title: Bioinformatical evaluation of modified nucleosides as biomedical markers in diagnosis of breast cancer.
abstract: It is known that patients suffering from cancer diseases excrete increased amounts of modified nucleosides with their urine. Especially methylated nucleosides have been proposed to be potential tumor markers for early diagnosis of cancer. For determination of nucleosides in randomly collected urine samples, the nucleosides were extracted using affinity chromatography and then analyzed via reversed phase high-performance liquid chromatography (HPLC) with UV-detection. Eleven nucleosides were quantified in urine samples from 51 breast cancer patients and 65 healthy women. The measured concentrations were used to train a Support Vector Machine (SVM) and a k-nearest-neighbor classifier (k-NN) to discriminate between healthy control subjects and patients suffering from breast cancer. Evaluations of the learned models by computing the leave-one-out error and the prediction error on an independent test set of 29 subjects (15 healthy, 14 breast cancer patients) showed that by using the eleven nucleosides, the occurrence of breast cancer could be forecasted with 86% specificity and 94% sensitivity when using an SVM and 86% for both specificity and sensitivity with the k-NN model.
authors.affiliation: University Hospital Tübingen, Department of Pharmacology and Toxicology, Division of Clinical Pharmacology, Otfried-Müller-Str. 45, D-72076 Tübingen, Germany.
authors.forename: Dino
authors.initials: D
authors.lastname: Bullinger
authors.forename: Holger
authors.initials: H
authors.lastname: Fröhlich
authors.forename: Fabian
authors.initials: F
authors.lastname: Klaus
authors.forename: Hans
authors.initials: H
authors.lastname: Neubauer
authors.forename: Antje
authors.initials: A
authors.lastname: Frickenschmidt
authors.forename: Carsten
authors.initials: C
authors.lastname: Henneges
authors.forename: Andreas
authors.initials: A
authors.lastname: Zell
authors.forename: Stefan
authors.initials: S
authors.lastname: Laufer
authors.forename: Christoph H
authors.initials: CH
authors.lastname: Gleiter
authors.forename: Hartmut
authors.initials: H
authors.lastname: Liebich
authors.forename: Bernd
authors.initials: B
authors.lastname: Kammerer
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000737:chemistry / Q000652:urine*; D001943:Breast Neoplasms / Q000175:diagnosis*; D002851:Chromatography, High Pressure Liquid / Q000295:instrumentation / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D005260:Female; D006801:Humans; D008875:Middle Aged; D008968:Molecular Conformation; D009705:Nucleosides / Q000737:chemistry / Q000652:urine*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013237:Stereoisomerism
chemical_list: D014408:Biomarkers, Tumor; D009705:Nucleosides