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Translating Proteomics & Metabolomics into the Clinical Laboratory 

Day 1  |  Day 2 

Translating Proteomics and Metabolomics into the Clinical Laboratory represents solutions and case studies for an array of problems related to clinical laboratory applications for protein-based and small molecule multiplex assays. Logistical and technological challenges will be addressed by a group of world-class experts and thought leaders from the IVD industry and academia. Mass spectrometry, protein array and multiplex immunoassay platforms will be featured during the meeting. Special emphasis will be placed on regulatory issues and solutions.

Recommended Short Courses* 

(SC5) Automation Solutions for Molecular Diagnostics (Aug 22, 2–5pm) 
(SC9) Mass Spec Methods for the Clinical Lab (Aug 24, 6:30–8:30pm) 

*Separate Registration Required 

TUESDAY, August 23

7:30 am Registration and Morning Coffee



8:30 Chairperson’s Opening Remarks

Daniel W. Chan, Ph.D., Professor and Director, Center for Biomarker Discovery and Translation, and Clinical Chemistry Division, Johns Hopkins University

8:40 Keynote Presentation: 

Translating Proteomics and Metabolomics into the Clinical Labortatory: The Future is Now

Daniel ChanDaniel W. Chan, Ph.D., Professor and Director, Center for Biomarker Discovery and Translation, and Clinical Chemistry Division, Johns Hopkins University

Despite the success of discovering many disease associated biomarkers, very few biomarkers have been translated into clinical diagnostics. To be successful in the translation, we need to develop a roadmap and identify several key steps that are critical in this process. These steps include defining a specific clinical “intended use” for unmet clinical needs, generating sufficient evidence in preliminary validation studies to support the investment for a large-scale validation study, developing assays with analytical performance suitable for the clinical laboratory and conducting clinical trials to demonstrate clinical utilities in order to obtain regulatory approval and gain acceptance by the clinical community. Specific examples will be shown to demonstrate the opportunities and challenges for the development of clinical proteomic diagnostics. The successful translation of these biomarkers into clinical practice will require close collaboration between researcher, industry, regulatory agency and clinician

9:10 Regulatory Perspective on Translating Proteomic Biomarkers to Clinical Diagnostics

Jinong LiJinong Li, Ph.D., DABCC, Regulatory Scientist, FDA/CDRH/OIVD/DCTD






Kellie B. Kelm, Ph.D., Regulatory Scientist, FDA/CDRH/OIVD/DCTD

Issues associated with the translation of complex proteomic biomarkers from discovery to clinical diagnostics have been widely discussed among academic researchers, government agencies, as well as assay and instrumentation manufacturers. Here, we provide an overview of the regulatory framework and type of information that is typically required in order to evaluate in vitro diagnostic tests regulated by the Office of In Vitro Diagnostic Device Evaluation and Safety (OIVD) at the US Food and Drug Administration (FDA), with the focus on some of the issues specific to protein-based complex tests.  Items to be discussed include:
* Overview of FDA regulation pathways on IVD tests
* Regulatory considerations for premarket submissions of multiplex assays
* Discussion on the two mock submissions submitted by members of the Clinical Proteomics Technology Assessment for Cancer (CPTAC) program of the National Cancer Institute (NCI) and reviewed by FDA, (published in Clinical Chemistry)

10:10 Networking Coffee Break

11:00 Criteria for Medical Necessity for Protein and Metabolite-Based Multiplex Assays

Gilbert S. Omenn, M.D., Ph.D., Director, Center for Computational Medicine & Bioinformatics Professor of Internal Medicine, Human Genetics and Public Health, University of Michigan

Major advances in proteomics and metabolomics are enhancing the sensitivity and reproducibility of these measurements with plasma and other clinical specimens. Differential diagnosis may require recognition of post-translational modifications, splice variants, and even sequence polymorphisms of proteins, as well as modeling of effects on interacting signaling pathways. Clinical laboratory criteria, including medical necessity for reimbursement, put a premium on positive-predictive value, narrow coefficient of variation, and results that make a difference in clinical decision-making for patients. The classifiers must be transparent, preferably with open code, to enhance reproducibility and confidence in moving toward personalized medicine.


11:30 Enabling Technologies for the Specific Immunoglobulin Analysis in the Diagnosis of Allergic and Autoimmune Diseases

Per Matsson, Ph.D., CTO, Phadia; Associate Professor, Uppsala University

The diagnostic industry is under great change and new emerging technologies allow the possibility to analyze more variables faster and more accurately. Specific Immunoglobulin analysis is today a routine for the diagnosis of allergic and autoimmune diseases. We can presently only analyze different antigens for S-IgE (allergy) or S-IgG (autoimmunity) through traditional sequential immuno-assay systems. The need for more and simultaneous information has encouraged us to search for new possibilities. Therefore, we have developed the possibility to simultaneously analyze >100 different antigens with a minute amount of patient sample. After reviewing a large number of assay technologies we now have the possibility to use multiplexed technologies both in the point-of-care setting, as well as the basis for new laboratory systems. These enabling technologies allow for the development of new information in immunology.

12:00 pm The PreDx® Diabetes Risk Score: A Prognostic Algorithm for Type 2 Diabetes Developed Using a High-Throughput, Quantitative Immunoassay Platform

Steven WatkinsSteven M. Watkins, Ph.D., CSO, Tethys Bioscience, Inc.

The PreDx Diabetes Risk score is a commercial prognostic test that provides patients with their absolute risk for type 2 diabetes within the next five years. The test was developed by a quantitative screen of protein concentrations in several large epidemiological cohorts that contained diabetes outcomes. A description of the test as well as a summary of the research technology and validation data will be provided in this talk.


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

1:30 Session Break


1:55 Chairperson’s Remarks

Nigel J. Clarke, Ph.D., Director of Mass Spectrometry, Scientific Director, R&D, Steroids, Nichols Institute, Quest Diagnostics


2:00 Mass Spectrometry as an Enabling Technology in Diagnostics

Cory Bystrom, Ph.D., Associate Scientific Director, Mass Spectrometry, Nichols Institute, Quest Diagnostics

Diagnostic use of Liquid Chromatography-Mass Spectrometry has taken off over the last 5 years. The assays provide higher specificity, sensitivity and require smaller sample volumes - ideal for precious samples e.g. pediatrics. The instrumentation allows for multiplexed assays further providing sample savings. These factors have lead to professional bodies endorsing the use of this technology. The ability to automate assays on LC-MS/MS entices labs to adopt the methodology. Since LC-MS/MS is becoming prevalent it is important that users be aware of LC-MS/MS performnce compared to RIAs and ICMAs. This presentation will detail assays through development, validation and use. Examples will differentiate LC-MS/MS results from traditional assays

2:40 Quantifying Proteins by LC-MS/MS

Andrew HoofnagleAndrew N. Hoofnagle, M.D., Ph.D., Assistant Professor, Laboratory Medicine, Departments of Laboratory Medicine and Medicine, University of Washington

There have been significant advances in the quantification of proteins by liquid chromatography-tandem mass spectrometry. Targeted proteomics workflows have major advantages over traditional automated immunoassays in the clinical laboratory. In addition, they are more precise than shotgun proteomics approaches. Using standard isotope dilution methods, we have developed several assays that demonstrate the utility of targeted mass spectrometry for the quantification of proteins in human samples. We will discuss the development of these assays and their application to tumor marker detection in serum and to studying the mechanisms of lipoprotein metabolism.

Sponsored by
Promise Advanced Proteomics 
3:10 Absolute Protein Quantification by MS
Virginie Brun, Ph.D., CSO & Cofounder, Promise Advanced Proteomics  
Promise proposes an innovative technology (PSAQ™) based on the use of full-length stable isotope-labeled protein standards and mass spectrometry analysis. Compared to ELISA, this method allows better results in terms of precision, specificity and accuracy, for the dosage of proteins such as biomarkers in complex biological matrices.

3:25 Networking Refreshment Break with Exhibits and Poster Viewing 

4:00 Evaluation of Cancer Biomarkers using Multiple Reaction Monitoring Cubed (MRM³)

Genevieve Choquet-Kastylevsky, M.D., Ph.D., Scientific Advisor, BioMarker Department, R&D, BioMerieux

Stable isotope dilution-selected reaction-monitoring mass spectrometry (SID-SRM-MS), or stable isotope dilution-multiple reaction-monitoring mass spectrometry (SID-MRM-MS), carried out in triple quadrupole instruments has emerged as a promising alternative to ELISA for validation of putative protein biomarkers discovered during proteomics projects.

4:30 Enhanced Detection of Low-Abundance Protein Modifications and Potential Biomarkers by Hexapeptide Libraries

Sri BandhakaviSricharan Bandhakavi, Ph.D., Sr. Scientist, New Technologies R&D, Life Science Group, Bio-Rad

Dynamic range compression (DRC) by hexapeptide libraries increases MS/MS-identification of lower-abundance proteins in biological samples. However, two questions impede fully realizing DRC’s potential. First, does DRC enhance identification of protein post-translational modifications (PTMs)? Second, can DRC be incorporated into differential analyses? Using DRC, we doubled identified salivary glyco- and phospho-proteins by MS/MS. Secondly, DRC enabled identification of novel changes to lower-abundance salivary proteins from breast cancer patients. Thus, DRC offers value for enhancing protein/PTM-based biomarker detection studies.ol

5:00 Opening Reception in the Exhibit Hall with Exhibits and Poster Viewing

6:00 Close of Day

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