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Innovative Sample Prep and Target Enrichment in Clinical Diagnostics - 2012 - Day 1

Conference Proceeding CD Now Available
  • Speaker Presentations
  • Poster Abstracts
  • and More!

Archived Content

Wednesday, April 18

7:30 am Registration and Morning Coffee

8:15 Welcoming Remarks from Conference Producer


Pre-Analytical Processing and Specimen Quality as the Key to Precision Testing 

8:25 Chairperson’s Opening Remarks 

James H. Nichols, Ph.D., DABCC, FACB, Professor of Pathology, Tufts University School of Medicine, Medical Director, Clinical Chemistry, Baystate Health, Springfield, MA

8:30 What’s in Your Sample?

Catherine A. Hammett-Stabler, Ph.D., DABCC, FABC, Professor of Department of Pathology and Laboratory Medicine, University of North Carolina

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.

9:00 Pre-Analytical Challenges in Point-of-Care Testing

James H. Nichols, Ph.D., DABCC, FACB, Professor of Pathology, Tufts University School of Medicine, Medical Director, Clinical Chemistry, Baystate Health, Springfield, MA

As implementation of point-of-care testing (POCT) becomes more widespread, it is important to consider how pre-analytical factors can impact the test result, and ultimately patient care. In this presentation, we will identify important pre-analytical challenges that are present in the POCT process. We will also discuss how laboratories can develop a quality control plan to reduce the risk of errors at the point of care and how manufacturers can assist in development of these QC plans.

9:30 Pre-Analytical Variables of Specimen Processing in Molecular Diagnostics

Helen D. Fernandes, Ph.D., Director, Molecular Diagnostics, Associate Professor, Department of Pathology & Laboratory Medicine New Jersey Medical SchoolThe expanding scope of molecular based assays in clinical diagnostics has mushroomed from detection and quantification of pathogens to next generation sequencing of exomes, genomes and targets. As the field has developed, so have the variety of specimens used and the analytical techniques employed. Specimen type, storage and handling conditions/treatments, extraction methodologies, as well as quality and quantity of nucleic acid recovered, are part of the pre-analytical variables that can affect optimal performance of the assay. Degradation of nucleic acid, particularly target RNA and excess contamination with proteins or inhibitory agents can contribute to inaccurate interpretation of test results. Since molecular diagnostic methods using nucleic acid amplification are inherently variable, minimizing the preanalytical variables surrounding sample acquisition, transport, storage and extraction would help to ascertain a more reliable and reproducible test outcome.

10:00 Sponsored Presentation (Opportunity Available) 

10:30 Networking Coffee Break with Poster Viewing


Sample Prep and Target Enrichment in Molecular Diagnostics for Infectious Diseases 

11:00 Improved Sample/Enrichment from Whole Blood for the Diagnosis of Early Lyme Disease

Mark W. Eshoo, Ph.D., Director, New Technology Development, Ibis Biosciences, Inc., a subsidiary of Abbott Molecular

Early detection and treatment of Lyme disease is crucial to prevent late sequelae and to improve long-term prognosis. However, infection is often difficult to diagnose because of the variability of clinical manifestations and the biologically delayed antibody production upon which current serologic tests are based. Direct molecular tests for early Lyme disease have largely been unsuccessful possibly due to the low levels of circulating pathogen. To address this challenge, we have developed a sensitive assay to detect B. burgdorferi directly from whole blood collected during the initial patient visit. This method employs a nested isothermal pre-amplification of the Borrelia DNA followed by PCR and electrospray ionization mass spectrometry. We compared our assay with 2-tiered serology with specimens from 29 patients with clinically defined early Lyme disease. Results of this study demonstrate the ability to detect B. burgdorferi in early Lyme disease directly from whole blood specimens prior to seroconversion.

11:30 Electrokinetic Matrix Management for Pathogen Identification and Antimicrobial Susceptibility Testing in Whole Blood

Vincent Gau, Ph.D., President, Molecular Analysis, Genefluidics

An integrated sample preparation and diagnostic system to enable the point-of-care (POC), evidence-based selection of antibiotics for treatment of acute bacterial infections is presented to include sample/reagent delivery, mixing, lysing, 37°C incubation, stringency washing and electrochemical detection in a microfluidic cartridge. The feasibility, accuracy and reproducibility of cartridge-based rapid antimicrobial susceptibility testing are demonstrated on whole blood samples spiked with E.coli and Staphylococcus epidermidis. The AST culture time inside the cartridge can be as short as 30 minutes followed by the 30-min pathogen identification assay.

12:00 pm Using Next Generation Sequencing in Novel Pathogens Detection

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

12:30 pm Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Own


Sample Prep and Target Enrichment in Molecular Diagnostics of Cancer 

1:55 Chairperson’s RemarksJorge Leon, Ph.D., President, Leomics Consulting 

2:00 Capture of Tumor Cells with Albumin Microspheres

Louise de Grandpre, Senior Research Scientist, Research and Development, Iris Molecular Diagnostics

We have developed a method to capture cancer cells from liquids such as whole blood using antibody coated air-filled albumin microspheres. Overall, the process of cell capture with albumin microspheres is simple, quick and can accomplished with supplies found in any lab. Cells are incubated with antibody-coated microspheres and after centrifugation, captured cells rise to the top and unbound cells pellet at the bottom of the tube. Once cell separation is complete, the microspheres are disrupted, leaving an enhanced suspension of the target cells. The methodology of the invention will be discussed and results of cell capture in buffered solutions and whole blood will be presented.

2:30 Fluid Phase of Solid Tumors: Using CTCs as a Real Time Fluid Biopsy

Anand Kolatkar, Ph.D., Scripps Physics Oncology Center, The Scripps Research Institute

The fluid phase of solid tumors is a critical third microenvironment in the development and progression of carcinomas. Cells originating from primary or secondary sites travel through the blood circulatory system to either get cleared out or initiate new tumor growth. Translational research efforts are attempting to identify the various subtypes of circulating tumor cells (CTCs), their origins, their destinations and their impact on the disease. Understanding and characterizing CTCs is a first step towards utilizing them as both biopsy material and directly as a biomarker. It requires approaches of subtyping CTCs and characterizing them at the single cell level. While new technologies are being developed constantly, even early approaches show uses of certain CTCs as a biomarker. New correlations can be established between CTCs and other fluid phase materials.

3:00 Tumor Cell DNA Extraction from Urine Samples for Prostate Cancer Diagnostics

Heather R. Sanders, Ph.D., Principal Scientist, Oncology R&D, Quest Diagnostics Nichols InstituteBiomarker detection in urine has been examined as a non-invasive tool in prostate cancer diagnostics. We aimed to define the fraction of urine (cells/ sediment, cell-free/microvesicle-associated, or whole) that is most enriched for prostate-derived RNA. Cell-capturing filters and low MW filtration columns were employed to separate cells from urine and concentrate cell-free and whole urine for RNA extraction. Prostate biomarker transcripts were measured by qRT-PCR. It was concluded that the cell-free fraction of urine contained the highest level of prostate-derived RNA.

3:30 Networking Refreshment Break with Poster Viewing


Nucleic Acid Extraction and Sequencing 

Sponsored by
NuGen logo
4:00 Integrated Sample Preparation Solutions for RNA and DNA Sequencing Applications

Steven Kain, Ph.D., Director, Product Marketing, Sponsored by NuGEN Technologies


4:30 Target Enrichment Strategies for Next Generation Sequencing Technologies for the Study of Human Diseases: The Example of Hypertrophic Cardiomyopathies

Professor Francesco Salvatore, Professor and Scientific Coordinator of CEINGE

Valeria D’Argenio, M.D., Researcher, Clinical Biochemistry and Molecular Biology, University Federico II of Naples and CEINGE

Advances in genomic technologies have markedly accelerated the search for genetic causes of human diseases and answered previously difficult-to-answer questions regarding disease mechanisms. In particular, NGS technologies have emerged as a powerful tool for diagnostic purposes. Different strategies have been tested to overcome current PCR limitations and efficiently enrich different targets to be simultaneously analyzed in large group of patients. Here, we show some examples with their possible applications, in particular in the field of molecular diagnosis of cardiomyopathies.

5:10 DNA Extraction Technology Review: The Good, the Bad, the Ugly

Crystal R Icenhour, Ph.D., President & Chief Science Officer, Phthisis Diagnostics

Why does extracting DNA have to be so complicated – or does it? Explore good, bad, and ugly DNA extraction technologies from clinical samples, including complex sample types such as stool and sputum. Each technology’s pros and cons will be presented, providing guidance to clinical laboratories in selecting the technology that best suits their sample, budget, and workflow.

5:40 Welcome Reception

6:40 Close of Day 1

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