title: Clinical application of oligonucleotide probe array for full-length gene sequencing of TP53 in colon cancer.
abstract: OBJECTIVE
  TP53 mutations are the most frequent genetic alterations in colon cancer. We studied whether the recently developed oligonucleotide microarray technique, GeneChip p53 assay, can be applied to sensitive detection of TP53 gene mutations in surgical specimens from colon cancer patients.
  
  
  METHODS
  TP53 gene mutations in exons 2-11 in 20 colon cancers and the corresponding histopathologically normal mucosa at the surgical margins were assessed by GeneChip p53 assay, and the results were further evaluated by direct sequencing of the involved exon or by mutant-allele-specific amplification (MASA). The expression of TP53 protein was also evaluated immunohistochemically and the result was compared with the gene alteration.
  
  
  RESULTS
  The GeneChip p53 assay detected TP53 mutations in 65% of primary cancers; 61% of the mutations were within the evolutionarily conserved regions, and 46% of the mutations were within the zinc-binding domains (regions of loop 2 and loop 3). Direct sequencing confirmed these mutations. Immunohistochemical examination detected TP53 protein overexpression in 47% of primary cancers, but this protein did not accumulate with all types of TP53 mutations. In addition, the GeneChip assay detected a mutation identical to that in the primary tumor in 2 samples from the surgical margins, and MASA confirmed both mutations, implying the presence of occult cancer cells.
  
  
  CONCLUSIONS
  The GeneChip p53 assay is sufficiently sensitive to detect TP53 mutations in surgical specimens from colon cancers and may be applicable to screening examination in clinical laboratories as a routine procedure.
authors.affiliation: Medical Research Center, Nihon University School of Medicine, Tokyo, Japan.
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Takahashi
authors.forename: Yukimoto
authors.initials: Y
authors.lastname: Ishii
authors.forename: Toshihito
authors.initials: T
authors.lastname: Nagata
authors.forename: Masahito
authors.initials: M
authors.lastname: Ikarashi
authors.forename: Koichi
authors.initials: K
authors.lastname: Ishikawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Asai
mesh_terms: D000328:Adult; D000368:Aged; D016022:Case-Control Studies; D003110:Colonic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D004273:DNA, Neoplasm / Q000032:analysis; D005260:Female; D020869:Gene Expression Profiling; D016158:Genes, p53 / Q000235:genetics*; D006801:Humans; D007124:Immunoenzyme Techniques; D008297:Male; D008875:Middle Aged; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D017422:Sequence Analysis, DNA / Q000379:methods; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism
chemical_list: D004273:DNA, Neoplasm; D015345:Oligonucleotide Probes; D016159:Tumor Suppressor Protein p53