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

Steven A. Ahrendt, Sarel Halachmi, John T. Chow, Li Wu, Naomi Halachmi, Stephen C. Yang, Scott Wehage, Jin Jen, David Sidransky

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206 Scopus citations

Abstract

The p53 gene was sequenced in 100 primary human lung cancers by using direct dideoxynucleotide cycle sequencing and compared with sequence analysis by using the p53 GeneChip assay. Differences in sequence analysis between the two techniques were further evaluated to determine the accuracy and limitations of each method. p53 mutations were either detected by using both techniques or, if only detected by one technique, were confirmed by using mutation-specific oligonucleotide hybridization. Dideoxynucleotide sequencing of the conserved regions of the p53 gene (exons 5-9) detected 76% of the mutations 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 conserved 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 100% and 98%, respectively. The GeneChip p53 assay is a rapid and reasonably accurate approach for detecting p53 mutations; however, neither direct sequencing nor the p53 GeneChip are infallible at p53 mutation detection.

Original languageEnglish (US)
Pages (from-to)7382-7387
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume96
Issue number13
DOIs
StatePublished - Jun 22 1999

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    Ahrendt, S. A., Halachmi, S., Chow, J. T., Wu, L., Halachmi, N., Yang, S. C., Wehage, S., Jen, J., & Sidransky, D. (1999). Rapid p53 sequence analysis in primary lung cancer using an oligonucleotide probe array. Proceedings of the National Academy of Sciences of the United States of America, 96(13), 7382-7387. https://doi.org/10.1073/pnas.96.13.7382