters are requested to be available at their posters
Poster presenters are requested to be available at their posters
Courses: Sunday | Plenary Sessions: Monday | Main Conference: Tuesday | Wednesday
Manufacturing and Business Considerations for Successful Launch in Clinical Market
8:30
Chairperson's Remarks
Dick Keys, Ph.D., President, Advanced Biotectonics
Dick Keys, Ph.D., President, Advanced Biotectonics
Keynote Presentation
8:45
The Next Generation in Clinical Molecular DiagnosticsDNA sequencing has become a disruptive technology. Next generation sequencing (NGS) will be the dominant molecular technology in the molecular market within ten years and will radically impact many market segments. This presentation will discuss the major challenges for molecular diagnostics in moving NGS into clinical laboratories and predict how a resulting virtual Dx world with NGS as the major technology might look.
Trevor Hawkins, Ph.D., CEO, Next Generation Diagnostics, Siemens Healthcare Diagnostics
9:30
Preparing for Launch of a Gene Scanning Solutions Platform in an Industry-leading Imaging Company: Business and Technical Considerations
Canon U.S. Life Sciences is developing systems to meet the need for rapid, flexible assay of increasingly complex human genetic targets. Results from our prototype, microfluidic platform capable of both gene scanning and genotyping, will be presented. The challenge of launching in a market currently dominated by laboratory developed tests, but about to undergo rapid change, will also be addressed. .
Ivor Knight, Ph.D., Senior VP and CTO, Canon U.S. Life Sciences, Inc.
Canon U.S. Life Sciences is developing systems to meet the need for rapid, flexible assay of increasingly complex human genetic targets. Results from our prototype, microfluidic platform capable of both gene scanning and genotyping, will be presented. The challenge of launching in a market currently dominated by laboratory developed tests, but about to undergo rapid change, will also be addressed. .
Ivor Knight, Ph.D., Senior VP and CTO, Canon U.S. Life Sciences, Inc.
10:00
Intellectual Property Challenges in the Diagnostics Industry
Diagnostics, especially sophisticated gene profiling as well as highly sensitive mutation detection technologies, have come under significant pressure as to what U.S. law now permits as patentable (witness the Myriad case) as well as how U.S. courts treat these technologies in the court room. Is there a new paradigm for protection of diagnostics, for example, where a disease is indicated by combined higher and lower levels of a group of thousands of genes, or do the old rules that applied to detection of a single marker still apply? What will companies involved in diagnostics be challenged under U.S. laws governing intellectual property?
Elizabeth N. Spar, Ph.D., J.D., Intellectual Property Strategist, Edwards Wildman Palmer LLP
Diagnostics, especially sophisticated gene profiling as well as highly sensitive mutation detection technologies, have come under significant pressure as to what U.S. law now permits as patentable (witness the Myriad case) as well as how U.S. courts treat these technologies in the court room. Is there a new paradigm for protection of diagnostics, for example, where a disease is indicated by combined higher and lower levels of a group of thousands of genes, or do the old rules that applied to detection of a single marker still apply? What will companies involved in diagnostics be challenged under U.S. laws governing intellectual property?
Elizabeth N. Spar, Ph.D., J.D., Intellectual Property Strategist, Edwards Wildman Palmer LLP
10:30
Networking Refreshment Break in Poster and Exhibit Hall
11:00
Requirements for Successful Integration of Regulatory Submission Planning and Product Assurance into the Business Strategy for FDA Regulated Products
Focus of Discussion:
Focus of Discussion:
- Domestic and international regulatory agency intelligence networking to assess current expectations and changing trends including reimbursement schemes
- Implementation of actionable design controls for efficient use of limited resources
- Smart matching of skills and experience for flexible resource deployment with clearly defined organizational responsibilities and authorities
- Effective clinical evaluations and study outcomes based upon marketing claims via established competitive indications for use
- Timely interactive communications with regulatory authorities to enhanceapproval predictability to support business decision-making
Audience Interactive Panel Discussion
11:30
The Oligo Supply Chain for Diagnostics - Getting your Research to the Market
A panel of industry experts will discuss status and approaches used to support commercialization of oligonucleotides in IVDs, including companion diagnostics. Emerging companies face critical decisions when bringing their diagnostic product through development into manufacturing. Whether deciding to make oligos in-house or obtaining these from a contract manufacturer, oligonucleotide supply is critical. Following selection of oligo supplier, additional important choices must be made relative to supply chain management, raw materials, synthesis and purification methods, and analytical methods used for quality control; these can have significant impact on ordering lead time, cost, and reproducibility of the IVD. Planning the oligo strategy for scale-up and process validation to support IVD manufacturing needs careful consideration to ensure regulatory requirements are met. Audience participation is encouraged during this session.
Moderator:
Dick Keys, Ph.D., President, Advanced Biotectonics
Panelists:
Michael Christopherson, Ph.D., Group Leader, Oligonucleotide Manufacturing, Roche Molecular Systems
Chad Gerber, Director of GMP Manufacturing and Commercial Services, Biosearch Technologies, Inc.
Luc Marion, Operations Manager, EGT North America
Catherine M. McKeen, Ph.D., Technical Manager, Link Technologies Ltd., United Kingdom
Roman Terrill, Business Unit Leader, Clinical and Commercial Manufacturing, Integrated DNA Technologies, Inc.
Additional panelists to be announced
A panel of industry experts will discuss status and approaches used to support commercialization of oligonucleotides in IVDs, including companion diagnostics. Emerging companies face critical decisions when bringing their diagnostic product through development into manufacturing. Whether deciding to make oligos in-house or obtaining these from a contract manufacturer, oligonucleotide supply is critical. Following selection of oligo supplier, additional important choices must be made relative to supply chain management, raw materials, synthesis and purification methods, and analytical methods used for quality control; these can have significant impact on ordering lead time, cost, and reproducibility of the IVD. Planning the oligo strategy for scale-up and process validation to support IVD manufacturing needs careful consideration to ensure regulatory requirements are met. Audience participation is encouraged during this session.
Moderator:
Dick Keys, Ph.D., President, Advanced Biotectonics
Panelists:
Michael Christopherson, Ph.D., Group Leader, Oligonucleotide Manufacturing, Roche Molecular Systems
Chad Gerber, Director of GMP Manufacturing and Commercial Services, Biosearch Technologies, Inc.
Luc Marion, Operations Manager, EGT North America
Catherine M. McKeen, Ph.D., Technical Manager, Link Technologies Ltd., United Kingdom
Roman Terrill, Business Unit Leader, Clinical and Commercial Manufacturing, Integrated DNA Technologies, Inc.
Additional panelists to be announced
12:45
Networking Luncheon in Poster and Exhibit Hall
Last Chance for Poster and Exhibit Viewing
Last Chance for Poster and Exhibit Viewing
New Technologies
1:55
Chairperson's Remarks
Thomas Battersby, Ph.D., Senior Manager, Siemens Healthcare Diagnostics
Thomas Battersby, Ph.D., Senior Manager, Siemens Healthcare Diagnostics
2:00
Pathogenica: Rapid Clinical Diagnostic Assays for Next Generation Sequencing Platforms
Single molecule resolution of nucleic acids is now within the reach of moderately equipped research laboratories, leading to fascinating breakthroughs in our understanding of disease. Pathogenica will preview our forthcoming clinical applications of next generation sequencing for viral and bacterial genotyping, and describe our DxSeq technology that significantly reduces workflow time and complexity from tissue sample to sequencing result.
Graeme Doran, Ph.D., Chief Scientific Officer, Pathogenica, Inc.
Single molecule resolution of nucleic acids is now within the reach of moderately equipped research laboratories, leading to fascinating breakthroughs in our understanding of disease. Pathogenica will preview our forthcoming clinical applications of next generation sequencing for viral and bacterial genotyping, and describe our DxSeq technology that significantly reduces workflow time and complexity from tissue sample to sequencing result.
Graeme Doran, Ph.D., Chief Scientific Officer, Pathogenica, Inc.
2:30
Ultrasensitive Detection of Rare Single-Nucleotide Variants using Next Generation Sequencing
The viral load of an infected individual often contains a population of quasi-species each with different genetic mutations. A rare resistant variant may survive therapeutic lethal selection and proliferate causing prolonged illness. We describe a statistical and experimental method using targeted next-generation sequencing to identify rare single nucleotide variant events at a resolution of 0.1% in clinical samples of influenza.
Patrick Flaherty, Ph.D., Postdoctoral Fellow, Biochemistry, Stanford University
The viral load of an infected individual often contains a population of quasi-species each with different genetic mutations. A rare resistant variant may survive therapeutic lethal selection and proliferate causing prolonged illness. We describe a statistical and experimental method using targeted next-generation sequencing to identify rare single nucleotide variant events at a resolution of 0.1% in clinical samples of influenza.
Patrick Flaherty, Ph.D., Postdoctoral Fellow, Biochemistry, Stanford University
New, Unpublished Data
3:00
Hot Start dNTPs for Nucleic Acid Amplification and Detection
Hot Start dNTPs are a distinct approach to Hot Start activation in PCR that provide a specific, sensitive and flexible alternative to hot-start DNA polymerases. The versatility of this technology allows for routine use in PCR as well as more advanced nucleic acid detection schemes. This presentation will highlight the latest advancements to this technology and will feature the benefits of Hot Start dNTPs in multiplexed molecular diagnostic assays.
Natasha Paul, Ph.D., Scientific Investigator, TriLink BioTechnologies, Inc.
Hot Start dNTPs are a distinct approach to Hot Start activation in PCR that provide a specific, sensitive and flexible alternative to hot-start DNA polymerases. The versatility of this technology allows for routine use in PCR as well as more advanced nucleic acid detection schemes. This presentation will highlight the latest advancements to this technology and will feature the benefits of Hot Start dNTPs in multiplexed molecular diagnostic assays.
Natasha Paul, Ph.D., Scientific Investigator, TriLink BioTechnologies, Inc.
3:30
Networking Refreshment Break
New, Unpublished Data
4:00
Improved Telomere Labeling Using Modified PNA FISH Miniprobes
PNA probes with enhanced affinity for complementary targets are effective fluorescence in situ hybridization (FISH) probes. The higher affinity allows shorter FISH probes to be used, as shown by telomere staining experiments. Shorter probes should translate into brighter fluorescent signals and lower cost of synthesis. The "miniprobe" concept can be extended to nontelomeric DNA and RNA targets.
Bruce A. Armitage, Ph.D., Co-Founder, PNA Innovations, Inc.; Professor of Chemistry, Co-Director, Center for Nucleic Acids Science and Technology, Carnegie Mellon University
PNA probes with enhanced affinity for complementary targets are effective fluorescence in situ hybridization (FISH) probes. The higher affinity allows shorter FISH probes to be used, as shown by telomere staining experiments. Shorter probes should translate into brighter fluorescent signals and lower cost of synthesis. The "miniprobe" concept can be extended to nontelomeric DNA and RNA targets.
Bruce A. Armitage, Ph.D., Co-Founder, PNA Innovations, Inc.; Professor of Chemistry, Co-Director, Center for Nucleic Acids Science and Technology, Carnegie Mellon University
4:30
T2Candida: Fully Automated Whole Blood PCR for Candidemic Patients
T2 Biosystems' T2Dx instrument platform enables rapid, high sensitivity direct detection of Candida in whole blood, based on the T2MR detection technology. The T2Dx is designed to automate all steps starting from a whole blood sample to answer in ~2 hours. Pre-clinical studies including analytical data demonstrating assay sensitivity at 1-3 CFU/mL in whole blood will be presented along with a review of the particle reagents development process.
Tom Lowery, Ph.D., Vice President, Diagnostics R&D, T2 Biosystems, Inc.
T2 Biosystems' T2Dx instrument platform enables rapid, high sensitivity direct detection of Candida in whole blood, based on the T2MR detection technology. The T2Dx is designed to automate all steps starting from a whole blood sample to answer in ~2 hours. Pre-clinical studies including analytical data demonstrating assay sensitivity at 1-3 CFU/mL in whole blood will be presented along with a review of the particle reagents development process.
Tom Lowery, Ph.D., Vice President, Diagnostics R&D, T2 Biosystems, Inc.
5:00
Case
Study
Feasibility Study: Integrating Novel DNA Extraction for Developing POC System to Detect Clostridium difficileStudy
We are developing a point-of-care assay and portable platform for detecting Clostridium difficile from human stool and from swabs of medical devices based on the combination of (1) our novel PureLyse® rapid and disposable sample preparation system that can mechanically lyse cells and extract DNA in less than five minutes, (2) rapid isothermal amplification of DNA, and (3) fluorescence detection with our FluoriSense® portable fluorometer. This project has culminated in a feasibility study of clinical stool samples with a prototype partially integrated system for sample prep and PCR as the amplification method.
Bruce Irvine, Chief Technology Officer, Claremont BioSolutions LLC
5:30
Close of Diagnostics Conference
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