Rapid p53 sequence analysis in primary lung cancer using an oligonucleotide probe array

The p.53 gene was sequenced in 100 primary human lung cancers by using dire ct dideoxynucleotide cycle sequencing and compared with sequence analysis b y using the p53 GeneChip assay. Differences in sequence analysis between th e two techniques were further evaluated to determine the accuracy and limit ations of each method. p53 mutations were either detected by using both tec hniques or, if only detected by one technique, were confirmed by using muta tion-specific oligonucleotide hybridization. Dideoxynucleotide sequencing o f the conserved regions of the p53 gene (exons 5-9) detected 76% of the mut ations within this region of the gene. The GeneChip p53 assay detected 81% of all (exons 2-11) mutations, including 80% of the mutations within the co nserved regions of the gene. The GeneChip assay detected 46 of 52 missense mutations (88%), but 0 of 5 frameshift mutations. The specificity of direct sequencing and of the p53 GeneChip assay at detecting p53 mutations were 1 00% and 98%, respectively. The GeneChip p53 assay is a rapid and reasonably accurate approach for detecting p53 mutations; however, neither direct seq uencing nor the p53 GeneChip are infallible at p53 mutation detection.