Jan 31, 2018 | Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing
Researchers are finding multiple approaches to metabolomic research and development involving disparate technology platforms and instrumentation
Human metabolome has been discovered to be a wealth of medical laboratory biomarkers for diagnosis, therapy, and patient monitoring. Because it can provide a dynamic phenotype of the human body, there are many potential clinical laboratory applications that could arise from metabolomics, the study of metabolites.
Researchers are discovering numerous ways the expanding field of metabolomics could transform the future of healthcare. However, to fully exploit the potential of human metabolome, developers must choose from various approaches to research.
“The metabolites we’re dealing with have vast differences in chemical properties, which means you need multi-platform approaches and various types of instrumentation,” James MacRae, PhD, Head of Metabolomics at the Francis Crick Institute in London, told Technology Networks. “We can either use an untargeted approach—trying to measure as much as possible, generating a metabolic profile—or else a more targeted approach where we are focusing on specific metabolites or pathways,” he added.
A multi-platform approach means different diagnostic technologies required to assess an individual’s various metabolomes, which, potentially, could result in multi-biomarker assays for medical laboratories.
Measuring All Metabolites in a Cell or Bio System
Metabolomics is the study of small molecules located within cells, biofluids, tissues, and organisms. These molecules are known as metabolites, and their functions within a biological system are cumulatively known as the metabolome.
Metabolomics, the study of metabolome, can render a real-time representation of the complete physiology of an organism by examining differences between biological samples based on their metabolite characteristics.
“Metabolomics is the attempt to measure all of the metabolites in a cell or bio system,” explained MacRae in the Technology Networks article. “You have tens of thousands of genes, of which tens of thousands will be expressed—and you also have the proteins expressed from them, which will then also be modified in different ways. And all of these things impact on a relatively small number of metabolites—in the thousands rather than the tens of thousands. Because of that, it’s a very sensitive output for the health or physiology of your sample.
“With that in mind, metabolomics has great potential for application in most, if not all, diseases—from diabetes, heart disease, cancer, HIV, autoimmune disease, parasitology, and host-pathogen interactions,” he added.
The graphic above is taken from a study published in the Journal of the American College of Cardiology (JACC). It notes, “State-of-the-art metabolomic technologies give us the ability to measure thousands of metabolites in biological fluids or biopsies, providing us with a metabolic fingerprint of individual patients. These metabolic profiles may serve as diagnostic and/or prognostic tools that have the potential to significantly alter the management of [chronic disease].” (Image and caption copyright:Journal of the American College of Cardiology.)
• Genomics: the study of DNA and genetic information within a cell;
• Proteomics: the large-scale study of proteins; and,
• Transcriptomics: the study of RNA and differences in mRNA expressions.
Researchers caution that metabolomics should be used in conjunction with other methods to analyze data for the most accurate results.
“Taking everything together—metabolic profiling, targeted assays, label incorporation and computational models, and also trying to associate all of this with proteomics and
genomics and transcriptomic data—that’s really what encapsulates both the power and also the challenges of metabolomics,” MacRae explained.
Metabolome in Precision Medicine
Metabolomics may also have the ability to help researchers and physicians fine-tune therapies to meet the specific needs of individual patients.
“We know we’re all very different and we don’t respond to drugs in the same way, so we could potentially use metabolomics to help select the best treatment for each individual,” Warwick Dunn, PhD, Senior Lecturer in Metabolomics at the University of Birmingham, Director of Mass Spectrometry, Phenome Center Birmingham, and, Co-Director, Birmingham Metabolomics Training Center, UK, told Technology Networks.
“Our genome is generally static and says what might happen in the future. And the metabolome at the other end is the opposite—very dynamic, saying what just happened or could be about the happen,” Dunn explained. “So, we could apply it to identify prognostic biomarkers, for example, to predict if someone is at greater risk of developing diabetes five to ten years from now. And if you know that, you can change their lifestyle or environment to try and prevent it.”
Metabolomics continues to tap the many diagnostic possibilities posed by the human metabolome. And, the resulting human biomarkers derived from the research could result in a rich new vein of medical laboratory assays.
—JP Schlingman
Related Information:
Metabolomics and Health: On the Cusp of a Revolution
‘Metabolomics’ Distinguishes Pancreatic Cancer from Pancreatitis
Using Metabolomics to Prevent Colon Cancer
Applications of Metabolomics
The Emerging Role of Metabolomics in the Diagnosis and Prognosis of Cardiovascular Disease
Metabolomics Takes Another Step Forward as Methodology for Clinical Laboratory Testing with Development of an Assay for the Diagnosis of Concussion
Jan 4, 2017 | Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing
Researchers believe they have begun to crack open a ‘black box’ involving the genomes and diseases of individual patients
Researchers in Switzerland are developing a new way to use mass spectrometry to explain why patients respond differently to specific therapies. The method potentially could become a useful tool for clinical laboratories that want to support the practice of precision medicine.
It is also one more example of how mass spectrometry is being used by researchers to develop new types of diagnostic assays that perform as well as traditional clinical laboratory testing methods, such as chemistry and immunoassay.
Thus, the latest research from the Swiss Federal Institute of Technology in Lausanne (EPFL) and ETH Zurich (ETHZ), will be of interest to pathology laboratory managers and medical laboratory scientists. It combines SWATH-MS (Sequential Window Acquisition of all Theoretical Mass Spectra) with genomics, transcriptomics, and other “omics,” to explain why patients respond differently to specific therapies, and to formulate a personalized strategy for individual treatment. (more…)
Aug 17, 2016 | Compliance, Legal, and Malpractice, Instruments & Equipment, Laboratory News, Laboratory Operations, Laboratory Pathology
Powered by massive data sets, precision medicine is unlocking new insight into the treatment of diseases and conditions. At the same time, pathology groups and medical laboratories are leading the way to creating the storage solutions, analytic tools, and networks that will power tomorrow’s advances in precision medicine
There is exponential growth in the amount of data generated at medical laboratories, pathology groups, and hospital diagnostic facilities. As gene sequencing technologies and tools continue to decrease in price but increase in both speed and accessibility, the volume of data will grow further still.
This has major implications for the field of precision medicine. In order for physicians, hospitals, and clinical laboratories to move forward with precision medicine, to advance, it will be essential that they have sophisticated capabilities in data handling, storage, and analysis.
Yet, hospitals wanting to do more with precision medicine might not be the providers that unravel the technicalities of harnessing this new pool of big data. Pathology groups and medical laboratories are already familiar with the challenges of managing complex data, such as that created by genome sequencing and molecular diagnostic assays. As they continue to bolster their information technology (IT) staffing and infrastructure, these labs are positioned to be the keepers for much of the data driving new medical developments.
Hospital IT Departments Lag in Preparations to Handle Genomic Data
In a Health Catalyst survey, 59% of healthcare executives polled do not believe that precision medicine will play a significant role in their organizations by 2020. Nearly two-thirds of respondents have no plan to integrate genomic data into their electronic health record (EHR) systems.
Despite the trend against genomic data integration, the same survey noted that half of the respondents believe that DNA sequencing could improve patient treatment strategies within their organizations.
However, as medical laboratories have known for some time, obtaining data from molecular and genetic testing is only the beginning. Without the ability to analyze results, communicate information, and store lab test data for access by other parties, the potential benefits of precision medicine will remain unrealized.
Medical Laboratories Leading the Charge for Better Data Handling and Analysis
The good news is that within many health systems, medical laboratories are already adapting IT systems to manage the large data sets required for molecular diagnostics and genetic testing. One of the lessons these labs are learning is that the more molecular and genetic testing the do, the more informatics staff they need.
Simply said, these innovative labs are devoting more physical space to informatics and a larger proportion of the laboratory staff are informatics specialists. In The Dark Report, Gregory J. Tsongalis, PhD, Professor of Pathology and Director of Molecular Pathology at the Theodore Geisel School of Medicine at Dartmouth College, stated, “We just opened a new clinical lab facility of 11,000 square feet at the Geisel School. Over 25% of that space will be devoted to data management. Because of the increasing volume of data generated at this site, there are more computational technologists than lab technicians.” (See The Dark Report, “New Molecular Analyzers to Bring Big Data to All Labs, July 13, 2015.)
Gregory J. Tsongalis, PhD (center right), is Professor of Pathology and Director of Molecular Pathology at the Theodore Geisel School of Medicine at Dartmouth College. (Photo copyright: The Geisel School of Medicine at Dartmouth.)
Tsongalis believes that labs themselves are positioned to become the storage providers and gatekeepers for much of the data driving precision medicine. Noting an increasing shift toward staffing informaticists in clinical labs to handle data, he says, “This is probably one aspect of the big data trend where pathologists and lab scientists are ahead of health system administrators.”
Medical Labs Must Address Issues Associate with Handling Genomic Data
Regardless of who holds the increasing amount of genomic data coming out of assays and tests, healthcare providers, laboratories, and vendors must create a set of standards to address both integration with EHR systems, and maintaining privacy and security on a scale never-before addressed.
In an article published in Health Data Management, Deven McGraw, Deputy Director for Health Information Privacy at the Department of Health and Human Services Office for Civil Rights, stressed the importance of data security as the regulatory agency begins work on aspects of the Precision Medicine Initiative. “A robust data security framework will be built in from the start. This is a new model for scientific research, but it is not widespread,” McGraw stated.
The Action Collaborative on Developing Guiding Principles for Integrating Genomic Information into the Electronic Health Record Ecosystem also is piloting a collaborative between Intermountain Healthcare, ARUP Laboratories, and Cerner, to examine privacy standards as well as standards for integration and representation of genomic data sets.
As pools of healthcare data and medical laboratory test results continue to grow and clinical laboratories continue to explore new methods of genetic testing and analysis, partnerships such as the Action Collaborative will remain critical opportunities for medical laboratories and pathology groups to use their current advantage to further their future roles in precision medicine.
—Jon Stone
Related Information:
Survey: Most Healthcare Organizations Unprepared for Precision Medicine
Big IT Challenges Ahead for Precision Medicine
About the Precision Medicine Initiative Cohort Program
Fact Sheet: President Obama’s Precision Medicine Initiative
DIGITizE: Displaying and Integrating Genetic Information Through the EHR
Newer, Smaller Analyzers Will Bring Big Data to Labs
Jun 10, 2016 | Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
Some cancer researchers worry that these patients may not benefit from such clinical laboratory testing because effective therapeutic drugs don’t exist for their cancers
What can be more patient-centric than for a medical laboratory company to offer free genetic tests for cancer? That’s the strategy of a firm in Canada that is offering free cancer genomics testing to 1,500 cancer patients. However, some cancer researchers responded to this offer with skepticism.
In March, Contextual Genomics of Vancouver, British Columbia, began providing its cancer genomics test free to the first 1,500 patients whose oncologists submitted tumor samples. These specimens would be tested using the company’s Find It hotspot cancer panel.
“You could call it marketing, but it’s making this test available to people who haven’t had access to it before,” stated Chris Wagner, Contextual Genomics President and CEO, in a CBC News Canada interview.
Contextual Genomics says its Find It test focuses on “90 hotspots across 29 known cancer genes and analyzes seven exons of three genes,” with the specific genes and mutations selected because they are “actionable and can potentially direct patient treatment, indicate prognosis, and support diagnosis.” Oncologists that participate in this commercial pilot program will receive a comprehensive report that interprets the sequencing results. The report also identifies any approved drugs or clinical trials that target the patient’s gene mutations. (more…)
Feb 16, 2015
PRESS RELEASE
THE DARK REPORT
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FOR IMMEDIATE RELEASE
Media Contact: Ron Martin
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AUSTIN, Texas (February 16, 2015) – Pharmacogenomic testing, or PGx, is the study of how an individual’s genetic makeup affects their response to drugs. Through the use of PGx, patient-specific genomic markers are used to select the appropriate treatment for ensuring drug efficacy, while minimizing the risk of toxicity.
“Although the value of PGx testing is clear, it presents a number of challenges to physicians, clinical diagnostic laboratories, and healthcare institutions,” states Robert L. Michel, Editor-In-Chief of The Dark Report. “A primary challenge is the difficulty of analyzing the complex amount of information involved in PGx testing, and then turning that information into actionable intelligence that a busy physician can use to drive good medical care—and to do so in a cost-effective, efficient, and reliable manner.”
One potential solution is to invest in an outsourced, cloud-based PGx interpretation service, which allows for numerous advantages, including faster time to implementation, quicker turnaround times and more consistent end results, in addition to lower investment risk and an ultimate lower overall cost. Addressing this important topic is a recently published white paper from The Dark Report, entitled “A Lab Leader’s Guide to Pharmacogenomic Testing (PGx): Cloud-Based Software Reporting of PGx for Hospitals, Health Systems and Clinical Laboratories.” Published by The Dark Report and Dark Daily, it is available free to laboratory professionals as a PDF download.
This free white paper provides a greater understanding of the obstacles physicians, laboratories and hospitals face when launching a pharmacogenomics program, how PGx testing can be used to drive patient care, and the important role cloud-based software can play in making PGx testing a practical and cost-effective solution.
White paper topics specifically addressed include:
- The ways in which pharmacogenomics can lead to an ultimate overall decrease in healthcare costs
- Myriad benefits that pharmacogenomics testing can provide patients
- How numerous studies support the clinical usefulness of PGx testing
- Various barriers to entry into the pharmacogenomic testing market
- Outsourcing as a solution to making PGx testing a viable option for laboratories
- The many advantages to a service that specializes in PGx interpretation
- Today’s status of genomic testing in the lab market, and what the future may hold
For an enlightening overview of pharmacogenomic testing and how PGx fits into current and future healthcare goals, and examples of how a cloud-based, Software-as-a-Service platform can help healthcare providers overcome obstacles encountered when considering entering the pharmacogenomic testing market, click here. “A Lab Leader’s Guide to Pharmacogenomic Testing (PGx): Cloud-Based Software Reporting of PGx for Hospitals, Health Systems and Clinical Laboratories” is a free publication and part of the Dark Daily Resource Center, comprised of a growing library of white papers and other information resources tailored specifically to the needs of laboratory administrators, lab managers, pathologists, and lab industry consultants.
For additional information, Contact: Ron Martin, 512-264-7103
About THE DARK REPORT
Established in 1995, THE DARK REPORT is the leading source of exclusive business intelligence for laboratory CEOs, COOs, CFOs, Pathologists and Senior industry executives. It is widely read by leaders in laboratory medicine and diagnostics. The Dark Report produces the famous Executive War College on Laboratory and Pathology Management every spring, which showcases innovations by the nation’s and globe’s leading laboratory organizations. Dark Daily is an Internet-based e-briefing intelligence service, read worldwide by thought leaders in laboratory and pathology management. Other well-known conferences conducted by THE DARK REPORT are Lab Quality Confab (on the use of Lean and Six Sigma methods in labs and hospitals), Molecular Summit (on the integration of in vivo and in vitro diagnostics). THE DARK REPORT co-produces Frontiers in Laboratory Medicine annually in the United Kingdom; Executive Edge bi-annually in Canada; and The Business of Pathology bi-annually in Australia.
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