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.

Základní údaje

Originální název

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

Autoři

TIKKANEN, T. (246 Finsko), B. LEROY (250 Francie), J.L. FOURNIER (250 Francie), R.A. RISQUES (840 Spojené státy), Jitka MALČÍKOVÁ (203 Česká republika, garant, domácí) a T. SOUSSI (250 Francie)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30101 Human genetics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.453

Kód RIV

RIV/00216224:14740/18:00105801

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000434972700003

Klíčová slova anglicky

database; HGVS variant nomenclature; TP53 variants; variant annotation

Štítky

14110212, podil, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 13. 3. 2019 11:32, Mgr. Pavla Foltynová, Ph.D.

Anotace

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 a 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, roč. 39, č. 7, s. 925-933. ISSN 1059-7794. Dostupné z: 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 a 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, roč.~39, č.~7, s.~925-933. ISSN~1059-7794. Dostupné z: https://dx.doi.org/10.1002/humu.23543.

Podrobný výpis o publikaci