title: Evaluation of arrayed primer extension for TP53 mutation detection in breast and ovarian carcinomas.
abstract: Mutations in the tumor suppressor gene TP53 are associated with a wide range of different cancers and may have prognostic and therapeutic implications. Methods for rapid and sensitive detection of mutations in this gene are therefore required. In order to make screening more effective, a commercially available TP53 genotyping microarray from Asper Biotech has been constructed by arrayed primer extension (APEX). The present study is the first report that blindly evaluates the efficiency of the second generation APEX TP53 genotype chip outside the Asper laboratory and compares it to temporal temperature gradient electrophoresis (TTGE) and sequencing of TP53 for mutation detection in ovarian and breast cancer samples. All nucleotides in the TP53 gene from exon 2-9 are included on the chip by synthesis and application of sequence-specific oligonucleotides. The chip was validated by screening 48 breast and 11 ovarian cancer cases, all of which had previously been analyzed by TTGE and sequencing. APEX scored 17 of 20 sequence variants, missing one deletion, one insertion, and a missense mutation. Resequencing efficiency using APEX was 92% for both DNA strands and 99.5% for sense and/or antisense strand. We conclude that the APEX TP53 microarray is a robust, rapid, and comprehensive screening tool for sequence alterations in tumors.
authors.affiliation: The Norwegian Radium Hospital, Oslo, Norway.
authors.forename: Pedro
authors.initials: P
authors.lastname: Kringen
authors.forename: Anna
authors.initials: A
authors.lastname: Bergamaschi
authors.forename: Eldri Undlien
authors.initials: EU
authors.lastname: Due
authors.forename: Yun
authors.initials: Y
authors.lastname: Wang
authors.forename: Elda
authors.initials: E
authors.lastname: Tagliabue
authors.forename: Jahn M
authors.initials: JM
authors.lastname: Nesland
authors.forename: Aune
authors.initials: A
authors.lastname: Nehman
authors.forename: Neeme
authors.initials: N
authors.lastname: Tönisson
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Børresen-Dale
mesh_terms: D000483:Alleles; D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D003062:Codon; D053938:DNA Fragmentation; D004252:DNA Mutational Analysis / Q000379:methods*; D017931:DNA Primers / Q000737:chemistry / Q000235:genetics*; D004586:Electrophoresis; D005260:Female; D016158:Genes, p53; D006801:Humans; D007150:Immunohistochemistry; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016376:Oligonucleotides, Antisense / Q000737:chemistry; D010051:Ovarian Neoplasms / Q000235:genetics*; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013997:Time Factors; D016159:Tumor Suppressor Protein p53 / Q000235:genetics*
chemical_list: D003062:Codon; D017931:DNA Primers; D016376:Oligonucleotides, Antisense; D016159:Tumor Suppressor Protein p53