Protocols and tools
Protocols
To assess TP53 mutation status it is recommended to perform gene sequencing of all exons, including the splice junctions and completed with MLPA to detect large deletion/duplications. Immuno-histochemical analysis is not a good method for assessing TP53 mutation status, as it cannot distinguish between the various types of mutations, does not detect truncating mutations (false-negative results), and gives false-positive results (over-expressed WT protein).
Some example of sequencing protocols:
- Direct sequencing by Sanger
- TP53 sequencing by a next generation sequencing technology (NGS). The detailed list of primers can be downloaded here
- MLPA
- Some caution regarding TP53 variants detected by multigene panel testing by NGS: a study by Weitzel et al.,
- SNP sequencing and haplotyping
Recent developments on p53 antibodies
- Monoclonal Antibodies against Specific p53 Hotspot Mutants as Potential Tools for Precision Medicine
- Understanding p53 functions through p53 antibodies
Other tools
- Mutalyzer, a package to support checks of sequence variant nomenclature according to the guidelines of the Human Genome Variation Society
- Resources for the systematic analysis of p53 interactions with DNA and other transcription factors.
- p53retriever, for the detection and display of p53 putative response elements (REs) on DNA sequences
- TargetGeneReg, for displaying gene of interest in the p53 and cell cycle gene regulatory networks
- TP53 RNA expression data from TCGA at GEPIA
- Datamed, a search engine for TP53 datasets
- Human Splicing Finder
- Align-AGVGD, for the prediction of the functional impact of missense mutations
- SIFT, for the prediction of the functional impact of missense mutations
- Scorecons, for scoring residue conservation
- The Cancer Genome Interpreter, to identify driver mutations in tumor samples
- LFSPRO, a tool for estimating TP53 Mutation Carrier Probability
- Famdenovo, an algorithm that calculates the probability of a germline mutation to be de novo based on family history data
- Amino-acid letter codes and properties
- Genetic code
- LOVD, a software to build mutation databases