newsletter published in partnership between TMIC and
the Metabolomics Society
Issue 29 - January 2014
Metabolomics Society News
• Professor Jeremy Nicholson (Imperial College, London)Early-bird registration closes on 14th March 2014
• Professor Roy Goodacre (University of Manchester)
• Dr Julian Griffin (MRC Human Nutrition Research, Cambridge)
• Dr Steffen Neumann (Leibniz Institute of Plant Biochemistry, IPB Halle, Germany)
• Professor Paul Thomas (Loughborough University)
• Professor Jean-Luc Wolfender (University of Geneva, Switzerland)
* Additional fee applies, see registration website; Members will also have electronic access to all issues and therefore print copies of back issues will not be available to Members who register late in the calendar year.Further benefits for Student Members
** Not applicable for Student Members.
It is clearly observed in this survey that a synergistic relationship is required between technology providers (vendors) and users of these technologies in industry (for example, pharma, agrichemical, service providers) and academia. Examples of how these relationships can benefit both parties are shown in Figure 1 and are discussed below.
Scientist at Waters Corporation, Milford, Massachusetts,
USA, and Adjunct Professor at Georgetown University,
Washington, DC, USA
Giuseppe Astarita, a principal scientist at Waters Corporation (Milford, Massachusetts USA) and adjunct professor at Georgetown University (Washington, DC USA), specializes in the areas of lipidomics and metabolomics. His research interests include lipid mass spectrometry and metabolomics, as applied to translational medicine and biomarker discovery. Dr. Astarita is applying the latest technologies in the study of health and disease as well as food and nutrition. In his current position at Waters, he brings his background to bear in contributing to the development of the company's metabolomics business.
|2 Dec 2013
Time to put your feet up: A new automated metabolite analysis tool
Ideally, biologists studying differences in metabolite expression between two groups of samples, such as healthy and diseased tissue, would like a system that could simply take in samples at one end and then pop out interesting biological information at the other. This information would include which metabolites are differently expressed in the two samples and which metabolic pathways have been thrown out of kilter by the disease process.
Although biologists can already obtain this information, they generally have to work for it. First, they need to analyze the metabolite samples with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Then they need to convert the resultant data into a useable form by removing background noise, detecting individual peaks and aligning those peaks between different samples.
Once the data is in a useable form, the biologists then need to analyze it with appropriate statistical techniques in order to discover which metabolites are differently expressed between the healthy and diseased samples. Finally, they need to determine the identity of the differently expressed metabolites, usually by scrutinizing a spectral database, and then work out what metabolic pathways those metabolites might take part in.
Understandably, this all takes time and effort, and also requires expertise in bioinformatics and statistical analysis, which many biologists lack. Hence the attraction of a completely automated system that accepts samples at one end and produces information at the other. And just recently, such systems have begun to appear.
Earlier this year saw the release of a web-based software tool called XCMS Online, which was specifically designed to open up metabolomics to biologists with little knowledge of bioinformatics (see Metabolomics for all). In one simple automated process, XCMS Online detects peaks, aligns retention times between samples, determines metabolites that are present at different concentrations in different samples, assigns possible identities to those metabolites, and performs multivariate statistical analyses.
Now, XCMS Online has been joined by another web-based software tool called MetaboLyzer, which was also specifically designed to open up metabolomics to more biologists. Whereas XCMS Online covers the whole data analysis process, however, MetaboLyzer focuses on the stage after the initial noise reduction, peak detection and alignment steps. Albert Fornace and his colleagues at Georgetown University Medical Center in Washington, DC, US, who developed MetaboLyzer, chose to focus on this later stage because a lot of tools already exist for conducting the initial data processing. In addition, they thought there was more scope for improving the later analytical stage.
Traditionally, biologists conducting metabolite studies have tended to apply standard multivariate statistical techniques such as principle component analysis to the cleaned-up metabolite data. But these techniques were not specifically developed for metabolite data, which have their own unique idiosyncrasies that can create problems for these standard techniques.
One of the most important of these idiosyncrasies is that metabolite datasets often contain missing data, in which an ion with a certain mass-to-charge ratio simply doesn’t show up in the data for a specific sample when it does in other identical samples. Standard analytical techniques can struggle to deal with this missing data and so biologists have to resort to estimating likely values, which can mess up the resulting analysis.
With MetaboLyzer, Fornace and his colleagues adopted a different approach. The first thing MetaboLyzer does with metabolite data is to highlight those ions that are missing in a certain proportion of the samples, say over 10%, which are termed partial presence. Those ions that are present in more than 90% of the samples are termed complete presence.
Next, it determines which ions are present at different abundances in the two different sample groups, but employs a simpler statistical technique for partial presence data than for complete presence data. It then assigns metabolites to the ions found at different abundances in both the partial presence and complete presence data by scrutinizing four small-molecule databases
After this, it only conducts further analysis, including uncovering relationships between the different ions and producing heat maps and volcano plots, on the complete presence data. In this way, MetaboLyzer can focus its analytical efforts on the detailed data, while still having access to less detailed data that can back up any findings from the detailed data.
All of which helps with the automated uncovering of interesting biological information.
|1 Dec 2013
Enhancing Colon Cancer Screening through Polyp Detection
Metabolomic Technologies (MTI) has developed a technology that detects colonic polyps, the precursor to colorectal cancer (CRC), using a noninvasive urine test. Unlike fecal-based tests, PolypDx™ detects polyps before they become cancerous, according to the company. The assay, now in beta testing, has the potential to improve patient compliance. By enabling early intervention, it also may reduce the high healthcare costs associated with treating CRC, by reducing the numbers of surgeries and hospitalizations.
“In Canada, colonoscopies are not the first line of defense. Instead, our healthcare system uses fecal-based tests,” Reg Joseph, CEO, explains. For those tests, patients collect their samples at home and send them to a lab. With that approach, compliance rates across Canada are as low as 14%. “Because the fecal tests detect CRC only 50% of the time, often people without polyps and cancer undergo colonoscopies. Eighty percent of patients referred for colonoscopies that are based upon fecal tests do not have CRC. Because of the invasive nature of this procedure and lack of patient compliance, many are not screened in time.”
PolypDx addresses those issues, MTI reports. It is a single spot test that analyzes metabolites in the urine to determine whether patients have CRC and, more importantly, whether they have colonic polyps. The test has a sensitivity of 71% and a specificity of 61% in terms of polyp detection. In contrast, standard-of-care fecal-based tests are designed to detect CRC—not colonic polyps. When used to detect polyps, fecal-based tests have sensitivities of 1–15%. Therefore, PolypDx represents a significant advance in polyp detection.
“We’re continuing to improve sensitivity and specificity for PolypDx by screening against a larger metabolomic library,” Joseph says. The current version is based on an NMR platform. An improved version offering higher throughput and enhanced ease of use is being developed on a mass spectroscopy platform. It is expected to become available in 2015. Mass spec instruments are used routinely in large diagnostics labs, so this new test kit can be integrated easily into current workflows.
“We’re working with Alberta Health Services and DynaLIFEDx to look at scaling up this test for large population screening,” Joseph says. Alberta Health Services is collaborating with MTI to release the assay kit as early as possible. MTI plans to commercialize the first version of the test in late 2014.
Ultimately, MTI envisions PolypDx as a routine screening tool that will be used before patients undergo a colonoscopy. “We’d like to be able to screen thousands of patients per day using one instrument,” Joseph says.
“More than 95% of colon cancer patients develop cancer through adenomatous colonic polyps. If we can identify these patients before the onset of cancer, the chance of survival is more than 90%.” The PolypDx assay kit is expected to be priced at about $50. The annual U.S. burden for CRC treatment is $14 billion.
MTI’s platform also may be harnessed for other diseases. MTI is developing ColoDx™ for CRC. Additionally, “We can see the preliminary signatures for prostate and breast cancers.” Urine-based assays for those diseases are in the early development phase.
The technology spun out of the University of Alberta in Canada, which is known globally for metabolomics research. Company founders, gastroenterologist Richard Fedorak, M.D., and colorectal surgeon Haili Wang, M.D., collaborated with the university’s metabolomics group, which was collecting bio-samples to identify potential diagnostics for a variety of diseases. A retrospective study led to a prospective study and, eventually, PolypDx.
“MTI is actively seeking partnerships and strategic commercial partners,” Joseph says.
MTI is collaborating with BGI-Shenzhen to develop the assays for the Chinese market. The assay is undergoing validation and clinical trials in China. According to Yong Zhang, Ph.D., head, proteomic division, BGI-Shenzhen, “Our company is the best positioned to co-develop MTI’s diagnostic tests for the Chinese market, assist with the regulatory process, and market the technology.”
“In the West, the regulatory landscape for multivariate tests like metabolomics is a bit gray. China, however, has a progressive regulatory framework that is focused around driving down the costs of disease for a large, new middle class that is demanding high-quality healthcare.” Therefore, “Preventive strategies—including diagnostics—are on the fast track.” Additionally, the University of Alberta has had research collaboration with BGI-Shenzhen for the past five years. Leveraging that relationship enables MTI to showcase a translational project and make a real difference, quickly, in individuals’ health.
Joseph says MTI’s finances are sound. MTI is funded by angel and super angel investors and by grants from Alberta Innovates—Health Solutions, the National Research Council of Canada’s Industrial Research Assistance Program, and Alberta Enterprise and Advanced Education. “Our burn rate isn’t excessively high, so regional financing will take us through the next few years.”
|22 Nov 2013
The NIH Metabolomics Program’s Standards Synthesis Centers
The National Institute of Health’s Common Fund Metabolomics program aims to increase capacity in metabolomics by supporting the development of next generation technologies. The goal is to enhance the sensitivity and speed with which specific elements of the cellular metabolome can be identified and quantified. As a component of this program, two metabolite standards synthesis centers (Research Triangle Institute and Stanford Research Institute) have been awarded contracts to chemically synthesize metabolite standards and make them available to the scientific community. Nominations are being sought from the metabolomics research community for metabolite standards that are not readily available from other sources. Nominations can be made at: http://www.metabolomicsworkbench.org/standards/nominatecompounds.cgi and metabolites will be prioritized for synthesis after review by the program’s executive committee.
Source: Pothur Srinivas, personal communication, November 22, 2013
|3-5 Feb 2014
Applications of NMR in Industry Conference
|3-7 Feb 2014
The Imperial International
Phenome Training Centre is offering "Hands-on
LC-MS for Metabolic Profiling"
|Early March 2014
mzTab for Metabolomics
|17-21 Mar 2014
EMBO Practical Course on
Metabolomics Bioinformatics for Life
This course will provide an overview of key issues that affect metabolomics studies, bioinformatics tools, and procedures for the analysis of metabolomics data. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics.
This course is aimed at PhD students and researchers with a minimum of one year’ s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants must have experience using R (including a basic understanding of the syntax and ability to manipulate objects) and the UNIX/LINUX operating system.
For more information, visit http://www.ebi.ac.uk/training/course/metabolomics-2014.
|7-11 Apr 2014
Workshop Metabolomics 2014
The workshop flyer is available here. For more details, please visit http://www.plantsandmetabolomics.nl/
|30 Apr 2014
Analytical Tools for
Cutting-edge Metabolomics - a joint meeting of
the Analytical Division of the RSC and the
international Metabolomics Society
Analytical chemistry has been one of the driving forces behind the development of metabolomics research over the past decade. The conference will bring together exceptional scientists for a program consisting of plenary and invited talks, posters, as well as an oral session devoted to early career researchers. It will be an excellent opportunity for analytical chemists to learn more about metabolomics and its application, and for metabolomics scientists to improve their knowledge of cutting-edge bioanalytical tools.
Deadline for submission of abstracts: 14 March 2014
Prof. Jeremy Nicholson, Imperial College, London UK - Plenary speaker
Dr Julian Griffin, MRC Human Nutrition Research, Cambridge, UK
Prof. Roy Goodacre, University of Manchester, UK
Prof. Jean-Luc Wolfender, University of Geneva, Switzerland
Dr Steffen Neumann, Leibniz Institute of Plant Biochemistry, IPB Halle, Germany
Prof Paul Thomas, Loughborough University
|16-17 Jun 2014
Informatics and Statistics
for Metabolomics (2014)
A poster announcing this workshop can be found here.
The workshop will cover many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomic databases and exploring chemical databases. Participants will be given various data sets and short assignments to assist with the learning process.
This course is intended for graduate students, post-doctoral fellows, clinical fellows and investigators who are interested in learning about both bioinformatic and cheminformatic tools to analyze and interpret metabolomics data.
Prerequisite: Your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements). If you do not access to a laptop, you may loan one from the CBW. Please contact email@example.com for more information.
Pre-Readings: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before. Please complete the following: R Tutorial
|23-26 Jun 2014
Metabolomics 2014: 10th
Annual International Conference of the
We are delighted to host the 10th Anniversary of the International Conference of the Metabolomics Society (Metabolomics2014) at Keio University in Tsuruoka City, where the very first meeting of the society was held in 2005. Since then, Tsuruoka has grown to “a city of metabolomics”; various additional research buildings have been built, and two spin-out companies established. Tsuruoka is a pretty city located 500 km north of Tokyo (about 1 hour flight), and surrounded by beautiful Japanese nature, historic spots, and exotic culture. You will also enjoy the best authentic Japanese food and sake (rice wine), as well as hot springs. So, come celebrate the 10th anniversary of the society, and enjoy high-quality scientific presentations by top-notch researchers around the world.
Early registration and abstract submission due March 31, 2014.
For detailed information about Metabolomics 2014, visit http://metabolomics2014.org.
|10-12 Sep 2014
Call for Papers
If you would like to be considered for an oral presentation at this meeting, Submit an abstract for review now!
Oral Presentation Submission Deadline: 31 January 2014
Call for Posters
You can also present your research on a poster while attending the meeting. Submit an abstract for consideration now!
Poster Submission Deadline: 27 August 2014
Drug Discovery and Pharma
Human Health and Nutrition
Microbial, Invertebrate and Environmental Applications
Data Analysis and Integration with Systems Biology
For more details, please visit the conference website.
|28 Jun to 2 Jul 2015
Metabolomics 2015: 11th
Annual International Conference of the
Stay abreast of the latest Metabolomics Society news via the Twitter feed on the front page of the website (http://www.metabolomicssociety.org). Also you can follow us on Twitter: Metabolomics Society @MetabolomicsSoc and Metabolomics journal @Metabolomics. And you can visit us on Facebook.
Please come back later for detailed information about Metabolomics 2015 by visiting http://metabolomics2015.org.
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advertising positions in metabolomics. If you have a job
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|Experimental Officer in Bioinformatics||University of Birmingham||
University of Birmingham
|BBSRC and Thermo Scientific-funded PhD studentship (clinical metabolomics and metabolite annotation)||University of Birmingham||Birmingham, UK||29-Dec-2013||31-Jan-2014||FindaPhD.com|
|BBSRC and Thermo Scientific-funded PhD studentship (environmental metabolomics and safety assessment of engineered nanomaterials)||University of Birmingham||Birmingham, UK||29-Dec-2013||17-Jan-2014||FindaPhD.com|
|Research Scientist (NMR Spectroscopist to support Business Development group)||Bruker BioSpin||
|Assistant Research Scientist (NMR Spectroscopist to support R&D efforts for Business Development group)||Bruker BioSpin||Billerica, USA||2-Dec-2013||Bruker BioSpin|
Ian J. Forsythe, M.Sc.MetaboNews
Department of Computing Science
University of Alberta
221 Athabasca Hall
Edmonton, AB, T6G 2E8, Canada
This newsletter is published in partnership between The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) and the Metabolomics Society (http://www.metabolomicssociety.org) for the benefit of the worldwide metabolomics community.
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