- 作者: Ping Qiu; Xiao-Yan Cai; Wei Ding; Qing Zhang; Ellie D Norris; Jonathan R Greene
- 作者服務機構: Molecular Design and Informatics, Schering-Plough Research Institute, Kenilworth, New Jersey, USA
- 中文摘要: --
- 英文摘要:
The genotype of Hepatitis C Virus (HCV) strains is an important determinant of the
severity and aggressiveness of liver infection as well as patient response to antiviral
therapy. Fast and accurate determination of viral genotype could provide direction in the
clinical management of patients with chronic HCV infections. Using publicly available
HCV nucleotide sequences, we built a global Position Weight Matrix (PWM) for the
HCV genome. Based on the PWM, a set of genotype specific nucleotide sequence
“signatures” were selected from the 5’ NCR, CORE, E1, and NS5B regions of the HCV
genome. We evaluated the predictive power of these signatures for predicting the most
common HCV genotypes and subtypes. We observed that nucleotide sequence signatures
selected from NS5B and E1 regions generally demonstrated stronger discriminant power
in differentiating major HCV genotypes and subtypes than that from 5’ NCR and CORE
regions. Two discriminant methods were used to build predictive models. Through 10
fold cross validation, over 99% prediction accuracy was achieved using both support
vector machine (SVM) and random forest based classification methods in a dataset of
1134 sequences for NS5B and 947 sequences for E1. Prediction accuracy for each
genotype is also reported. - 中文關鍵字: --
- 英文關鍵字: --