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Jack K. Horner Science Applications International Corporation P. O. Box 3827 Santa Fe, NM 87501

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. Problem and Method.

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Jack K. Horner Science Applications International Corporation P. O. Box 3827 Santa Fe, NM 87501

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  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 A 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 A 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] A Phylogenetic ...

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