The optimization of pre-analytical/pre-detection processing should closely follow or even precede the emergence of new omics assays. Innovative sample prep and target enrichment technologies have the ability to significantly increase the sensitivity and specificity of a test that is run on a heterogeneous sample or a sample that contains low concentration of an analyte. Appropriate and novel sample preparation is a pivotal part of assay development and validation that guarantees its repeatability and robustness. The ninth annual Sample Prep Technologies conference is designed to discuss the major challenges and the latest advances in sample preparation for advanced omics assays in clinic as well as in biodetection and biosurveillance fields.

Day 1 | Day 2 | Download Brochure 

Thursday, June 25 

7:15 am Registration & Morning Coffee


8:10 Chairperson’s Opening Remarks

Scott D. Jewell, Ph.D., Professor and Director, Program for Technologies and Cores Van Andel Research Institute

8:15 Assessment of the Biological Quality of Biospecimens

Scott-JewellScott D. Jewell, Ph.D., Professor and Director, Program for Technologies and Cores Van Andel Research Institute

Biospecimen quality is affected by preanalytical variable and the analytes from the biospecimen are the targets of that quality assessment. Purity, size, integrity and a functional assessment of nucleic acids are used to measure genomic biospecimen quality. However, a more complex measurement of quality is the assessment of the biology of the biospecimen. We investigate these questions using animal models to provide further improvements in best practices. 

8:45 Joint Presentation: Sample Prep as the Core Feature of Innovative, Highly Integrated, Molecular Systems

Randy-RasmussenRandy Rasmussen, Ph.D., President and COO, BioFire Diagnostics

Stephanie Thatcher, Ph.D., Director, Systems Integration, BioFire Diagnostics

Development of molecular detection systems focuses on nucleic acid amplification and detection. This half of the problem gets the grants, the patents and the research time. Unfortunately these systems are often brought to their knees by snot, blood, poop and sputum. The hardest part of highly integrated systems is the sample prep and yet it is the part that is hardest to get people to work on. We will describe the process of learning this lesson with the FilmArray system, how we approach sample prep, and what important factors you should consider during development.

9:30 Sensitive Molecular Detection Of Bacterial And Candidal Infections In Direct Whole Blood Specimens

Gregory RichmondGregory Richmond, Ph.D., Principal Scientist, Ibis Biosciences, Abbott

We describe a sample preparation and detection system that provides for the rapid detection and identification of bacterial and Candidal nucleic acid directly in whole blood specimens from patients with suspected bloodstream infections. A lysis method and DNA purification system were designed for processing 5 ml of whole blood. PCR amplification formulations were optimized for high levels of human DNA. The system provides for rapid and sensitive molecular detection of diverse agents of these clinically important infections in approximately 6h.

10:00 Coffee Break in the Exhibit Hall with Poster Viewing


10:40 Chairperson’s Remarks

Patrick Hurban, Ph.D., Vice President, Research and Development, Expression Analysis, The Quintiles Company

10:45 Use of a Next-Generation Sequencing Assay to Compare Results Obtained from Matched Formalin-Fixed and Frozen Tissue Specimens

Patrick-HurbanPatrick Hurban, Ph.D., Vice President, Research and Development, Expression Analysis, The Quintiles Company

Formalin-fixed tissues present many sample preparation, extraction and method development challenges. It can also be challenging to understand whether certain findings stem from intrinsic genetic properties of the sample, or alternatively, are a product of how the sample was handled. Despite advancements in preservation methods, vast collections of FFPE material await analysis. Results will be presented comparing matched formalin-fixed and frozen tumor samples analyzed using a sensitive next-generation sequencing assay.

11:15 Best Practices for Fusion Detection by Targeted RNA Sequencing: Pre-Analytical Considerations, Assay Validation and More

Robert-DaberRobert D. Daber, Ph.D., Director, Research and Development and Sequencing Operations, Bio-Reference Laboratories

This presentation will discuss challenges and benefits of NGS based targeted RNA sequencing in the detection of gene fusion events, including, nucleic acid isolation, sample preparation and downstream data processing. There are a number of specific challenges related to RNA sequencing, standardized quality control metrics both before and after library prep are clearly needed.

11:45 Q&A with Speakers

12:00 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:00 Dessert Break in the Exhibit Hall with Poster Viewing

1:40 Chairperson’s Remarks

Chalom Sayada, M.D., Ph.D., Co-founder & CEO, Advanced Biological Laboratories SA

1:45 Highly Effective Automated Nucleic Acid Extraction from Diverse Samples for Quantitative Real Time PCR and Next Generation Sequencing

Jenkuei-LiuJenkuei Liu, Ph.D., Senior Staff Scientist, Bioproduction, ThermoFisher Scientific 

Special formulation of magnetic particles and chemical RNase inhibitors and procedures will help solve problem that many people have had for their nucleic acid-based assays for different samples. Automation provide high throughput method. We will present data showing examples of results obtained from multiple sample types used in multiple applications. With the features that include highly efficient recovery, RNase-inhibition, simultaneous extraction of multiple microbial genomes, compatibility with multiple assays, excipients, and convenience for automation, more applications using these reagents can be developed. 

2:15 Multiplex Targeted Sequencing Of Small Clinical Samples

Curt-ScharfeCurt Scharfe, M.D., Ph.D., Senior Scientist, Stanford Genome Technology Center, Stanford University

Clinical molecular testing increasingly depends on the development and deployment of novel sample preparation technologies. In collaboration with physicians and clinical laboratories we are developing genomic and sequencing assays for the screening and diagnosis of cystic fibrosis, clinical viral infections, newborn and neurodevelopmental conditions and inherited cardiomyopathies. These projects have involved invention of a novel multiplex capture technology, and several innovative improvements in DNA sample preparation. Both approaches have increased speed and accuracy, while lowering costs.

2:45 Refreshment Break in the Exhibit Hall with Poster Viewing

3:15 Optimization of Sample Preparation and Assay Validation in Virology and Oncology through the DeepChek & OncoChek Platforms

Chalom-SayadaChalom Sayada, M.D., Ph.D., Co-founder & CEO, Advanced Biological Laboratories SA

Clinical environments wishing to provide genotyping services in the field of Virology or Human Genetics using Next Generation Sequencing (NGS) need robust, standardized, registered and well-validated software systems. These should be tailored to the optimized management of genomic data resulting in personalized healthcare. Dedicated downstream analysis systems help to perform an accurate, quick and simple analysis of NGS data. This begins with sample preparation and the generation of reads by any type of sequencing platform and ends with simple and easily-understandable reporting ideally suited to clinical interpretation and the connection to the local LIMS. Coupling advanced IT solutions to a well-established sequencing workflow usually helps labs with the validation of new sample prep and innovative assays, enhancing patient management.

Covaris3:45 Simultaneous Extraction and Purification of NGS-Grade DNA and RNA from FFPE Tissue Samples with Covaris truXTRAC™

Hamid Khoja, Principal Scientist, Covaris Inc.

truXTRAC™ utilizes the highly controlled Covaris Adaptive Focused Acoustics™ (AFA) technology for the effective removal of paraffin from FFPE cores, sections, and slides, enabling rapid tissue rehydration, tissue digestion, crosslink reversal, and efficient extraction of NGS-grade nucleic acids without the use of any dangerous organic solvents or messy mineral oils.

4:00 Sponsored Presentation (Opportunity Available)

4:15 Panel Discussion: Matching Nucleic Acid Extraction Method with the Goals of an Assay

Patrick Hurban, Ph.D., Vice President, Research and Development, Expression Analysis, The Quintiles Company

Topics to be Discussed:

  • Recognizing bias in extraction methodology 
  • Optimizing extraction: when is it good enough? 
  • Balancing the desire to optimize with the desire to harmonize across assays  


Robert D. Daber, Ph.D., Director, Research and Development and Sequencing Operations, Bio-Reference Laboratories

Jenkuei Liu, Ph.D., Senior Staff Scientist, Bioproduction, ThermoFisher Scientific

Curt Scharfe, M.D., Ph.D., Senior Scientist, Stanford Genome Technology Center, Stanford University

4:45 Workshop Registration

5:30-8:30 Dinner Workshop* - How to Launch a Laboratory Test: Everything You Wanted to Know But Were Afraid to Ask


Steven-GutmanSteven Gutman, M.D., Strategic Advisor, NA, Myraqa, Inc.


Bruce QuinnBruce Quinn, M.D., Ph.D., Senior Health Policy Specialist, Foley Hoag LLP


View Detailed Agenda 

*separate registration required

Day 1 | Day 2 | Download Brochure 

Friday, June 26 

8:00 am Morning Coffee


8:25 Chairperson’s Remarks

Samantha Maragh, Ph.D., Human Geneticist & Molecular Biologist, National Institute of Standards & Technology

8:30 National Cancer Institute Resources to Guide Fit-For-Purpose Biospecimen Collection and Utilization

Helen-MooreHelen Moore, Ph.D., Branch Chief, Biorepositories & Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute

The National Cancer Institute has led the way in developing Best Practices for Biospecimen Resources, sponsoring new research in Biospecimen Science, and building groundbreaking research biospecimen collections including postmortem biospecimens for the NIH GTEx program. New projects to build evidence-based best practices for frozen and FFPE tissues will be described.

9:00 Assessment of FFPE Samples for Success in NGS

Helen-FernandesHelen Fernandes, Ph.D., Associate Professor, Pathology and Laboratory Medicine, Weill Cornell Medical College

This presentation will discuss several important issues, such as: RNA detection in cancer tissues stored in FFPE samples, profiling microRNA expression, FFPE DNA quality control and its correlation with NGS data, and understanding pre-analytic effects on RNA gene expression.

9:30 The Impact of Preanalytical Variables on Biomarker Research

David_Craft David Craft, Ph.D., Senior Manager Sciences, Preanalytical Systems, BD Diagnostics

The use of biomarkers can potentially improve the efficiency of the drug development process. The preanalytical phase has great potential for errors.  This presentation will focus on the potential impact of sample handling on RNA, proteins, cells within blood / tissue and how this variability can be controlled.

10:00 Coffee Break


10:10 Chairperson’s Remarks

Alexis Sauer-Budge, Ph.D., Senior Research Scientist, Fraunhofer Center for Manufacturing Innovation; Adjunct Research Assistant Professor, Biomedical Engineering, Boston University

10:15 Rapid Sample Preparation of Viable Bacteria Directly from Blood Specimens

Alexis-Sauer-BudgeAlexis Sauer-Budge, Ph.D., Senior Research Scientist, Fraunhofer Center for Manufacturing Innovation; Adjunct Research Assistant Professor, Biomedical Engineering, Boston University

Traditionally, bacterial pathogens in the blood have been identified using culture-based methods that can take several days to obtain results. This can lead to physicians making treatment decisions based on an incomplete diagnosis contributing to patient morbidity. To decrease diagnosis time, we are developing a novel sample preparation device for isolating and concentrating dilute bacteria from blood. This presentation will describe the sample preparation device for methodology to isolate viable bacteria from blood which is clean enough for direct PCR or other downstream detection technologies.  

10:45 Bacterial Separation and Portable Detection: Preanalytical Consideration and Technology

Sam-NugenSam R. Nugen, Ph.D., Assistant Professor, Department of Food Science, University of Massachusetts, Amherst

The lack of a practical method for bacterial separation remains a hindrance for the low-cost and successful development of rapid detection methods from complex samples. We have developed T7 bacteriophage magnetic probes, where T7 bacteriophage is bound to magnetic particles. The capture efficiencies of bacteriophages on microbeads and nanoparticles for the separation of E. coli K12 were determined. The results indicated that bacteriophage magnetic particles achieved a capture efficiency of 93.7 ± 1.1% in 15 minutes.  

11:15 Microfluidic PCR Amplification for Next-Generation Sequencing of GAA to Detect Mutations that Cause Pompe Disease

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

We designed a next-generation sequencing assay using primer pairs for PCR amplification and library preparation of up to 48 samples in one Fluidigm Access Array for next-generation sequencing using the MiSeq. This assay can be scaled up using additional Access Arrays in one MiSeq run. The PCR amplification of GAA is challenging due to difficult regions in the gene. All transcribed exon sequences as well as exon/intron borders including those intron sequences containing mutations as identified in the Human Genome Mutation Database (HGMD) were targeted for amplification. Primers were designed not to overlap known HGMD mutations, and variants found in dbSNP were avoided when possible. The data was filtered at a quality score of ≥ 30 and trimmed. We characterized reference materials including those with missense, nonsense, and splicing mutations; and small insertions and deletions. Large deletions that included exon 18 were independently characterized.

11:45 Pre-Analytical Variables – Most Vulnerable but Underappreciated Phase in Biomarker Validation

Apurva-SrivastavaApurva K. Srivastava, Ph.D., Principal Scientist, Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc.

Contrary to prevalent belief, pre-analytic factors contribute to the most errors documented in clinical laboratories as compared to analytical factors where most efforts are devoted during assay validation. Dr. Srivastava will discuss the general pre-analytical variables for protein assays and how they affect accuracy in clinical laboratory tests. The focus of his presentation will be on identifying the phases of pre-analytical factors with reference to pharmacodynamic/proof-of-mechanism (POM) phospho-protein biomarkers in clinical trials. As a take home message, participants will learn that pre-analytic variables are an underappreciated area in biomarker validation process and improvements in this process will significantly impact accuracy of test results and enable laboratories to focus their quality assurance efforts.

12:15 pm Close of Conference  

Day 1 | Day 2 | Download Brochure 

For more details on the conference, please contact:
Marina Filshtinsky, M.D.
Senior Director, Conferences
Knowledge Foundation, a division of CHI
Phone: (+1) 781-972-5496

For partnering & sponsorship information, contact:
Sherry Johnson
Business Development Manager
Knowledge Foundation, a division of CHI
Phone: (+1) 781-972-1359

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