Overcoming the challenges of implementing high value tests in the clinical lab

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Educational Grants supported in part by:
& Brian Kelly

Invited Speakers

Tue April 05 @ 15:00 (03:00 PM) in De Anza
Beyond the Human Genome: A Million Person Precision Population Health Project
Leroy Hood
Institute for Systems Biology

The vision of this project is that we will develop the infrastructure to employ a data-driven approach to optimizing the health trajectory of individuals for body and brain. We have two large populations (5000 and 10,000) that have validated this approach for body and brain health, respectively. These studies have led to us pioneering the science of wellness and prevention. This project will require the acquisition of key partners for execution, which will be delineated. We are approaching the Federal Government for funding, as we did for the first Human Genome Project. This project will lead to striking new knowledge about medicine, it will catalyze the initiation of start-up companies and it will catalyze a paradigm shift in healthcare from a disease orientation to a wellness and prevention orientation. This will catalyze the largest paradigm shift in medicine, ever.
Tue April 05 @ 16:00 (04:00 PM) in De Anza
The Clinical Laboratory Perspective on Wellness Testing: Let’s Take a Look Under the Hood
Geoff Baird
University of Washington

As medical science continues to make gains in the elucidation of disease pathophysiology and the discovery of cures , some have questioned the value of dedicating dwindling financial resources to maintaining wellness rather than to fighting disease per se. While both approaches are meritorious and complementary, neither approach is alone sufficient to ensure the health of a population. One major problem with the focus on wellness is the Bayesian dilemma that the positive predictive value of clinical laboratory testing in apparently healthy people is often low, as the specificities of few clinical tests are high enough to ensure that most positive results are true. The impact of this dilemma on laboratory-based wellness approaches will be discussed.
Tue April 05 @ 16:00 (04:00 PM) in De Anza

Mari DeMarco
University of British Columbia

Wed April 06 @ 08:00 (08:00 AM) in De Anza
Glycoproteins as Biomarkers for Cancers
Carlito Lebrilla
UC Davis

Wed April 06 @ 09:00 (09:00 AM) in De Anza
How Can Proteomics Fulfill the Unmet Needs of Effective Drug Treatment Stratification for Patients with Ovarian Cancer?
Stefani Thomas
University of Minnesota

The mutational status of a solid tumor can predict the therapeutic efficacy of a specific drug in a molecularly defined subset of patients. Targeted therapies are available to treat advanced (stage II – IV) ovarian cancer with mutations in BRCA1/2 genes. Unfortunately, there is considerable inter-patient heterogeneity in BRCA1/2–based determinations of drug treatment sensitivity. Determining the proteome-level mechanisms of drug treatment sensitivity could enhance our ability to select the ovarian cancer patient populations that would benefit the most from these targeted therapies, consequently improving survival and overall treatment response. Our laboratory is applying mass spectrometry-based proteomics to identify protein signatures of drug treatment sensitivity and subsequent patient stratification for treatment. This presentation will provide an overview of the experimental models and analytical approaches that we are utilizing toward a long-term goal of identifying prognostic protein biomarkers of drug treatment sensitivity in patients with high-grade serous ovarian cancer.
Wed April 06 @ 09:45 (09:45 AM) in De Anza
N-linked Glycans in Human Disease: From New Tools to Translational and Preclinical Studies
Peggi Angel
MUSC Proteomics Center

N-glycosylation plays a significant role in immune cell recruitment, influences disease progression and outcome and response to therapy. Here, we discuss simplified workflows capable of reporting N-glycan expression patterns in tissues, cells and biofluids. We present translational and pre-clinical work investigating glycosylation patterns in cardiovascular disease, cancer risk and cancer. A long-term goal is to leverage glycosylation patterns to non-invasively monitor disease status and therapeutic efficacy.
Thu April 07 @ 08:00 (08:00 AM) in De Anza

Barbara Engelhardt
Princeton University

Thu April 07 @ 09:00 (09:00 AM) in De Anza

Meena Choi
Genentech

Fri April 08 @ 09:00 (09:00 AM) in De Anza
Addressing Hurdles in Clinical Translation of Targeted Proteomics
Jeffrey Whiteaker
Fred Hutchinson Cancer Research Center
Quantifying proteins and post-translational modifications will improve precision medicine, but several hurdles remain to adopting proteomics to the clinical laboratory. Dr. Whiteaker will discuss successes and remaining challenges for incorporating targeted proteomic measurements in clinical trials and other clinical applications.
Fri April 08 @ 10:00 (10:00 AM) in De Anza
Newborn Screening by Mass Spec Meets Newborn Screening by DNA Sequencing
Michael Gelb
University of Washington

Our laboratory has been developing tandem mass spectrometry (MS/MS) for worldwide expansion of newborn screening (NBS) panels to include an ever-increasing collection of treatable genetic diseases. There is widespread discussion on the use of whole genome and whole exome DNA sequencing in population-wide NBS. The intersection of biochemical- and DNA-based NBS is an interesting topic now under heavy discussion.

We will highlight the development of liquid chromatography-MS/MS (LC-MS/MS) for multiplex NBS of a large panel of treatable genetic diseases in newborns. Next generation sequencing (NGS) is also employed currently as a second-tier analysis after LC-MS/MS assays. We will also illustrate how it is possible to carry out first-tier NGS followed by second-tier LC-MS/MS NBS.

LC-MS/MS is used together with enzyme substrates and biomarkers to monitor the activity of a large collection of enzymes and to measure the abundance of biomarkers in dried blood spots on NBS cards. We will focus on multiplex methods and then zoom in one a more detailed analysis of one disease called metachromatic leukodystrophy (MLD). We carried out a pilot MLD NBS study and determined that the rate of false positives out of 28,000 newborns screened is essentially zero showing the power of LC-MS/MS for NBS of this lysosomal storage disorder. In the second arm of the study, we have been measuring the activity of the enzyme relevant to MLD on a large collection of gene variants that are found in allele databases and for which no pathogenic information is reported. We show how we can integrate these efforts to provide for a highly efficient NBS program for MLD.


We screened ~28,000 newborns for elevated sulfatide lipid, the biomarker that is relevant to MLD and found 180 high sulfatide newborns. These were submitted to an assay of the activity of the relevant enzyme, arylsulfatase A, and all but two showed normal levels of activity. DNA sequencing was carried out on 2 newborns, one with 0% and one with 8% of normal ARSA activity. The newborn with 0% activity was confirmed to have MLD, the other was shown to not have MLD. On the DNA front, we created a phenotype matrix that allows one to input the ARSA enzymatic activity of each variant to provide a composite genotype, and to make a prediction of the phenotype associated with this genotype. We show that this method is 83% accurate at predicting the true set of phenotypes observed in MLD patients.

Massively multiplexed NBS of genetic diseases in newborns is possible using LC-MS/MS, and when used with second-tier NGS leads to a successful NBS platform. We show that it is also possible to carry out NGS as a first-tier NBS step and to clarify the results with second-tier biochemical assays based on LC-MS/MS. Thus LC-MS/MS meets DNA and DNA meets LC-MS/MS, and this provides a framework for the future employment of both LC-MS/MS and NGS in expansion of population based NBS.

Fri April 08 @ 10:50 (10:50 AM) in De Anza
Utilization of Mass Spectrometry to Discover and Develop Novel Biomarkers to Support Drug Development
Veronica Anania
Genentech

Biomarkers play an important role in the drug development process including providing necessary insights into target engagement, dose selection and mechanism of action of candidate therapeutics. LC-MS is uniquely positioned to enable accurate quantitation of both small and large molecule biomarker candidates, however, the process of going from biomarker discovery to a multiplexed targeted MRM panel in clinical samples is long and resource intensive. Moreover, biomarker candidates often fail to replicate when tested in large clinical cohorts. Recent advances in data-independent MS (DIA-MS) have made this technology more accessible and certain benefits of DIA-MS including reproducible label-free analysis of hundreds of samples, ability to capture low abundance ions over a high dynamic range, and deep proteome coverage makes this technology well suited to streamline translational proteomics. One major hurdle for using DIA-MS to support drug development is that the quantitative range for most DIA-MS methods has not been well characterized and thus, quantitative conclusions drawn by prior studies that have employed this approach have been controversial. Here, we describe challenges associated with applying DIA-MS methods to address questions associated with clinical development and introduce best practices for establishing quantitative criteria for DIA-MS approaches in clinical trial samples. Results and lessons learned from both discovery and targeted clinical biomarker studies will be discussed and a model for a more streamlined biomarker development workflow that conserves resources and provides more comprehensive proteomic information from clinical trial samples will be discussed.