Proteomic biomarker identification for diagnosis of early relapse in ovarian cancer.
Ovarian cancer recurs at the rate of 75% within a few months or several years later after therapy. Early recurrence, though responding better to treatment, is difficult to detect. Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry has showed the potential to accurately identify disease biomarkers to help early diagnosis. A major challenge in the interpretation of SELDI-TOF data is the high dimensionality of the feature space. To tackle this problem, we have developed a multi-step data processing method composed of t-test, binning and backward feature selection. A new algorithm, support vector machine-Markov blanket/recursive feature elimination (SVM-MB/RFE) is presented for the backward feature selection. This method is an integration of minimum weight feature elimination by SVM-RFE and information theory based redundant/irrelevant feature removal by Markov Blanket. Subsequently, SVM was used for classification. We conducted the biomarker selection algorithm on 113 serum samples to identify early relapse from ovarian cancer patients after primary therapy. To validate the performance of the proposed algorithm, experiments were carried out in comparison with several other feature selection and classification algorithms.
Oh
Jung Hun
JH
Department of Computer Science and Engineering, University of Texas, Arlington, TX 76019, USA.
Nandi
Animesh
A
Gurnani
Prem
P
Knowles
Lynne
L
Schorge
John
J
Rosenblatt
Kevin P
KP
Gao
Jean X
JX
D000465:Algorithms; D001185:Artificial Intelligence; D014408:Biomarkers, Tumor / Q000097:blood*; D003936:Diagnosis, Computer-Assisted / Q000379:methods; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009363:Neoplasm Proteins / Q000097:blood*; D009364:Neoplasm Recurrence, Local / Q000097:blood / Q000175:diagnosis*; D010051:Ovarian Neoplasms / Q000097:blood / Q000175:diagnosis*; D010363:Pattern Recognition, Automated / Q000379:methods; D011379:Prognosis; D020543:Proteome / Q000032:analysis*; D018570:Risk Assessment; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D020543:Proteome