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Related Experiment Videos

p53 Mutation analysis in breast tumors by a DNA microarray method.

Meredith Tennis1, Shiva Krishnan, Matthew Bonner

  • 1Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057-1465, USA. pgs2@georgetown.edu

Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology
|January 26, 2006
PubMed
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The p53 gene is frequently mutated in breast cancer. A high-throughput sequencing method using Affymetrix GeneChip technology effectively identified p53 mutations in archived tumor samples, aiding cancer etiology research.

Area of Science:

  • Oncology
  • Genetics
  • Molecular Biology

Background:

  • The p53 gene is a critical regulator of cell growth and DNA repair.
  • Inactivation of the p53 gene is a common event in human cancers, particularly breast cancer.
  • High-throughput sequencing methods are essential for large-scale cancer etiology studies.

Purpose of the Study:

  • To evaluate the utility of Affymetrix GeneChip technology for high-throughput p53 mutation detection in breast cancer.
  • To identify novel mutation hotspots in the p53 gene within a population-based study.
  • To validate the accuracy of the Affymetrix assay against manual sequencing.

Main Methods:

  • A population-based case-control study involving 392 breast cancer subjects.
  • p53 gene amplification using Polymerase Chain Reaction (PCR).

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  • High-throughput sequencing of p53 using Affymetrix GeneChip technology.
  • Manual sequencing of p53 exons 5-9 for validation.
  • Assay of paraffin-embedded archival tumor tissues (breast and lung).

    • Main Results:

    • 138 out of 392 (35%) breast tumors exhibited p53 mutations.
    • 88% of identified mutations were located in exons 5 to 8.
    • New mutation hotspots were identified at codons 179, 195, 196, 213, 217, 249, 254, 278, 281, and 298.
    • Affymetrix assay showed 100% concordance with manual sequencing for detectable mutations.
    • Successful analysis of archival tumor samples dating back to 1958.

    Conclusions:

    • Affymetrix GeneChip technology is a reliable and efficient method for high-throughput p53 mutation analysis, even with archival tissues.
    • The study identified novel p53 mutation hotspots, contributing to a better understanding of breast cancer mutational spectra.
    • This methodology supports large-scale investigations into gene-environment interactions in cancer etiology.