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@article{1173878,
author = {Grodecká, Lucie and Lockerová, Pavla and Ravčuková, Barbora and Buratti, Emanuele and Baralle, Francisco E. and Dušek, Ladislav and Freiberger, Tomáš},
article_location = {SAN FRANCISCO},
article_number = {2},
doi = {http://dx.doi.org/10.1371/journal.pone.0089570},
keywords = {POLYPYRIMIDINE TRACT RECOGNITION; HUMAN-DISEASE GENES; CONFORMATIONAL SELECTION; COMPUTATIONAL TOOLS; SEQUENCE MOTIFS; FACTOR U2AF(35); MSH2 MISSENSE; SITE; ENHANCERS; U2AF(65)},
language = {eng},
issn = {1932-6203},
journal = {PLoS One},
title = {Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools},
url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089570},
volume = {9},
year = {2014}
}
TY - JOUR
ID - 1173878
AU - Grodecká, Lucie - Lockerová, Pavla - Ravčuková, Barbora - Buratti, Emanuele - Baralle, Francisco E. - Dušek, Ladislav - Freiberger, Tomáš
PY - 2014
TI - Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools
JF - PLoS One
VL - 9
IS - 2
SP - "nestránkováno"
EP - "nestránkováno"
PB - PUBLIC LIBRARY SCIENCE
SN - 19326203
KW - POLYPYRIMIDINE TRACT RECOGNITION
KW - HUMAN-DISEASE GENES
KW - CONFORMATIONAL SELECTION
KW - COMPUTATIONAL TOOLS
KW - SEQUENCE MOTIFS
KW - FACTOR U2AF(35)
KW - MSH2 MISSENSE
KW - SITE
KW - ENHANCERS
KW - U2AF(65)
UR - http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089570
L2 - http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089570
N2 - Mutations in the first nucleotide of exons (E+1) mostly affect pre-mRNA splicing when found in AG-dependent 39 splice sites, whereas AG-independent splice sites are more resistant. The AG-dependency, however, may be difficult to assess just from primary sequence data as it depends on the quality of the polypyrimidine tract. For this reason, in silico prediction tools are commonly used to score 39 splice sites. In this study, we have assessed the ability of sequence features and in silico prediction tools to discriminate between the splicing-affecting and non-affecting E+1 variants. For this purpose, we newly tested 16 substitutions in vitro and derived other variants from literature. Surprisingly, we found that in the presence of the substituting nucleotide, the quality of the polypyrimidine tract alone was not conclusive about its splicing fate. Rather, it was the identity of the substituting nucleotide that markedly influenced it. Among the computational tools tested, the best performance was achieved using the Maximum Entropy Model and Position-Specific Scoring Matrix. As a result of this study, we have now established preliminary discriminative cut-off values showing sensitivity up to 95% and specificity up to 90%. This is expected to improve our ability to detect splicing-affecting variants in a clinical genetic setting.
ER -
GRODECKÁ, Lucie, Pavla LOCKEROVÁ, Barbora RAVČUKOVÁ, Emanuele BURATTI, Francisco E. BARALLE, Ladislav DUŠEK a Tomáš FREIBERGER. Exon First Nucleotide Mutations in Splicing: Evaluation of In Silico Prediction Tools. \textit{PLoS One}. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2014, roč.~9, č.~2, s.~''nestránkováno'', 13 s. ISSN~1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0089570.
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