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Study by EDRN Researchers Shows that SELDI-TOF-MS Analysis is Reproducible Across Six Labs


Chipping away at the theory that protein peaks are not reproducible from instrument to instrument, a new study by six of the National Cancer Institute’s Early Detection Research Network centers showed that SELDI-TOF-MS analysis of 28 prostate cancer and control samples produced reproducible results across all six labs.

In the study, published in this month’s issue of Clinical Chemistry, 28 blinded samples, including 14 prostate cancer samples and 14 control samples, were analyzed by each of the participating institutions. The institutions used an algorithm developed two years earlier by researchers in lead author Oliver John Semmes’ laboratory at the Eastern Virginia Medical School’s Virginia Prostate Center.

Results showed that researchers from all six sites correctly identified the 28 blinded samples. And though the data do not prove that a diagnostic application based on the technology is reproducible, they may bring mass specs one step closer to the world of clinical diagnostics.

“This was a validation of instrument reproducibility and portability,” said Semmes. “The take-home message is that inter-lab reproducibility is equal to intra-lab reproducibility. People were telling us that peaks found at one place were not reproducible at another place. That’s just not true.”

The participating sites for the study included the Virginia Prostate Center at Eastern Virginia Medical School; the Fred Hutchinson Cancer Center; the Center for Prostate Disease Research at the Uniformed Services University of the Health Sciences; the University of Pittsburgh Cancer Institute’s Hillman Cancer Center; the Department of Pathology at Johns Hopkins Medical Institute; the Department of Pathology at the University of Alabama Birmingham; and the Department of Medicine at the University of Texas Health Sciences Center.

Semmes emphasized that while the study proved that instrument results are reproducible, it doesn’t prove that a diagnostic application based on the technology is reproducible. “To really test this, you need to take samples from a separate population, drop them down and see how everybody does,” said Semmes.

To validate the profile, Semmes’ research group is spearheading a study involving 1,200 samples from eight institutions. The researchers seek to prove that the profile of peaks found is specific and sensitive for prostate cancer.

The 1,200 samples include prostate cancer samples, samples from people with other conditions such as inflammation, other types of cancer, and controls.

“There are a lot of confounders put in [to the validation study] because it’s important that we be able to distinguish the correct disease,” said Semmes.

The prostate cancer samples in the validation study include samples from high- and low-grade disease patients, as well as patients with benign tumors, said Semmes. Samples are stratified by prostate specific antigen scores.

“What we’re doing now may not help identify early- versus late-stage disease, but it may discriminate high- versus low-grade disease, and benign versus malignant disease,” said Semmes.

Currently, a PSA test together with a digital rectal examination is standard procedure for screening men over 50 for prostate cancer. Today, the PSA test is not very specific, and it is estimated that 75 percent of men with elevated PSA levels undergo essentially worthless biopsies, said Semmes.

“You’d like to know early, but if you could just know for sure if it is a true cancer, and if it is high or low grade, that would be useful, too,” said Semmes.

Aside from validating the prostate cancer profile, researchers are now also working on identifying and characterizing proteins from the profile peaks. They were not previously identified because researchers wanted to maintain blind samples, Semmes said.

“We believe that you can’t not identify the proteins because without the IDs, the FDA’s not going to approve” the profile as a diagnostic test, said Semmes. “At least they don’t sound like they would approve a signal without any reference to a protein.”

In November, Lawrence Lesko, FDA’s director of clinical pharmacology and biopharmacuetics, told ProteoMonitor that a number of companies have said that they intend to submit protein signature patterns to the FDA for approval as diagnostic tests, but no such signatures have yet been approved by the FDA.

Stephen Naylor, an adjunct professor of genetics and genomics at Boston University School of Medicine, said that the researchers should be applauded for making the effort to look at inter-lab reproducibity. However, the study is not very significant in terms of finding bilogical markers that are relevant to prostate cancer, he said.

“They’re differentiating a group of samples that have some disease associated with them versus a control set. Whether this could be used to diagnose prostate cancer versus ovarian cancer is not at all clear,” said Naylor.

Semmes agreed that the significance of the protein panel as a diagnostic measure is not clear. However, proving that results from mass spec instruments are reproducible brings mass specs one step closer to being used as a clinical diagnostic tool, he said.

Gail Page, the president of the diagnostics division of Ciphergen, which manufactures SELDI technology, said her company is excited at the EDRN’s reproducibility results.

“It is our ultimate goal to translate our biomarker discovery programs covering a range of life-threatening diseases into commercially viable diagnostic assays that could lead to earlier detection of disease and improved health outcomes,” said Page. “We are very excited about these promising results which demonstrate that SELDI-TOF-MS is reproducible and accurate when standardized operating procedures are followed similar to those followed in a CLIA-certified laboratory.”


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