From aptamer-based biomarker discovery to diagnostic and clinical applications: an aptamer-based, streamlined multiplex proteomic assay

Recently, we reported an aptamer-based, highly multiplexed assay for the purpose of biomarker identification. To enable seamless transition from highly multiplexed biomarker discovery assays to a format suitable and convenient for diagnostic and life-science applications, we developed a streamlined, plate-based version of the assay. The plate-based version of the assay is robust, sensitive (sub-picomolar), rapid, can be highly multiplexed (upwards of 60 analytes), and fully automated. We demonstrate that quantification by microarray-based hybridization, Luminex bead-based methods, and qPCR are each compatible with our platform, further expanding the breadth of proteomic applications for a wide user community

Age-Dependent Changes in the Cerebrospinal Fluid Proteome by Slow Off-Rate Modified Aptamer Array

An important precondition for the successful development of diagnostic assays of cerebrospinal fluid (CSF) biomarkers of age-related neurodegenerative diseases is an understanding of the dynamic nature of the CSF proteome during the normal aging process. In this study, a novel proteomic technology was used to quantify hundreds of proteins simultaneously in the CSF from 90 cognitively normal adults 21 to 85 years of age. SomaLogic's highly multiplexed proteomic platform can measure more than 800 proteins simultaneously from small volumes of biological fluids using novel slow off-rate modified aptamer (SOMAmer) protein affinity reagents with sensitivity, specificity, and dynamic ranges that meet or exceed those of enzyme-linked immunosorbent assays. In the first application of this technology to CSF, we detected 248 proteins that possessed signals greater than twofold over background. Several novel correlations between detected protein concentrations and age were discovered that indicate that both inflammation and response to injury in the central nervous system may increase with age. Applying this powerful proteomic approach to CSF provides potential new insight into the aging of the human central nervous system that may have utility in discovering new disease-related changes in the CSF proteome

Aptamer-based multiplexed proteomic technology for biomarker discovery

Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma). Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding DNA aptamer concentration signature, which is then quantified with a DNA microarray. In essence, our assay takes advantage of the dual nature of aptamers as both folded binding entities with defined shapes and unique sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to discover unique protein signatures characteristic of various disease states. More generally, we describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine

A real-world approach to Evidence-Based Medicine in general practice: a competency framework derived from a systematic review and Delphi process

Background Evidence-Based Medicine (EBM) skills have been included in general practice curricula and competency frameworks. However, GPs experience numerous barriers to developing and maintaining EBM skills, and some GPs feel the EBM movement misunderstands, and threatens their traditional role. We therefore need a new approach that acknowledges the constraints encountered in real-world general practice. The aim of this study was to synthesise from empirical research a real-world EBM competency framework for general practice, which could be applied in training, in the individual pursuit of continuing professional development, and in routine care. We sought to integrate evidence from the literature with evidence derived from the opinions of experts in the fields of general practice and EBM. Methods We synthesised two sets of themes describing the meaning of EBM in general practice. One set of themes was derived from a mixed-methods systematic review of the literature; the other set was derived from the further development of those themes using a Delphi process among a panel of EBM and general practice experts. From these two sets of themes we constructed a real-world EBM competency framework for general practice. Results A simple competency framework was constructed, that acknowledges the constraints of real-world general practice: (1) mindfulness - in one’s approach towards EBM itself, and to the influences on decision-making; (2) pragmatism – in one’s approach to finding and evaluating evidence; and (3) knowledge of the patient – as the most useful resource in effective communication of evidence. We present a clinical scenario to illustrate how a GP might demonstrate these competencies in their routine daily work. Conclusion We have proposed a real-world EBM competency framework for general practice, derived from empirical research, which acknowledges the constraints encountered in modern general practice. Further validation of these competencies is required, both as an educational resource and as a strategy for actual practice.</p

Building a Clinical Research Network in Trauma Orthopaedics: The Major Extremity Trauma Research Consortium (METRC)

OBJECTIVESLessons learned from battle have been fundamental to advancing the care of injuries that occur in civilian life. Equally important is the need to further refine these advances in civilian practice, so they are available during future conflicts. The Major Extremity Trauma Research Consortium (METRC) was established to address these needs.METHODSMETRC is a network of 22 core level I civilian trauma centers and 4 core military treatment centers-with the ability to expand patient recruitment to more than 30 additional satellite trauma centers for the purpose of conducting multicenter research studies relevant to the treatment and outcomes of orthopaedic trauma sustained in the military. Early measures of success of the Consortium pertain to building of an infrastructure to support the network, managing the regulatory process, and enrolling and following patients in multiple studies.RESULTSMETRC has been successful in maintaining the engagement of several leading, high volume, level I trauma centers that form the core of METRC; together they operatively manage 15,432 major fractures annually. METRC is currently funded to conduct 18 prospective studies that address 6 priority areas. The design and implementation of these studies are managed through a single coordinating center. As of December 1, 2015, a total of 4560 participants have been enrolled.CONCLUSIONSSuccess of METRC to date confirms the potential for civilian and military trauma centers to collaborate on critical research issues and leverage the strength that comes from engaging patients and providers from across multiple centers