title: Integrating microarray and proteomics data to predict the response on cetuximab in patients with rectal cancer.
abstract: To investigate the combination of cetuximab, capecitabine and radiotherapy in the preoperative treatment of patients with rectal cancer, fourty tumour samples were gathered before treatment (T0), after one dose of cetuximab but before radiotherapy with capecitabine (T1) and at moment of surgery (T2). The tumour and plasma samples were subjected at all timepoints to Affymetrix microarray and Luminex proteomics analysis, respectively. At surgery, the Rectal Cancer Regression Grade (RCRG) was registered. We used a kernel-based method with Least Squares Support Vector Machines to predict RCRG based on the integration of microarray and proteomics data on To and T1. We demonstrated that combining multiple data sources improves the predictive power. The best model was based on 5 genes and 10 proteins at T0 and T1 and could predict the RCRG with an accuracy of 91.7%, sensitivity of 96.2% and specificity of 80%.
authors.affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering (ESAT), SCD-SISTA (BIOI), Kasteelpark Arenberg 10--bus 2446, B-3001 Leuven, Heverlee, Belgium. anneleen.daemen@esat.kuleuven.be
authors.forename: Anneleen
authors.initials: A
authors.lastname: Daemen
authors.forename: Olivier
authors.initials: O
authors.lastname: Gevaert
authors.forename: Tijl
authors.initials: T
authors.lastname: De Bie
authors.forename: Annelies
authors.initials: A
authors.lastname: Debucquoy
authors.forename: Jean-Pascal
authors.initials: JP
authors.lastname: Machiels
authors.forename: Bart
authors.initials: B
authors.lastname: De Moor
authors.forename: Karin
authors.initials: K
authors.lastname: Haustermans
mesh_terms: D000465:Algorithms; D000911:Antibodies, Monoclonal / Q000627:therapeutic use*; D061067:Antibodies, Monoclonal, Humanized; D000970:Antineoplastic Agents / Q000627:therapeutic use*; D001185:Artificial Intelligence; D000069287:Capecitabine; D000068818:Cetuximab; D003131:Combined Modality Therapy; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D003841:Deoxycytidine / Q000031:analogs & derivatives / Q000627:therapeutic use; D005472:Fluorouracil / Q000031:analogs & derivatives / Q000627:therapeutic use; D006801:Humans; D016018:Least-Squares Analysis; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D040901:Proteomics / Q000706:statistics & numerical data*; D012004:Rectal Neoplasms / Q000235:genetics / Q000378:metabolism / Q000628:therapy*
chemical_list: D000911:Antibodies, Monoclonal; D061067:Antibodies, Monoclonal, Humanized; D000970:Antineoplastic Agents; D003841:Deoxycytidine; D000069287:Capecitabine; D000068818:Cetuximab; D005472:Fluorouracil