title: Tissue biomarker development in a multicentre trial context: a feasibility study on the PETACC3 stage II and III colon cancer adjuvant treatment trial.
abstract: OBJECTIVE
  We evaluated the feasibility of biomarker development in the context of multicenter clinical trials.
  
  
  METHODS
  Formalin-fixed, paraffin-embedded (FFPE) tissue samples were collected from a prospective adjuvant colon cancer trial (PETACC3). DNA was isolated from tumor as well as normal tissue and used for analysis of microsatellite instability, KRAS and BRAF genotyping, UGT1A1 genotyping, and loss of heterozygosity of 18 q loci. Immunohistochemistry was used to test expression of TERT, SMAD4, p53, and TYMS. Messenger RNA was retrieved and tested for use in expression profiling experiments.
  
  
  RESULTS
  Of the 3,278 patients entered in the study, FFPE blocks were obtained from 1,564 patients coming from 368 different centers in 31 countries. In over 95% of the samples, genomic DNA tests yielded a reliable result. Of the immmunohistochemical tests, p53 and SMAD4 staining did best with reliable results in over 85% of the cases. TERT was the most problematic test with 46% of failures, mostly due to insufficient tissue processing quality. Good quality mRNA was obtained, usable in expression profiling experiments.
  
  
  CONCLUSIONS
  Prospective clinical trials can be used as framework for biomarker development using routinely processed FFPE tissues. Our results support the notion that as a rule, translational studies based on FFPE should be included in prospective clinical trials.
authors.affiliation: University Institute of Pathology, University of Lausanne Medical Center, Lausanne, Switzerland. fred.bosman@chuv.ch
authors.forename: Fred T
authors.initials: FT
authors.lastname: Bosman
authors.forename: Pu
authors.initials: P
authors.lastname: Yan
authors.forename: Sabine
authors.initials: S
authors.lastname: Tejpar
authors.forename: Roberto
authors.initials: R
authors.lastname: Fiocca
authors.forename: Eric
authors.initials: E
authors.lastname: Van Cutsem
authors.forename: Richard D
authors.initials: RD
authors.lastname: Kennedy
authors.forename: Daniel
authors.initials: D
authors.lastname: Dietrich
authors.forename: Arnaud
authors.initials: A
authors.lastname: Roth
mesh_terms: D000971:Antineoplastic Combined Chemotherapy Protocols; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism*; D002166:Camptothecin / Q000008:administration & dosage / Q000031:analogs & derivatives; D017024:Chemotherapy, Adjuvant; D003110:Colonic Neoplasms / Q000188:drug therapy* / Q000401:mortality; D018572:Disease-Free Survival; D005472:Fluorouracil / Q000008:administration & dosage; D014453:Glucuronosyltransferase / Q000235:genetics / Q000378:metabolism; D006801:Humans; D000077146:Irinotecan; D053842:Microsatellite Instability; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011446:Prospective Studies; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics / Q000378:metabolism; D016283:Proto-Oncogene Proteins p21(ras); D051901:Smad4 Protein / Q000378:metabolism; D019098:Telomerase / Q000378:metabolism; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism; D018631:ras Proteins / Q000235:genetics / Q000378:metabolism; D000099148:UGT1A1 Enzyme
chemical_list: D014408:Biomarkers, Tumor; D002166:Camptothecin; D005472:Fluorouracil; D014453:Glucuronosyltransferase; D000077146:Irinotecan; D011518:Proto-Oncogene Proteins; D048493:Proto-Oncogene Proteins B-raf; D016283:Proto-Oncogene Proteins p21(ras); D051901:Smad4 Protein; D019098:Telomerase; D016159:Tumor Suppressor Protein p53; D018631:ras Proteins; D000099148:UGT1A1 Enzyme; C117307:KRAS protein, human; C497796:SMAD4 protein, human; C482119:BRAF protein, human; C509186:TERT protein, human