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

J 2018

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

TIKKANEN, T., B. LEROY, J.L. FOURNIER, R.A. RISQUES, Jitka MALČÍKOVÁ et. al.

Basic information

Original name

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

Authors

TIKKANEN, T. (246 Finland), B. LEROY (250 France), J.L. FOURNIER (250 France), R.A. RISQUES (840 United States of America), Jitka MALČÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution) and T. SOUSSI (250 France)

Edition

Human Mutation, New York, Wiley-Liss, 2018, 1059-7794

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

30101 Human genetics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.453

RIV identification code

RIV/00216224:14740/18:00105801

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1002/humu.23543

UT WoS

000434972700003

Keywords in English

database; HGVS variant nomenclature; TP53 variants; variant annotation

Abstract

V originále

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/.

Citovat

TIKKANEN, T., B. LEROY, J.L. FOURNIER, R.A. RISQUES, Jitka MALČÍKOVÁ and T. SOUSSI. Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing. Human Mutation. New York: Wiley-Liss, 2018, vol. 39, No 7, p. 925-933. ISSN 1059-7794. Available from: https://dx.doi.org/10.1002/humu.23543.

@article{1489193,
   author = {Tikkanen, T. and Leroy, B. and Fournier, J.L. and Risques, R.A. and Malčíková, Jitka and Soussi, T.},
   article_location = {New York},
   article_number = {7},
   doi = {http://dx.doi.org/10.1002/humu.23543},
   keywords = {database; HGVS variant nomenclature; TP53 variants; variant annotation},
   language = {eng},
   issn = {1059-7794},
   journal = {Human Mutation},
   title = {Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing},
   url = {https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23543},
   volume = {39},
   year = {2018}
}

TY  - JOUR
ID  - 1489193
AU  - Tikkanen, T. - Leroy, B. - Fournier, J.L. - Risques, R.A. - Malčíková, Jitka - Soussi, T.
PY  - 2018
TI  - Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing
JF  - Human Mutation
VL  - 39
IS  - 7
SP  - 925-933
EP  - 925-933
PB  - Wiley-Liss
SN  - 10597794
KW  - database
KW  - HGVS variant nomenclature
KW  - TP53 variants
KW  - variant annotation
UR  - https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23543
N2  - 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/.
ER  -

TIKKANEN, T., B. LEROY, J.L. FOURNIER, R.A. RISQUES, Jitka MALČÍKOVÁ and T. SOUSSI. Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing. \textit{Human Mutation}. New York: Wiley-Liss, 2018, vol.~39, No~7, p.~925-933. ISSN~1059-7794. Available from: https://dx.doi.org/10.1002/humu.23543.

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