Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing

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Authors	TIKKANEN T. LEROY B. FOURNIER J.L. RISQUES R.A. MALČÍKOVÁ Jitka SOUSSI T.
Year of publication	2018
Type	Article in Periodical
Magazine / Source	Human Mutation
MU Faculty or unit	Central European Institute of Technology
Citation
Web	https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23543
Doi	http://dx.doi.org/10.1002/humu.23543
Keywords	database; HGVS variant nomenclature; TP53 variants; variant annotation
Description	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 TP53Website, http://p53. fr or directly at http://vps338341.ovh.net/.