Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing
Language English Country United States Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
Grant support
R01 CA181308
NCI NIH HHS - United States
PubMed
29696732
DOI
10.1002/humu.23543
Knihovny.cz E-resources
- Keywords
- HGVS variant nomenclature, TP53 variants, database, variant annotation,
- MeSH
- Molecular Sequence Annotation MeSH
- Databases, Genetic * MeSH
- Genetic Variation genetics MeSH
- Genomics trends MeSH
- Internet MeSH
- Humans MeSH
- Mutation MeSH
- Tumor Suppressor Protein p53 genetics MeSH
- Software * MeSH
- Computational Biology trends MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Tumor Suppressor Protein p53 MeSH
- TP53 protein, human MeSH Browser
Accurate annotation of genomic variants in human diseases is essential to allow personalized medicine. Assessment of somatic and germline TP53 alterations has now reached the clinic and is required in several circumstances such as the identification of the most effective cancer therapy for patients with chronic lymphocytic leukemia (CLL). Here, we present Seshat, a Web service for annotating TP53 information derived from sequencing data. A flexible framework allows the use of standard file formats such as Mutation Annotation Format (MAF) or Variant Call Format (VCF), as well as common TXT files. Seshat performs accurate variant annotations using the Human Genome Variation Society (HGVS) nomenclature and the stable TP53 genomic reference provided by the Locus Reference Genomic (LRG). In addition, using the 2017 release of the UMD_TP53 database, Seshat provides multiple statistical information for each TP53 variant including database frequency, functional activity, or pathogenicity. The information is delivered in standardized output tables that minimize errors and facilitate comparison of mutational data across studies. Seshat is a beneficial tool to interpret the ever-growing TP53 sequencing data generated by multiple sequencing platforms and it is freely available via the TP53 Website, http://p53.fr or directly at http://vps338341.ovh.net/.
Central European Institute of Technology Masaryk University Brno Czech Republic
Department of Oncology Pathology Cancer Center Karolinska Karolinska Institutet Stockholm Sweden
Department of Pathology University of Washington Seattle Washington
Genevia Technologies Tampere Finland
INSERM Centre de Recherche des Cordeliers U1138 Paris France
References provided by Crossref.org
ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia-2024 update
