Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP
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Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP. / Johansen, Morten Bo; Izarzugaza, Jose M G; Brunak, Søren; Petersen, Thomas Nordahl; Gupta, Ramneek.
In: P L o S One, Vol. 8, No. 7, 07.2013, p. e68370.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP
AU - Johansen, Morten Bo
AU - Izarzugaza, Jose M G
AU - Brunak, Søren
AU - Petersen, Thomas Nordahl
AU - Gupta, Ramneek
PY - 2013/7
Y1 - 2013/7
N2 - We have developed a sequence conservation-based artificial neural network predictor called NetDiseaseSNP which classifies nsSNPs as disease-causing or neutral. Our method uses the excellent alignment generation algorithm of SIFT to identify related sequences and a combination of 31 features assessing sequence conservation and the predicted surface accessibility to produce a single score which can be used to rank nsSNPs based on their potential to cause disease. NetDiseaseSNP classifies successfully disease-causing and neutral mutations. In addition, we show that NetDiseaseSNP discriminates cancer driver and passenger mutations satisfactorily. Our method outperforms other state-of-the-art methods on several disease/neutral datasets as well as on cancer driver/passenger mutation datasets and can thus be used to pinpoint and prioritize plausible disease candidates among nsSNPs for further investigation. NetDiseaseSNP is publicly available as an online tool as well as a web service: https://www.cbs.dtu.dk/services/NetDiseaseSNP.
AB - We have developed a sequence conservation-based artificial neural network predictor called NetDiseaseSNP which classifies nsSNPs as disease-causing or neutral. Our method uses the excellent alignment generation algorithm of SIFT to identify related sequences and a combination of 31 features assessing sequence conservation and the predicted surface accessibility to produce a single score which can be used to rank nsSNPs based on their potential to cause disease. NetDiseaseSNP classifies successfully disease-causing and neutral mutations. In addition, we show that NetDiseaseSNP discriminates cancer driver and passenger mutations satisfactorily. Our method outperforms other state-of-the-art methods on several disease/neutral datasets as well as on cancer driver/passenger mutation datasets and can thus be used to pinpoint and prioritize plausible disease candidates among nsSNPs for further investigation. NetDiseaseSNP is publicly available as an online tool as well as a web service: https://www.cbs.dtu.dk/services/NetDiseaseSNP.
U2 - 10.1371/journal.pone.0068370
DO - 10.1371/journal.pone.0068370
M3 - Journal article
C2 - 23935863
VL - 8
SP - e68370
JO - PLoS ONE
JF - PLoS ONE
SN - 1932-6203
IS - 7
ER -
ID: 58426758