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As the need for faster, more accurate, and effective molecular-based tests grows, Cambridge Healthtech Institute’s 6th Annual Molecular Diagnostics for Infectious Disease conference showcases cutting-edge technologies and tests being brought into routine clinical practice for rapid pathogen detection and identification. Several technologies and tests featured include next-gen sequencing, GI panels, and molecular-based tests for sepsis and blood borne infections. Outcome studies measuring the impact of the diagnostic on patient health and outcome, critical to the successful adoption of these molecular diagnostics in the clinic, will be discussed.


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Advanced Diagnostics for Infectious Disease 


10:30 am Registration

PLENARY SESSION: Think Tank on Next-Generation Sequencing Diagnostics

11:00 Chairperson’s Opening Remarks

Harry Glorikian, Healthcare Consultant

11:10 Discussion: Regulatory Review of Clinical Sequencing Assays

Harry GlorikianModerator: Harry Glorikian, Healthcare Consultant


Jennifer DickeyGuest Speaker: Jennifer Dickey, RAC, Ph.D., Office of In Vitro Diagnostics, DIHD, US Food and Drug Administration


In November of 2013, the FDA issued the first clearances of Next Gen Sequencing- (NGS) based assays. There have additionally been a number of clinical trials approved recently that utilize NGS-based assays for patient enrollment or stratification. In light of the expanding roles that new sequencing technologies are playing in clinical decision making, this talk will focus on critical elements that FDA considers when evaluating NGS validation using the recent clearances/approvals as examples. There will also be a discussion of any new communications that FDA has issued in regard to the regulatory review of NGS- based assays. Following the discussion there will be a Q&A with the audience.

11:55 Next-Generation Sequencing in Clinical Practice: Case Reports of Clinical Utility and Reimbursement  

Elaine LyonModerator: Elaine Lyon, Ph.D., Medical Director, Molecular Genetics, ARUP


Case Presenters:

Andrea Ferreira-Gonzalez Andrea Ferreira-Gonzalez, Ph.D., Professor, Pathology; Director, Molecular Diagnostics Lab, Virginia Commonwealth University


Madhuri HegdeMadhuri Hegde, Ph.D., FACMG, Professor, Human Genetics; Executive Director, Emory Genetics Laboratory, Emory University School of Medicine


The landscape of next-generation sequencing diagnostics is changing rapidly. Clinical laboratories are offering highly complex tests using new technologies, but face challenges in reimbursement. To be reimbursed for these tests, laboratories will need to address clinical utility as well as clinical validity. Clinical cases that demonstrate the utility of genomic oncological and inherited disease testing will be presented. Experiences with reimbursement of these tests will be discussed.

12:40 pm Enjoy Lunch on Your Own


1:50 Chairperson’s Opening Remarks

Nathan A. Ledeboer, Ph.D., D(ABMM), Assistant Professor & Medical Director, Clinical Microbiology, Medical College of Wisconsin

2:00 Impact of Molecular Diagnostics on Infection-Related Patient Outcomes

Jerod NagelJerod Nagel, Pharm.D., BCPS (AQID), Clinical Specialist, Infectious Diseases, Clinical Assistant Instructor, Director Infectious Diseases Residency, University of Michigan Hospital and Health Systems, University of Michigan, College of Pharmacy

The advancement of molecular diagnostics has improved the ability to identify pathogens and resistance mechanisms in a timely manner. Demonstrating the impact on patient outcomes and overall hospital expenditure should be an important component in deciding the role of molecular diagnostics in clinical laboratories. This presentation aims to review the outcomes associated with new diagnostics and discuss strategies to optimize patient outcomes.

2:30 Unbiased Next-Generation Sequencing — Moving Towards Clinically Actionable Diagnostic Assays for Pathogens

Charles ChiuCharles Chiu, M.D., Ph.D., Assistant Professor, Lab Medicine and Medicine, Infectious Diseases, University of California San Francisco

Unbiased next-generation sequencing technology enables the detection of novel or uncommon pathogens directly from clinical samples, but its routine implementation in clinical and public health settings has been hindered by issues of cost, turnaround time, and bioinformatics analysis of complex datasets. Here we will describe the use of the technology in the clinical laboratory to validate novel, ultra-sensitive assays that have the potential to transform infectious diseases diagnosis, including a case where NGS rapidly identified a rare pathogen leading to a dramatic, real-time impact on the care and treatment of an immunocompromised child with a fulminant, unknown encephalitis.


2:50 From Culture to the Future: Molecular Detection of Enteric Pathogens

Nathan A. LedeboerNathan A. Ledeboer, Ph.D., D(ABMM), Assistant Professor & Medical Director, Clinical Microbiology, Medical College of Wisconsin

The diagnosis of enteric pathogens is particularly challenging given the large amount of vastly diverse indigenous gastrointestinal flora present in stool. Stool cultures have low sensitivity due to variable amounts of pathogen shedding and obscuring normal flora. Studies have shown a diagnostic yield of stool culture as low as 1.5%, with a cost per positive culture as high as $1,200. Molecular methods boast increased sensitivity and specificity when compared to stool culture. Several molecular methods including real-time PCR, microarray, and liquid array assays have been described. This presentation will evaluate the performance of molecular gastroenteritis assays and begin to evaluate the clinical and cost saving benefits.

3:10 The Use of Molecular Stool Panels in the Diagnosis of Infectious Gastroenteritis

Susan M. Novak-WeekleySusan M. Novak-Weekley, Ph.D., D(ABMM), Director, Microbiology, Kaiser Permanente, SCPMG Regional Reference Laboratories

Infectious gastroenteritis is a major public health concern. The landscape is changing within the clinical laboratory setting in regards to diagnosis of bacterial, viral and parasitic stool pathogens. Several manufacturers are developing multiplex molecular panels for the diagnosis of these pathogens. This session will discuss the newer panels coming out on the market and performance data related to those assays. How these panels will fit into the laboratory and clinical setting will also be discussed.

3:30 Dual Site Clinical Evaluation of the xTAG Gastrointestinal Pathogen Panel for Detection of Infectious Gastroenteritis

Anami_Patel_LuminexAnami Patel, Ph.D, MB (ASCP) DLM, Technical Director, Molecular Diagnostics Laboratory, Le Bonheur Children’s Hospital

We evaluated the clinical performance and laboratory cost and time efficiencies gained through use of the xTAG gastrointestinal pathogen in vitro diagnostic (IVD) assay in a comparison between clinical and public health laboratories. The site reproducibility study showed 98.7% agreement with high positive and negative agreement values (96.2% and 99.8%, respectively).  High throughput detection of multiple GI pathogens improved turnaround time, consolidated laboratory workflow, and simplified stool culture practices, thus reducing the overall cost and number of specimens processed.

4:00 Refreshment Break in the Exhibit Hall with Poster Viewing


4:45 From Genome to Biomarker: The Path Forward

David A. RaskoDavid A. Rasko, Ph.D., Associate Professor, Microbiology & Immunology, University of Maryland School of Medicine Institute for Genome Sciences

The advent of more decreased sequencing costs and increased throughput have allowed movement beyond the examination of prototype isolates and into the use of microbial genomic data for other purposes. Microbial pathogens are identified based on virulence factors that are often encoded on mobile elements, and thus have variable presence or absence. Identification of stable genomically derived biomarkers will allow more robust identification of bacterial pathogens. Genomic sequencing is opening this avenue of biomarker development.

5:15 Next-Generation Sequencing for Pathogen Detection - HIVE Platform Solutions and Applications to Viral Detection and Other Bioinformatics Pipelines

Vahan SimonyanVahan Simonyan, Ph.D., HIVE Project Lead, CBER, FDA

Next-generation sequencing production has exponentially increased in recent years due to the reduction in cost and improvements in performance of the technology. A single sample generally provides ample coverage but, due to the highly complex genomes of many pathogenic organisms, development of improved computational methods and platforms is now necessary to meet the increasing demands of related studies. HIVE, the High-performance Integrated Virtual Environment, is a cloud-based environment specifically developed to meet the growing storage and analysis challenges associated with NGS data and other big data types. The HIVE platform provides secure web access for registered users to store, annotate, analyze and retrieve big data, as well as a visually dynamic interface for viewing computational results. HIVE can be used for pathogen detection through the following applied pipelines: big data management (NGS, mass spec, etc.); alignment of unknown or mixed samples to reference viral genome sets; computation and comparison of SNP profiles of patients or pathogen samples; discovery of recombination events implicated in virulence recovery and pathogenicity; facilitation of collaborative discovery and annotations.

5:45 Novel Methods for Sample Preparation & Target Enrichment in Molecular and Protein Diagnostics for Infectious Disease and Beyond - Lessons from Mass Spec and NGS

Michael SuperMichael Super, Ph.D., Senior Staff Scientist, Advanced Technology Team, Wyss Institute at Harvard

We have developed methods for sample extraction from complex biological environments using broad-spectrum pathogen binding proteins attached to nanomagnetic particles. These have been used to enrich samples for molecular and protein analysis without the need for culturing, thereby saving significant time and providing same-day pathogen identification. An overview of the challenges of sample prep in the current environment of NGS and genomic testing will also be discussed.

6:15 Close of Day

6:00 Dinner Short Course Registration


Recommended Dinner Short Course*

6:30-8:30 pm NGS for Infectious Disease Diagnostics - View Detailed Agenda 

*Separate registration required

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