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Cambridge Healthtech Institute’s Third Annual

Sample Prep and Target Enrichment in Molecular DiagnosticsSample Prep and Target Enrichment in
Molecular Diagnostics    

Sample Quality and Sample Prep for NGS and Other Technologies 

Part of the Precision Diagnostics Summit
June 16-17, 2014 | Hilton Boston Back Bay| Boston, MA

Pre-detection/pre-analytical processing is a pivotal part of molecular diagnostics in general and in nucleic acid testing in particular. Next Generation Sequencing that is making its way into clinical laboratory imposes especially high requirements of precision on sample quality and pre-analytical processing.  As a rule, the modernization of pre-analytical processing should closely follow or even precede the emergence of new molecular diagnostics technologies. Target enrichment as part of pre-analytical processing has the ability to significantly increase sensitivity and specificity of a test that is run on a heterogeneous sample or a sample that contains a low concentration of analyte. Cambridge Healthtech Institute’s Third Annual 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, particularly in next generation sequencing and other nucleic testing technologies.

Final Agenda

MONDAY, June 16, 2014

7:15 am Registration & Morning Coffee

Standardizing SAMPLE QUALITY AND Preanalytical Processing 

7:45 Welcome Remarks from Marina Filshtinsky, M.D., Conference Director

7:55 Chairperson’s Opening Remarks

8:00 The Biomarker Development for Precision Medicine Sample Prep Considerations: A Systems Approach Beginning with the Right Stuff

CarolynComptonCarolyn Compton, M.D., Ph.D., Professor, School of Life Sciences, Arizona State University

The future of precision medicine depends on the development of diagnostic analyses that accurately reflect the biomolecular phenotype of the disease, both for accurate classification and appropriate therapeutic management.  In order to develop and use diagnostics, the biospecimens that serve as the test material must be systematically collected, processed and stabilized according to standards that render the samples fit for the analytic approach used in the diagnostic test.  Rigorous adherence to standards under a quality management system that includes documentation of of process steps and recording of deviations from protocol is required. Reproducibility and clinical validity cannot be achieved with complex diagnostic analyses without the assurance of the provenance of the specimens being tested. The biomarker qualification program of the Center for Drug Evaluation and Research at the Food and Drug Administration emphasizes the need to document the biospecimen quality of diagnostic biomarkers used for drug development and the Center for Devices and Radiologic Health has similar requirements for approval of diagnostic devices. It is imperative that the diagnostics development community address the need for standardized processes and fit-for-purpose biospecimens to accelerate the delivery of accurate, reproducible, clinically relevant molecular diagnostics for precision medicine.

8:30 The Challenges of Developing and Implementing Biospecimen Evidence-Based Practices

HelenMooreHelen Moore, Ph.D., Program Director, Biorepositories & Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute

The U.S. National Cancer Institute has led progress in biobanking with the NCI Best Practices for Biospecimen Resources and the Biospecimen Research Network (BRN). Incorporating new scientific data into best practices is another challenge.

9:00 A Call to Standardize Preanalytic Data Elements for Biospecimens

JamesRobbJames Robb, M.D., FCAP, Leidos Biomedical Research, Inc.

Biospecimens must have appropriate clinical annotation to ensure optimal quality for both patient care and research. A quantitative list of 170 clinical preanalytic variables (data fields), along with their relative importance, which can vary depending on downstream use, institutional needs, and information technology capabilities, have been developed and published by the College of American Pathologists. Notes, definitions, and negative impacts have been provided for each variable. This list can be used as a guide for site-specific implementation into patient care and/or research biorepository processes.

9:30 Ultracold vs. LN2 Cryopreservation for Biospecimens Destined for Genomically-Informed Precision Medicine

MarkCosentinoMark Cosentino, D.P.M., Ph.D., Head, BioProcessing and DNA Extraction, Staging Laboratories, Biogen

The storage temperature of biospecimens of various material types tends to be selected based on historical antidotal information. What is needed is scientific-based research to define “Best Practices” that links the appropriate storage temperature of analytes to specific downstream testing applications. This is not a trivial matter. The presentation will discuss the possibility of storing biospecimens below the Glass Transition Temperature of Water (GTTW). An experimental approach and call for scientific collaboration will also be discussed.

Wafergen10:00 Development of an NGS Mediated Assay Targeting High Frequency Somatic Alterations in AML Patients Utilizing the WaferGen SmartChip TE System

Mark_LandersMark Landers, Director, Research Services, Research & Development, AltheaDx

We have developed an NGS mediated assay targeting 30 of the most frequently mutated genes reported in AML disease progression for the purposes of supporting translational research.  The WaferGen SmartChipTM TE panel reliably detects point mutations across all exons of the targeted genes as well as specific genomic rearrangements including FLT3 ITD and MLL PTD.


 10:15 Sponsored Presentation (Opportunity Available) 



10:30 Coffee Break with Exhibit and Poster Viewing

10:55 Chairperson's remarks
Veronique Neumeister, M.D., Specialized Translational Services Laboratory, Department of Pathology, Yale University
11:00 Quantitative Measurement of Protein Degradation in FFPE Samples

VeroniqueNeumeisterVeronique Neumeister, M.D., Specialized Translational Services Laboratory, Department of Pathology, Yale University

Companion diagnostic tests are critically dependent on tissue quality. However, tissue handling and processing are not always tightly controlled and pre-analytical variables can significantly alter tissue quality. Cold ischemic time is amongst the most important variables. This presentation will discuss the effect of this variable in the diagnostic and research setting and show data on analytes that are particularly sensitive to this issue. Tools to control tissue quality will be discussed and the construction of an internally calibrated tissue quality index (TQI) as a way to monitor tissue quality for immunological assessments will be illustrated.

11:30 Practical Approaches to Expanding Biorepository Representation: Innovative Tissue Print Technologies for Collecting High Quality Snap-Frozen Specimens for Biomarker Research

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. . Remnant tissues obtained from fresh surgical specimens are the mainstay for biorepositories that provide high quality snap-frozen samples for research, but many critical areas of a surgical resection and most diagnostic biopsies cannot be easily “divvied up” before the tissue is submitted for processing as a formalin-fixed paraffin embedded (FFPE) specimen. 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.


12:00 Development, Validation and Implementation of Sample Prep Procedures for Clinical Whole Exome Sequencing at the Broad Institute

BiallLennonNiall J. Lennon, Ph.D., Director, Technology Development, Genomics Platform & Clinical Applications Development, Clinical Research Sequencing Platform, Broad Institute of MIT & Harvard

The development of the Whole Exome Sequencing assay offered by the Broad clinical lab will be discussed as an example of the need for, and application of, process design and quality management systems in molecular diagnostics. Though the documentation and validation requirements may differ between clinical and research processes there are a common set of challenges that must be tackled through the identification and elimination of process variability, rigorous supply chain control, enhanced tracking and troubleshooting, and automation of both lab and analytical pipeline functions.

12:30 Use of a Next-Generation Sequencing Assay to Compare Results Obtained from Matched Formalin-Fixed and Frozen Tissue Specimens

PatrickHurbanPatrick Hurban, Ph.D., Senior Director, Translational Research and Development, Global Head, Genomic 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.

1:00 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch On Your Own

1:55 Chairperson's remarksPatrick Hurban, Ph.D., Senior Director, Translational Research and Development, Global Head, Genomic Research and Development, Expression Analysis, The Quintiles Company

2:00 Development, Validation, and Implementation of Clinical Targeted Next Generation Sequencing using Anchored Multiplex PCR (AMP) 

Long Phi LeLong Phi Le, M.D., Ph.D., Medical Director, Clinical Research Sequencing Platform, Broad Institute; Assistant Professor of Pathology, Massachusetts General Hospital

Targeted next-generation sequencing (NGS) is an important approach for both research and clinical applications. This presentation will describe a novel method termed anchored multiplex polymerase chain reaction (AMP) which offers a rapid, economical, and scalable target enrichment solution. We share our experience with developing, validating, and implementing AMP in several clinical assays for fusion transcript detection and cancer genotyping (single nucleotide variants, insertions/deletions, and copy number) using formalin-fixed paraffin-embedded specimens. The use of pre-analytical steps to assess nucleic acid quality from FFPE specimens and post-analytical steps to qualify sequencing data will be discussed in the context of clinical testing.

Covaris2:30 A Novel Method of Active Paraffin Removal, and Efficient Extraction of NGS-Quality DNA from FFPE Tissues

Hamid Khoja, Ph.D., Principal Scientist, Covaris Inc.

FFPE tissue preservation, conceived primarily to facilitate histological analysis, is now routinely used in clinical oncology as a source of DNA for targeted and whole genome sequencing. The paraffin matrix and chemical crosslinks of FFPE-preserved samples present significant challenges for the robust extraction of nucleic acids. To provide reliable access to DNA of clinical FFPE samples, we present a novel method for consistent and reproducible extraction and purification of DNA from FFPE samples using Covaris Adaptive Focused Acoustics™(AFA).

3:00 Comparison of Various Preanalytical Strategies in Molecular Testing for Infectious Diseases

DavidHillyardDavid R. Hillyard, M.D., Medical Director, Molecular Infectious Diseases, Arup Laboratories

Molecular infectious disease testing places unique demands on pre-analytic methods for organismal disruption, nucleic acid release, purification, and concentration. For both high throughput core platforms and the increasing number of near point-of-care devices, nucleic extraction is a key pre-analytic step for good test performance. This presentation will review both currently available and emerging approaches to pathogen nucleic acid extraction, and issues relevant to its integration with downstream amplification and analysis technologies.

3:30 Refreshment Break with Exhibit & Poster Viewing

4:00 Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems

LynnBryLynn Bry, Ph.D., M.D., Associate Professor of Pathology, Brigham and Women’s Hospital

4:30 Panel Discussion: Matching Nucleic Acid Extraction Method with the Goals of an Assay

Moderator: Patrick Hurban, Ph.D., Senior Director, Translational Research and Development, Global Head, Genomic Research and Development, Expression Analysis, The Quintiles Company

Panelists: Monday Speakers

5:10 Welcome Reception with Exhibit & Poster Viewing

6:00 Short Course Registration

6:15-9:00pm Dinner Short Course: How to Launch a Laboratory Test: Everything You Wanted to Know but Were Afraid to Ask *

Instructors: Steven Gutman, M.D., Strategic Advisor, NA, Myraqa, Inc.

Tonya Dowd, Director, Reimbursement Policy, Quorum Consulting, Inc.

* Separate Registration Required

Tuesday, June 17

Cutting-Edge Innovations in Molecular Testing:
The Future is Now

8:15 am Breakout Discussions with Continental Breakfast 

Nucleic Acid ExtractionModerator: Kai Wang, Ph.D., Principle Scientists, Institute of Systems Biology
Working with FFPE SamplesModerator: 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 

Sample Prep – Less Diagnostics 

Mark A. Reed, Harold Hodgkinson Professor of Electrical Engineering, Departments of Electrical Engineering and Applied Physics, Yale University
Barry Lutz, Ph.D., Research Assistant Professor, Department of Bioengineering, University of Washington

9:10 Chairperson’s RemarksBarry Lutz, Ph.D., Research Assistant Professor, Department of Bioengineering, University of Washington 

9:15 Challenges and Prospects of Circulating RNA

KaiWangKai Wang, Ph.D., Principle Scientists, Institute of Systems Biology

Since extracellular microRNAs (miRNAs) were discovered, their impact on biomarker related applications has been a surprising and exciting field. The discovery of exogenous RNAs in circulation further expands the possibility of using circulating RNA to assess the interactions between host and microbiome. The fundamental requirement for biomarker development is a reliable and accurate measurement method, which is still lacking for miRNA and other short RNAs in circulation. Factors that are known to affect circulating RNA measurements include sample type, sample preparation, storage condition, measurement platform, and many others. While new measurement methods are needed, caution needs to be taken in interpreting circulating RNA based results.

9:45 Electronic Label-Free Biosensing Assays

MarkReedMark A. Reed, Harold Hodgkinson Professor of Electrical Engineering, Departments of Electrical Engineering and Applied Physics, Yale University

Nanoscale electronic devices have the potential to achieve exquisite sensitivity, selectivity, and portability as sensors for detection of protein biomarkers. Nanowire-FETs compatible with standard microelectronics technology enable a high yield and low-cost technology with simple system integration. This talk discusses the application of this technology to a wide range of label-free biochemical and macromolecule sensing at clinically important concentrations for biomarker assays.

DNAgenotek10:15 MAX Lysis: A Novel Chemical Lysis Reagent Replaces Bead beating for Spores and Other Difficult-to-Lyse Organisms

CKellyCassandra Kelly-Cirino, Ph.D., Senior Scientist, Product Development, Research & Development, DNA Genotek
DNA Genotek has developed a liquid reagent, MAX Lysis, which efficiently releases DNA from hardy bacteria including Bacillus anthracis, Clostridium botulinum, C. difficile and Mycobacterium tuberculosis without the need for bead beating or sonication. This reagent provides for a safer laboratory workflow and can be automated for use in high-throughput testing. 

10:30 Coffee Break with Exhibit and Poster Viewing

11:00 MAD NAAT: Multiplexable Autonomous Disposable Nucleic Acid Amplification Test for Low-Resource Settings

BarryLutzBarry Lutz, Ph.D., Research Assistant Professor, Department of Bioengineering, University of Washington

We are developing tests for DNA and RNA that can be performed anywhere, including your home. All steps from sample preparation to visual readout are carried out automatically without an instrument. Data collection by a cell phone will allow transmission of results to a healthcare provider and medical record. Project goals include commercializable tests as well as broad platform capabilities for future tests.

11:30 A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing

KamleshPatelKamlesh Patel, Ph.D., Manager, Advance Systems Engineering and Deployment, Sandia National Labs

DNA sequencing is advancing at an unprecedented rate, but sample preparation methods rely on manual bench-top processes, which are labor-intensive. The introduction of fast, low-throughput sequencers warrant a need to automate these protocols. We report on our work to integrate novel digital microfluidic technology to automate DNA library preparation workflows for characterization of novel and emerging pathogens from clinical samples.

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


1:00 Chairperson’s Remarks

1:05 PLENARY KEYNOTE: Sample Preparation Considerations for Digital Technologies

N Reginald BeerN. Reginald Beer, Ph.D., Medical Diagnostics Initiative Leader, Center for Micro and Nanotechnologies, Lawrence Livermore National Laboratory

Digital PCR provides extremely accurate quantification as compared to traditional standard curve methods but pre-detection processing remains pivotal. Critical factors such as sample preparation, sample homogeneity, reaction volume measurements, thermal cycler uniformity, template GC content and methylation can all effect data quality. In this talk we will discuss the benefits of digital technologies as well as steps to ensure accurate measurement. Attention will be given to future trends driving the field and moving out of the lab and onto the bench.

1:35 How To Choose The Right Assay On The Right Platform: A Clinical Diagnostic Laboratory Perspective

Elizabeth Duffy HynesElizabeth Duffy Hynes, Laboratory Manager for Clinical Development, Laboratory for Molecular Medicine, Partners HealthCare Center for Personalized Genetic Medicine

Clinical diagnostic and research laboratories may have similar fundamental criteria for evaluating instruments, technologies, and platforms, but there are additional facets and layers of stringency that need to be considered when in a clinical setting. At a technical level,  assays have to have the best possible sensitivity and specificity scores and cutting-edge technologies should be proven to meet or exceed gold standard metrics, or current standard of care. Routine laboratory operations considerations, such as cost,  hands on time, ease of use, and turn-around-time, among others must also be evaluated. Of course, these factors must be carefully balanced with proven clinical utility in order to provide the highest quality healthcare service to patients and their physicians. Experiences and decision making processes of the Laboratory for Molecular Medicine will be discussed.

2:05 Close of Sample Preparation Conference