Oligonucleotide probe array for p53 gene alteration analysis in DNA from formalin-fixed paraffin-embedded breast cancer tissues

Mutations in the TP53 tumor-suppressor (p53) gene represent the most common molecular changes in various malignancies, including breast cancer (BC). We sequenced the p53 gene in DNA extracted from archival paraffin-embedded BC tissues and compared the results obtained from direct sequencing with those obtained by oligonucleotide probe array (OPA). DNA was extracted from 34 samples. OPA correctly detected 13 genetic alterations in 14 cases, with a mutation frequency of 41.2%. No changes were detected in exons 3, 4, 9, 10, and 11 and no polymorphisms were found. Direct manual sequencing in which DNA was amplified by PCR showed 21 genetic mutations in 19 (55.9%) cases. Eightmutations were identified by both OPA and PCR methods. Although OPA detected fewer gene alterations than direct sequencing, the difference was not significant (P = 0.11). In conclusion, the OPA may be safely used to identify individual genetic variations of human p53 gene in BC specimens.