Navigation Links
Signaling protein builds bigger, better bones in mice

In a new study, researchers present a “cautionary tale?about what may go wrong when using the fledgling science of proteomics to devise a diagnostic test for cancer.

In the February 16 issue of the Journal of the National Cancer Institute, researchers from The University of Texas M. D. Anderson Cancer Center detail why an experimental test intended to identify early ovarian cancer from a small sample of blood is unlikely to lead to a reliable clinical test right away.

After conducting repeated checks of the data that supported the test’s effectiveness, the researchers say their findings indicate that claims about the experimental protein-based assay are not biologically plausible.

“We view this as a cautionary tale. If you are not careful with this new technology, whose quirks we don’t fully understand, you can find results that may be due to something other than biology,?says the study’s lead author, Keith Baggerly, Ph.D., an associate professor in the Department of Biostatistics & Applied Mathematics.

He adds that this study “illustrates the need for researchers to set standards by which to conduct proteomics research,?meaning that protocols involved in these investigations should be common across laboratories so that results from one lab can be verified by others.

"We are moving in that direction,?he adds. “The technology being used to develop a variety of proteomic diagnostic tests is getting better and we are getting more reproducible results.?
Researchers worldwide are excited about the notion of using protein “barcodes?to identify individual cancers before symptoms appear, but Baggerly and others maintain that the promise of this emerging field of proteomics has not yet been met due to the difficulty in finding complex, reproducible patterns of proteins.

According to Baggerly, that now appears to be the case with the experimental ovarian cancer test at issue, which was first proposed in 2002 by researc hers in the journal, Lancet. That study reported dramatic results using mass spectrometry to search for a pattern of proteins in blood. In several sets of blinded samples, the test detected all patients who had ovarian cancer and only misdiagnosed three healthy individuals.

But among others who subsequently tested the study’s data for reproducibility were Baggerly and his colleagues (Kevin Coombes, Ph.D., and Jeffrey Morris, Ph.D., from M. D. Anderson Cancer Center, and Sarah Edmonson, M.D., from Baylor College of Medicine). They say the issue centers on how the mass spectrometer data were analyzed.

A mass spectrometer is an instrument that can quantitatively measure the concentration of hundreds of proteins from a single sample. In short, it does this by using an electric current to propel ionized proteins toward a detector. The number of ions hitting the detector at each mass-to-charge ratio (also known as m/z ratio) is recorded to produce a protein spectrum. A peak in the graph of the spectrum represents a protein (the identity of which is often unknown).

The goal is to find a pattern of peaks that will distinguish between patients with cancer and those who are cancer-free. The authors of the Lancet study have reported different proteomic patterns in three separate data sets. Researchers at the State University of New York, Stony Brook, reanalyzed the data to look for reproducible patterns. In 2003, they reported finding a single pattern involving 18 peaks (or unidentified proteins) that could diagnose ovarian cancer across two of these data sets.

The M. D. Anderson researchers examined the quality of the data sets and concluded that this systematic protein pattern “is biologically implausible.?Baggerly explains that discriminatory peaks appear to be spread across the entire m/z spectrum in the second data set, but “changes in protein expression associated with cancer should affect only a few specific peaks, not the entire spectrum .?/p>

Furthermore, the researchers say some of the protein peaks were found in regions of the spectra where, for technical reasons, mass spectrometry cannot be sampling proteins, and thus may be simply representing experimental “noise.?Such results may come about from such procedural problems as incomplete randomization of samples, Baggerly says.

The study raises a question that is broader than the effectiveness of the experimental ovarian cancer test, the researchers say. “Are we going to be able to measure what we want to measure??Baggerly asks. “Given issues in technology and a lack of standards, I think it will be a few years before we can know what works.?/p>

The study was funded by the National Cancer Institute.


'"/>

Source:


Related biology news :

1. Computational Method Speeds Mapping of Cell Signaling Networks
2. Signaling for cartilage
3. New, automated tool successfully classifies and relates proteins in unprecedented way
4. New binding target for oncogenic viral protein
5. Controversial drug shown to act on brain protein to cut alcohol use
6. Timing is everything: First step in protein building revealed
7. UWs Rosetta software to unlock secrets of many human proteins
8. Researchers find how protein allows insects to detect and respond to pheromones
9. Ancient olfaction protein is shared by many bugs, offering new pest control target
10. Automatic extraction of gene/protein biological functions from biomedical text
11. Discovery of key proteins shape could lead to improved bacterial pneumonia vaccine
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:4/6/2017)... Forecasts by Product Type (EAC), ... End-Use (Transportation & Logistics, Government & Public Sector, Utilities ... Generation Facility, Nuclear Power), Industrial, Retail, Business Organisation (BFSI), ... you looking for a definitive report on the $27.9bn ... ...
(Date:4/5/2017)... April 4, 2017 KEY FINDINGS ... expand at a CAGR of 25.76% during the forecast ... the primary factor for the growth of the stem ... https://www.reportbuyer.com/product/4807905/ MARKET INSIGHTS The global stem cell ... application, and geography. The stem cell market of the ...
(Date:3/30/2017)... 2017  On April 6-7, 2017, Sequencing.com will host ... hackathon at Microsoft,s headquarters in Redmond, ... on developing health and wellness apps that provide a ... Genome is the first hackathon for personal genomics ... companies in the genomics, tech and health industries are ...
Breaking Biology News(10 mins):
(Date:6/27/2017)... ... June 27, 2017 , ... DuPont Pioneer (DuPont) and ERS ... the ERS patent portfolio covering CRISPR-Cas genome editing technology for all agricultural uses ... (IP) of the CRISPR-Cas technology from co-inventor and co-owner Emmanuelle Charpentier, Ph.D. ...
(Date:6/23/2017)... ... June 23, 2017 , ... Biova, LLC., the leader in water soluble ... of Directors. Dr. Henig will bring a wealth of scientific experience in the food, ... Chief Technical and Scientific Officer of four major global companies in the last 4 ...
(Date:6/22/2017)... ... June 21, 2017 , ... Beaker, the industry’s ... in the life sciences industry, today announces a strategic partnership with Alcami Corporation, ... full advantage of Beaker’s expertise in executive recruitment solutions, providing Alcami with access ...
(Date:6/22/2017)... ... June 22, 2017 , ... For the months ... produced a Spotlight series on “Cell Therapy Regulation” for its regenerative ... experts on the unique regulatory challenges of stem cell medical research. , Stem ...
Breaking Biology Technology: