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New Mass Spectrometry Blood Test Can "Fingerprint" Prostate, Ovarian Cancers, Dartmouth Researchers Say

By J. Strax

PSA Rising /New York/ February 12, 2004 -- Prostate cancer and ovarian cancer diagnosis may soon be achievable with almost perfect accuracy and specificity using data from a mass spectrometer, an instrument that produces charged particles (ions) from the chemical substances that are to be analyzed -- such as blood -- and uses electric and magnetic fields to measure the mass ("weight") of the charged particles.

If this replaces the PSA test to detect prostate cancer, it will come about partly from the efforts of two young computer scientists and their mentor at Dartmouth College, Ryan Lilien, a Dartmouth M.D./Ph.D. student, Hany Farid, Assistant Professor of Computer Science , and Bruce Donald, the Foley Professor of Computer Science, collaborated on this project, which was published in the Journal of Computational Biology in December 2003.

"Our algorithm, named Q5, works on the assumption that the molecular composition of the blood changes between healthy and disease states," says Donald, the senior researcher on the project. "The goal of our work is to develop minimally invasive diagnostic methods with high predictive accuracy, and this is a promising first step."

"Our algorithm detected ovarian cancer with virtually 100% accuracy and prostate cancer with approximately 95% accuracy," explains Lilien, the lead author on the paper. "Q5 analyzes the mass spec data and offers control over the threshold between healthy and disease classification. Although we only tested against ovarian and prostate cancer, we think it's possible that Q5 may be used to test for other cancers and diseases."

Mass spectrometry is used for all kinds of chemical analyses, from detection of pollutants like dioxin to finding high-grade petroleum in sludge. It's used to detect steroids in the urine of athletes and contaminants in herbal supplements. It's used to screen newborns for inherited disorders and to listen for a signal put out by crystals in blood cells invaded by malaria.

In 2001 Matritech Inc. announced that that a prostate cancer marker identified by Matritech's scientists detected prostate cancer with greater sensitivity than the prostate specific antigen (PSA) test. In addition, Matritech reported that a MALDI mass spectrometer, a type of instrument used routinely in most clinical laboratories, can be used to detect this marker.

Speed, accuracy and portability are what make today's briefcase-size high-throughput mass spectrometers irresistable as screening devises. Combined with the approriate data analyser the equipment can identify and characterize hundreds of complex proteins near-instantaneously. This makes mass spectrometry a star player in the emerging new discipline known as proteomics, which seeks to detect and evaluate the thousands of proteins expressed by the genome and then understand how these molecules work in concert to maintain life.

The Dartmouth team claim to have come up with a predictive calculation (or algorithm) that "detected ovarian cancer with virtually 100 percent accuracy and prostate cancer with approximately 95 percent accuracy." "Q5 analyzes the mass spec data and offers control over the threshold between healthy and disease classification. Although we only tested against ovarian and prostate cancer, we think it's possible that Q5 may be used to test for other cancers and diseases."

Mathematical computations are routinely developed, varied and refined to analyze mass spectrometry data. Q5 uses mathematical techniques called Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) to differentiate between the mass spectra of healthy and diseased blood samples. Q5 learns with each sample it tests, resulting in better accuracy. The algorithm compares the molecular fingerprint of each sample to identify features that differ between the healthy and disease states.

The researchers explain that there is much still to be learned from the different types of information within a sample of blood, and Q5 is one means of extracting new and important data.

"Most exciting to us, unlike previous mass spec disease diagnosis methods, Q5 provides clues about the molecular identities of abnormal proteins and peptides, which often cause disease. These altered proteins can serve as biomarkers, helping doctors make diagnosis and also helping researchers design better targeted drugs," says Donald.

This research is funded by the National Institutes of Health, the National Science Foundation, the John Simon Guggenheim Foundation, and an Alfred P. Sloan Fellowship.

Institutional source, Department of Computer Science, Dartmouth College. This page made and last edited by J.Strax, Feb 12, 2004.