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Published on: September 20, 2016
Specific mutation screening of TP53 gene by low-density DNA microarray
Angélica Rangel-López1, Alfonso Méndez-Tenorio, Kenneth L Beattie
1Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN Siglo XXI-IMSS, Mexico City, Mexico ; Unidad de Investigación Médica en Enfermedades Nefrológicas, Hospital de Especialidades, CMN Siglo XXI-IMSS, Mexico City; Mexico ; Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, IPN Mexico City, Mexico.
Abstract:
TP53 is the most commonly mutated gene in human cancers. Approximately 90% of mutations in this gene are localized between domains encoding exons 5 to 8. The aim of this investigation was to examine the ability of the low density DNA microarray with the assistance of double tandem hybridization platform to characterize TP53 mutational hotspots in exons 5, 7, and 8 of the TP53. Nineteen capture probes specific to each potential mutation site were designed to hybridize to specific site. Virtual hybridization was used to predict the stability of hybridization of each capture probe with the target. Thirty-three DNA samples from different sources were analyzed for mutants in these exons. A total of 32 codon substitutions were found by DNA sequencing. 24 of them a showed a perfect correlation with the hybridization pattern system and DNA sequencing analysis of the regions scanned. Although in this work we directed our attention to some of the most representative mutations of the TP53 gene, the results suggest that this microarray system proved to be a rapid, reliable, and effective method for screening all the mutations in TP53 gene.
Insights
This study introduces a DNA microarray system for rapidly screening TP53 gene mutations, a common occurrence in human cancers. The developed method accurately identifies TP53 hotspots, offering a reliable tool for cancer mutation analysis.
Area of Science:
- Molecular Biology
- Genetics
- Oncology
Background:
- The TP53 gene is frequently mutated in human cancers, with hotspots located in exons 5 to 8.
- Accurate and efficient methods are needed to characterize TP53 mutations for cancer research and diagnostics.
Purpose of the Study:
- To evaluate a low-density DNA microarray with a double tandem hybridization platform for characterizing TP53 mutational hotspots.
- To assess the reliability and effectiveness of this microarray system in identifying TP53 mutations in cancer-related exons.
Main Methods:
- Design of 19 capture probes specific to TP53 mutation sites in exons 5, 7, and 8.
- Utilizing virtual hybridization to predict probe-target binding stability.
- Analysis of 33 DNA samples using the microarray system and DNA sequencing.
Main Results:
- A total of 32 codon substitutions were identified via DNA sequencing.
- The microarray system demonstrated perfect correlation with DNA sequencing for 24 of these mutations.
- The system proved effective in scanning specific regions of the TP53 gene.
Conclusions:
- The DNA microarray system is a rapid, reliable, and effective method for screening TP53 gene mutations.
- This technology shows promise for comprehensive TP53 mutation analysis in various cancer types.
- The findings support the utility of microarray platforms in cancer genomics research.
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