title: Rapid and sensitive p53 alteration analysis in biopsies from lung cancer patients using a functional assay and a universal oligonucleotide array: a prospective study.
abstract: OBJECTIVE
  Molecular profiling of alterations associated with lung cancer holds the promise to define clinical parameters such as response to treatment or survival. Because <5% of small cell lung cancers and <30% of non-small cell lung cancers are surgically resectable, molecular analysis will perforce rely on routinely available clinical samples such as biopsies. Identifying tumor mutations in such samples will require a sensitive and robust technology to overcome signal from excess amounts of normal DNA.
  
  
  METHODS
  p53 mutation status was assessed from the DNA and RNA of biopsies collected prospectively from 83 patients with lung cancer. Biopsies were obtained either by conventional bronchoscopy or computed tomography-guided percutaneous biopsy. Matched surgical specimens were available for 22 patients. Three assays were used: direct sequencing; a functional assay in yeast; and a newly developed PCR/ligase detection reaction/Universal DNA array assay.
  
  
  RESULTS
  Using the functional assay, p53 mutation was found in 62% of biopsies and 64% of surgical specimens with a concordance of 80%. The sensitivity of the functional assay was determined to be 5%. Direct sequencing confirmed mutations in 92% of surgical specimens but in only 78% of biopsies. The DNA array confirmed 100% of mutations in both biopsies and surgical specimens. Using this newly developed DNA array, we demonstrate the feasibility of directly identifying p53 mutations in clinical samples containing <5% of tumor cells.
  
  
  CONCLUSIONS
  The versatility and sensitivity of this new array assay should allow additional development of mutation profiling arrays that could be applied to biological samples with a low tumor cell content such as bronchial aspirates, bronchoalveolar lavage fluid, or serum.
authors.affiliation: EA3493, UPMC-IC of [corrected] Laboratoire de génotoxicologie des tumeurs, Paris, France.
authors.forename: Coralie
authors.initials: C
authors.lastname: Fouquet
authors.forename: Martine
authors.initials: M
authors.lastname: Antoine
authors.forename: Pascaline
authors.initials: P
authors.lastname: Tisserand
authors.forename: Reyna
authors.initials: R
authors.lastname: Favis
authors.forename: Marie
authors.initials: M
authors.lastname: Wislez
authors.forename: Fréderic
authors.initials: F
authors.lastname: Commo
authors.forename: Nathalie
authors.initials: N
authors.lastname: Rabbe
authors.forename: Marie France
authors.initials: MF
authors.lastname: Carette
authors.forename: Bernard
authors.initials: B
authors.lastname: Milleron
authors.forename: Francis
authors.initials: F
authors.lastname: Barany
authors.forename: Jacques
authors.initials: J
authors.lastname: Cadranel
authors.forename: Gérard
authors.initials: G
authors.lastname: Zalcman
authors.forename: Thierry
authors.initials: T
authors.lastname: Soussi
mesh_terms: D000368:Aged; D000483:Alleles; D001706:Biopsy; D015331:Cohort Studies; D004247:DNA / Q000378:metabolism; D004252:DNA Mutational Analysis / Q000379:methods*; D005260:Female; D016158:Genes, p53; D006801:Humans; D008175:Lung Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009696:Nucleic Acids / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000235:genetics*; D010957:Plasmids / Q000378:metabolism; D016133:Polymerase Chain Reaction; D011446:Prospective Studies; D012313:RNA / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism
chemical_list: D009696:Nucleic Acids; D009841:Oligonucleotides; D016159:Tumor Suppressor Protein p53; D012313:RNA; D004247:DNA