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Sample Prep Conference


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Pre-detection processing is a pivotal part of molecular diagnostics. Its modernization should closely follow or even precede the emergence of new diagnostic technologies. Cambridge Healthtech Institute’s Sample Prep and Target Enrichment in Molecular Diagnostics is designed to demonstrate the latest advances in pre-analytical processing, sample preparation and target enrichment in molecular diagnostics and particularly in nucleic acid testing. IVD industry scientists and academia researchers who are working in this exciting area should attend this meeting.

 

 

TOPICS INCLUDE:

  • Nucleic Acid Extraction and Enrichment 
  • Pre-Detection Issues with Tissue Samples 
  • Sample Prep in Molecular Testing for Infectious Diseases 
  • Sample Prep Considerations for Validation of Clinical Tests 
 

DINNER SHORT COURSE:

Guidelines for Commercial Launch
of Novel Diagnostics

Instructors:
Jorge Leon, Ph.D., President, Leomics Associates, Inc.
David Parker, Ph.D., Vice President, Market Access Strategy, Precision Health Holdings
 

Day 1 | Day 2 | Download Brochure  

Wednesday, April 10

7:15 AM Registration and Morning Coffee

7:45-7:55 am Welcome Remarks from Marina Filshtnsky, Conference Producer

7:55-8:00 Chairperson's Opening Remarks

Brandon Young, Director of the Genomics and Cell-Based Screening Cores of Scripps Florida


» 8:00-8:30 Keynote Presentation:

The Sample – Often Forgotten, but Critical to The Result

Catherine A. Hammett-Stabler, Ph.D., DABCC, FACB, Professor of Pathology and Laboratory Medicine; Director, Core Laboratory McLendon Clinical Laboratories

When developing a new test we typically spend a great deal of time and effort optimizing the analytical portion. We need to spend just as much time validating and optimizing the sample. All too often this critical component is neglected. This session will discuss the many issues such as collection, processing, and storage that contribute to sample characteristics and dramatically impact your results.

Tissue as a Sample for Nucleic Acid Testing and Omics Research 

8:30-9:00 Tissue Samples for Genomic Analysis: RNA Sequence Analysis of Tissue Samples Preserved in PAXgene Tissue Fixative and RNAStable Dry Storage

Kristin Ardlie, Ph.D., Director, Biological Samples Platform, The Broad Institute

The Genotype Tissue Expression Project (GTEx) aims to study human gene expression and regulation in multiple tissues to provide insight into the mechanisms of gene regulation.  The collection of tissues (~30 per donor) and the preservation of RNA presents a unique challenge for the project, since all tissues are obtained from recently deceased donors. The PAXgene® Tissue System was implemented to allow for greater flexibility at both the collection sites and for shipping to processing and analysis centers. Data on histology, RNA quality, and RNA sequence data analysis from these samples will be presented.

9:00-9:30 Current National Guidelines for Creating High Quality Tissue Biospecimens

James Robb, M.D., FCAP, SAIC-Frederick Consulting Pathologist to the National Cancer Institute, NIH, HHS

Evidence-based national guidelines for creating high quality tissue biospecimens for clinically-applicable genomic testing for patient treatment, such as the CAP-ASCO breast cancer biomarker guidelines, have recently become available. Included topics are: annotating, collecting, transporting, processing, testing, storing, distributing, and post-distribution return of tissue biospecimens. Key points: Cold Ischemia Time <60 min (<20 min optimal) and Total Time In Formalin (6-72 hours). Areas of ongoing discussion and field experience from high quality tissue collection research programs will be discussed.

QIAGEN9:30-10:00 Comparison of Methods for Preserving Morphological, Molecular, and Protein Biomarkers in Tissue

Lynne Rainen, Ph.D., Scientific Director, PreAnalytiX GmbH

Current fixation methods used in traditional histology to prepare tissue specimens for morphological analysis are of limited use for molecular analysis. Formalin fixatives crosslink biomolecules, destroying or modifying nucleic acids and proteins during the fixation process. In contrast, snap-freezing in liquid nitrogen preserves biomolecules but ultimately leads to disruption of morphological structures.  This workshop will compare results of molecular, histological, and protein analyses obtained with formalin fixation and snap-freezing, to a new non-formalin fixative, the PAXgene® Tissue System.

10:00-10:30 First Do No Harm: Innovative Tissue Print Technologies for Collecting High Quality Snap-Frozen Samples for Research without Compromising the Diagnostic Specimen

Sandra M. Gaston, Ph.D., Director, Molecular Biomarkers Research Laboratory, Department of Pathology and Laboratory Medicine, Tufts Medical Center Assistant Professor of Pathology, Tufts University School of Medicine

Most human tissue samples obtained from clinical biopsy and surgical resections are only secondarily considered as research specimens, and any plan to collect tissue for research must put first priority on patient care. Our group has developed a set of tissue print micropeel technologies that offer an innovative and practical approach to obtaining high quality RNA and DNA from biopsies and other “high value” specimens without compromising pathology diagnosis. Application of these technologies for cancer biomarker discovery will be discussed. 

10:30-11:00 Coffee Break with Exhibit and Poster Viewing

11:00-11:30 A Quantitative Proteomic Analysis of FFPE Patient Melanoma

Nathan L. Avaritt , Biochemistry Department, University of Arkansas for Medical Sciences

Molecular pathways regulating melanoma initiation and progression are potential targets of therapeutic development for this aggressive cancer. We present the most comprehensive analysis of formalin-fixed paraffin-embedded human melanoma tissues using quantitative proteomics. Our results reveal that molecular pathways involved with tumor cell proliferation, motility, and apoptosis are
mis-regulated in melanoma. These data provide the most comprehensive proteome resource on patient melanoma and reveal insight into the molecular mechanisms driving melanoma progression.

11:30-12:00 pm Sample Prep Comparison for NGS Profiling of FFPE and Fresh Frozen Tumor Samples

Brandon Young, Director of the Genomics and Cell-Based Screening Cores of Scripps Florida

Archival samples preserved in FFPE present a difficult challenge due to sample degradation. Due to the nature of Next Generation Sequencing that relies on data generated from short reads the degradation is no longer the factor it once was.  Utilizing Nugen protocols we can now perform NGS experiments on FFPE and Fresh Frozen samples. It is now possible to directly compare retrospective tumor samples with new samples in a continued effort to advance translational genomics research on prospective patient samples.

Covaris12:00-12:15 pm Rationalizing Sample Prep with Adaptive Focused Acoustics (AFA): Improved FFPE Nucleic Acid Extraction for NGS

William M. Skea, Ph.D., Scientist, Covaris, Inc.

AFA technology offers a versatile solution to simplify Sample Preparation workflows and improve bioanalytical assay performance. One example is extracting nucleic acids from FFPE tissues; their growing use in genomics and transcriptomics studies requires high quality starting material and a seamless integration with Next Generation Sequencing.

Pressure Biosciences PBI12:15-12:30 Exploring Applications of High Pressure in Biological Sample Preparation 
Alexander Lazarev, Ph.D., Vice President, Research & Development, Pressure BioSciences, Inc.
Hydrostatic pressure is a significant thermodynamic parameter as importantas temperature. We present several examples of high hydrostatic pressure and pressure cycling technology (PCT) used to facilitate efficient and reproducible extraction of proteins, nucleic acids and lipids from complex biological matrices for -omics studies and targeted analysis. 

12:30-1:55 Lunch on Your Own

1:55-2:00 Chairperson's Remarks

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


Nucleic Acid Extraction and Sequencing  

2:00-2:30 Nucleic Acid Extraction and Sequencing Sample Prep for Next-Generation Sequencing: The Story of Two Approaches

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

2:30-3:00 Sample Prep Consideration for Validation of NGS-Based Clinical Tests

Corey Braastad, Ph.D., Scientific Director, Athena Diagnostics

3:00-3:30 Issues Concerning Extraction Efficiency, Methods, and Direct dPCR

Ross Haynes, Biological Science Technician, Biochemical Science Division, National Institute of Standards and Technology

Extraction of DNA from a sample is necessary in many applications, but leaves only a fraction of the total DNA for analysis. Liquid extraction methods attempt to maintain the entire DNA sample by avoiding washing and precipitation steps. Direct PCR methods bypass extraction entirely, theoretically allowing the analysis of the entire sample, but must overcome PCR inhibitors. Digital PCR has been shown to be less sensitive than qPCR to PCR inhibitors, but only because right shift of the amplification curve does not affect the result in digital PCR. NIST's experience with direct digital PCR will be discussed.

3:30-4:00 Refreshment Break with Exhibit and Poster Viewing

4:00-4:30 Selective Enrichment of Mitochondrial DNA

Eileen Dimalanta, Ph.D., Group Leader, Applications & Product Development, New England Biolabs

While many mitochondrial DNA (mtDNA) mutations are benign, some are associated with deficiencies in mitochondrial function and result in a substantial proportion of mitochondrial disorders in children and adults. Current methods of mtDNA mutation detection rely on long range PCR or hybridization based capture followed by Next-Gen sequencing. However, homologous well-characterized mtDNA sequences in the nuclear genome (NUMTs) may also be amplified, complicating the analysis of low-level heteroplastic abnormalities. To address this problem, we have developed a unique method for the separation of human genomic DNA from mtDNA. This simple methodology can be used to analyze low-level mtDNA mutations from a variety of clinical samples in a cost-effective manner utilizing established Next-Gen sequencing platforms, as well as newer single molecule sequencing technologies.

4:30-5:00 Panel Discussion: Nucleic Acid Sample Prep Considerations for Validation of Clinical Tests

  • Sample prep points to consider for validation of digital PCR
  • Issues specific to validation of amplicon based NGS tests
  • Considerations for validation of capture-based of NGS tests
  • Validation approaches in light of current NGS guidelines

Moderator: Jamie Platt, Ph.D., Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute
Panelists: Kristin Ardlie, Ph.D., Director, Biological Samples Platform, The Broad Institute
Ross Haynes, Biological Science Technician, Biochemical Science Division, National Institute of Standards and Technology
Corey Braastad, Ph.D., Scientific Director, Athena Diagnostics
 

5:10-6:00 Welcome Reception in the Exhibit Hall with Poster Viewing

6:00 Close of the day

6:00-6:15 Short Course Registration

  

6:15-9:00 Dinner Short Course: Guidelines for Commercial Launch of Novel Diagnostics*

Jorge Leon, Ph.D., President, Leomics Associates, Inc.
David Parker, Ph.D., Vice President, Market Access Strategy, Precision for Medicine

 

This short course is focused on development of molecular diagnostics as they make their way from identification of a medical need through to commercial launch. The course will emphasize identification of critical hurdles that when addressed early, can materially accelerate progress. Vital areas to be addressed include disease management, validation, reimbursement strategies including provider engagement, regulatory pathway decisions and education of the medical community. Examples and case studies of diagnostic companies will be shared to illustrate a real world roadmap including:

  • Disease Management
  • Assay Validation
  • Regulatory Pathways and Considerations
  • Reimbursement
  • Acceptance and Adoption

*Separate registration required


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