Evaluation of Oligonucleotide Arrays for Sequencing of the p53 Gene in DNA from Formalin-Fixed, Paraffin-Embedded Breast Cancer Specimens

Cooper, Melissa; Li, Shu Qiu; Bhardwaj, Tajinder; Rohan, Thomas E.; Kandel, Rita A.

doi:10.1373/clinchem.2003.025221

Cited by 22 publications

(21 citation statements)

References 37 publications

(28 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The proteinase K was inactivated by heating to 95jC for 15 minutes. An aliquot of the digest was amplified using PCR [a 33 P]dATP and exon-specific primers under the conditions described previously (39). An aliquot of the reaction product was separated on an 8% nondenaturing polyacrylamide gel and processed for autoradiography.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

p53 Alterations and Protein Accumulation in Benign Breast Tissue and Breast Cancer Risk: A Cohort Study

Rohan

Hartwick

et al. 2006

Cancer Epidemiology, Biomarkers &Amp; Prevention

Self Cite

View full text Add to dashboard Cite

Disruption of p53 gene function seems to have a pivotal role in carcinogenesis. p53 gene changes occur before the development of breast cancer and therefore might influence breast cancer risk. We investigated the association between p53 protein accumulation and p53 mutations detected in benign breast tissue and risk of subsequent breast cancer. We conducted a case-control study nested within the cohort of 4,888 women in the Canadian National Breast Screening Study who were diagnosed with biopsy-confirmed benign breast disease during active follow-up. Cases were women with benign breast disease who subsequently developed breast cancer; five controls were matched to each case. p53 protein accumulation was assessed immunohistochemically using sections of paraffin-embedded benign breast tissue from 104 cases and 385 controls; for 82 of these cases and 327 of the controls, DNA was successfully extracted from the breast tissue for p53 gene analysis using PCR-singlestrand conformation polymorphism/direct sequencing. p53 protein accumulation was associated with a 2-fold increase in risk of progression to breast cancer [adjusted odds ratio (OR), 2.16; 95% confidence interval (95% CI), 1.08-4.30], whereas p53 nucleotide changes overall were not associated with altered risk (adjusted OR, 1.22; 95% CI, 0.68-2.19); those with both p53 immunopositivity and a p53 nucleotide change had an OR (95% CI) of 3.20 (1.21-8.50). Nonpolymorphic intronic changes were associated with a 2.8-fold increase in risk (OR, 2.84; 95% CI, 1.09-7.41). The results of this study suggest that p53 protein accumulation and nonpolymorphic intronic changes in p53 are associated with increased risk of progression to breast cancer in women with benign breast disease. (Cancer Epidemiol Biomarkers Prev 2006;15(7):1316 -23)

show abstract

Section: Methodsmentioning

confidence: 99%

“…For some samples, the exon 4 portion of the exons 3 to 4 partial PCR product was unreadable. For these samples, PCR and sequencing were done with primers that were specific for exon 4 only, in order to read the 3 ¶ portion of exon 4 (39).…”

Section: Methodsmentioning

confidence: 99%

p53 Alterations and Protein Accumulation in Benign Breast Tissue and Breast Cancer Risk: A Cohort Study

Rohan

Hartwick

et al. 2006

Cancer Epidemiology, Biomarkers &Amp; Prevention

Self Cite

View full text Add to dashboard Cite

show abstract

“…Sequencing of known mutation hotspots of TP53 on exons 5-9 [38] was performed in selected cases (cases 2, 5 and 6 and matched adjacent normal breast tissues). The primers used for TP53 sequencing have been previously described [38,39].…”

Section: Tp53 Mutation Analysismentioning

confidence: 99%

“…The primers used for TP53 sequencing have been previously described [38,39]. 50 ng tumour DNA was amplified and sequencing reactions were carried out using the DNA Sequencing Kit BigDye Terminator v 1.1 Cycle Sequencing Ready Reaction Mix (Applied Biosystems, Warrington, UK), as previously described [40].…”

Section: Tp53 Mutation Analysismentioning

confidence: 99%

Molecular analysis reveals a genetic basis for the phenotypic diversity of metaplastic breast carcinomas

Geyer

Weigelt

Natrajan

et al. 2010

The Journal of Pathology

190

159

View full text Add to dashboard Cite

Cancers may be composed of multiple populations of submodal clones sharing the same initiating genetic lesions, followed by the acquisition of divergent genetic hits. Intra-tumour genetic heterogeneity has profound implications for cancer clinical management. To determine the extent of intra-tumour genetic heterogeneity in breast cancers, and whether the morphological diversity of breast cancers is underpinned by divergent genetic aberrations, we analysed the genomic profiles of microdissected, morphologically distinct components of six metaplastic breast carcinomas, tumours characterized by the presence of morphological areas with divergent differentiation. Each morphologically distinct component was separately microdissected and subjected to high-resolution microarray-based comparative genomic hybridization. Each component was also analysed by immunohistochemistry and in situ hybridization. Clonal relationship between the distinct components was tested by TP53 sequencing and human androgen receptor (HUMARA) X-chromosome inactivation assay. In the majority of cases, all morphologically distinct components from each case were clonal and displayed remarkably similar genetic profiles. In two cases, however, morphologically distinct components harboured specific genetic aberrations. In an adenosquamous carcinoma, the differences were such that only 20% of the genome harboured similar copy number changes. The squamous component displayed EGFR gene amplification, EGFR over-expression and lack of expression of hormone receptors, whereas the lobular component displayed the reverse pattern. The components of a biphasic spindle cell carcinoma harboured similar gains, losses, amplifications of 9p23 and 17q12 (HER2 ) and identical TP53 mutations, suggesting that these were relatively early events in the development of this tumour; however, each component displayed divergent focal amplifications. Importantly, the metastatic deposit of this case, despite harbouring a TP53 mutation identical to that found in the primary tumour, harboured additional specific focal amplifications. This proof-of-principle study provides direct evidence of intra-tumour genetic heterogeneity in breast cancers, and shows that in some cases morphological diversity may be underpinned by distinct genetic aberrations.

show abstract

“…Molecular characterization of tumors can provide signatures to categorize tumors. Tumors acquire many DNA changes but efforts to genotype breast cancer tissue DNA for mutations in critical oncogenes and tumor suppressor genes have met with limited success largely due to the limitations of existing DNA sequencing methods (Cooper et al 2004). Tumors are very heterogeneous tissues due to contaminating stromal cells, adipose and vascular tissue and the microevolution that occurs within a tumor; therefore, mutant DNA is frequently only a minor component of a tumor DNA sample.…”

Section: Introductionmentioning

confidence: 99%

Test for Sensitive Detection and Accurate Assignment of TP53 Variants in Tumor DNA

Telmer¹

2005

View full text Add to dashboard Cite

Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, Including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS.

show abstract

Evaluation of Oligonucleotide Arrays for Sequencing of the p53 Gene in DNA from Formalin-Fixed, Paraffin-Embedded Breast Cancer Specimens

Cited by 22 publications

References 37 publications

p53 Alterations and Protein Accumulation in Benign Breast Tissue and Breast Cancer Risk: A Cohort Study

p53 Alterations and Protein Accumulation in Benign Breast Tissue and Breast Cancer Risk: A Cohort Study

Molecular analysis reveals a genetic basis for the phenotypic diversity of metaplastic breast carcinomas

Test for Sensitive Detection and Accurate Assignment of TP53 Variants in Tumor DNA

Contact Info

Product

Resources

About