1. 11/26/2003A Phylogenetic...1 A Phylogenetic Method for Identifying a Stage I Ovarian Cancer Signature in the Mass-Spectrum of Serum Proteins Jack K. Horner Science Applications International Corporation P. O. Box 3827 Santa Fe, NM 87501 Email: jack.k.horner@saic.com

2. 11/26/2003A Phylogenetic...2 Problem and Method Problem: ovarian cancer (OC) can currently be diagnosed only at advanced stages, when prognosis is very poor Objective: find a method that detects OC at a stage at which it can be successfully treated Method (using serum protein mass-spectra) –form a set of known cancer, and known non-cancer, spectra; call this the “reference” set –merge reference set with unknown spectrum U –apply the phylogenetic maximum parsimony method to the merged set –declare U to have the same disease state as its siblings in the tree

3. 11/26/2003A Phylogenetic...3 Results (How well does the method work?) Correct classification rate 133 known cancer, and 95 known non-cancer, spectra ~370,000 points per spectrum Phylogenetic Analysis Using Parsimony (Ver. 4.0b10) MP heuristic search, seed from clock, 31 runs Mean.893 Std Err.003 Kurtosis -.297 Median.890 Std Dev.017 S.E. Kurt..880 Mode.890 Variance.000 Skewness.150 Minimum.860 Sum 27.670 S.E. Skew..440 Maximum.930 Range.070 Valid 31.000 95% Confidence Interval for the mean = [.8862 to.8989]