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Hum Mutat. 2018 Jul;39(7):925-933. doi: 10.1002/humu.23543. Epub 2018 May 17.

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

Author information

1
Genevia Technologies, Tampere, Finland.
2
Sorbonne Université, UPMC Univ Paris, Paris, France.
3
Department of Pathology, University of Washington, Seattle, Washington.
4
Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic.
5
Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
6
Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska Institutet, Stockholm, Sweden.
7
INSERM, Centre de Recherche des Cordeliers, U1138, Paris, France.

Abstract

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/.

KEYWORDS:

HGVS variant nomenclature; TP53 variants; database; variant annotation

PMID:
29696732
DOI:
10.1002/humu.23543
[Indexed for MEDLINE]
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