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Published February 9, 2004; Category: ARTS &
SCIENCES
Cancer diagnosis may one day employ mass spectrometer
Hany Farid (left), Bruce Donald (seated),
and Ryan Lilien have developed an algorithm named Q5
that uses data from a mass spectrometer to distinguish
between healthy blood and diseased blood. (photo by
Joseph Mehling '69)
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Dartmouth researchers have developed an algorithm that may
someday be used to analyze blood for diagnostic purposes.
Using data from a mass spectrometer, a device that generates a
molecular fingerprint of biological samples, the Dartmouth
team's calculations can distinguish healthy blood from
diseased blood.
This study by 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, appeared in the Journal
of Computational Biology in December.
"Our algorithm, named Q5, works on the assumption that the
molecular composition of the blood changes between healthy and
diseased 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."
Mathematical computations are routinely developed, varied
and refined to analyze mass spectrometry data. The algorithm
Q5 uses mathematical techniques called Principal Component
Analysis and Linear Discriminant Analysis to differentiate
between the mass spectra of healthy and diseased blood
samples, and 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.
"Our algorithm detected ovarian cancer with virtually 100
percent accuracy and prostate cancer with approximately 95
percent 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."
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.
By SUSAN
KNAPP | 
