Designing Verification Studies for New Markers

HomeResearch TopicsTranslational ProteomicsDesigning Verification Studies for New Markers
Designing Verification Studies for New Markers 2016-11-10T20:32:44+00:00

Notable peer-reviewed articles–integration of statistical, quality control, and sample collection protocols for MS-based verification of putative biomarkers.


Articles of note

Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies

Protein biomarkers are needed to deepen our understanding of cancer biology and to improve our ability to diagnose, monitor, and treat cancers. Important analytical and clinical hurdles must be overcome to allow the most promising protein biomarker candidates to advance into clinical validation studies. Although contemporary proteomics technologies support the measurement of large numbers of proteins in individual clinical specimens, sample throughput remains comparatively low. This problem is amplified in typical clinical proteomics research studies, which routinely suffer from a lack of proper experimental design, resulting in analysis of too few biospecimens to achieve adequate statistical power at each stage of a biomarker pipeline. Read more ›

Implementation of statistical process control for proteomic experiments via LC MS/MS

Statistical process control (SPC) is a robust set of tools that aids in the visualization, detection, and identification of assignable causes of variation in any process that creates products, services, or information. A tool has been developed termed Statistical Process Control in Proteomics (SProCoP) which implements aspects of SPC (e.g., control charts and Pareto analysis) into the Skyline proteomics software. It monitors five quality control metrics in a shotgun or targeted proteomic workflow. None of these metrics require peptide identification. Read more ›

Practical guidance for implementing predictive biomarkers into early phase clinical studies (free full-text)

The recent U.S. Food and Drug Administration (FDA) coapprovals of several therapeutic compounds and their companion diagnostic devices (FDA News Release, 2011, 2013) to identify patients who would benefit from treatment have led to considerable interest in incorporating predictive biomarkers in clinical studies. Yet, the translation of predictive biomarkers poses unique technical, logistic, and regulatory challenges that need to be addressed by a multidisciplinary team including discovery scientists, clinicians, biomarker experts, regulatory personnel, and assay developers. Read more ›

Regulatory perspective on translating proteomic biomarkers to clinical diagnostics

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. Read more ›

Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach (free full-text)

Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Read more ›