Abstract:
BACKGROUND:HIV/AIDS is a serious threat to public health. The emergence of drug resistance mutations diminishes the effectiveness of drug therapy for HIV/AIDS. Developing a computational prediction of drug resistance phenotype will enable efficient and timely selection of the best treatment regimens. RESULTS:A unified encoding of protein sequence and structure was used as the feature vector for predicting phenotypic resistance from genotype data. Two machine learning algorithms, Random Forest and K-nearest neighbor, were used. The prediction accuracies were examined by five-fold cross-validation on the genotype-phenotype datasets. A supervised machine learning approach for automatic prediction of drug resistance was developed to handle genotype-phenotype datasets of HIV protease (PR) and reverse transcriptase (RT). It predicts the drug resistance phenotype and its relative severity from a query sequence. The accuracy of the classification was higher than 0.973 for eight PR inhibitors and 0.986 for ten RT inhibitors, respectively. The overall cross-validated regression R(2)-values for the severity of drug resistance were 0.772-0.953 for 8 PR inhibitors and 0.773-0.995 for 10 RT inhibitors. CONCLUSIONS:Machine learning using a unified encoding of sequence and protein structure as a feature vector provides an accurate prediction of drug resistance from genotype data. A practical webserver for clinicians has been implemented.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Shen C,Yu X,Harrison RW,Weber ITdoi
10.1186/s12859-016-1114-6subject
Has Abstractpub_date
2016-08-31 00:00:00pages
278issn
1471-2105pii
10.1186/s12859-016-1114-6journal_volume
17 Suppl 8pub_type
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