Geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data.

Matthias Döring,Martin Däumer,Joachim Büch,Rolf Kaiser,Prabhav Kalaghatgi,Alexander Thielen,Georg Friedrich,Alejandro Pironti,Elena Knops,Nico Pfeifer,Martin Obermeier,Eva Heger,Thomas Lengauer

doi:10.1093/nar/gky349

Abstract

Identifying resistance to antiretroviral drugs is crucial for ensuring the successful treatment of patients infected with viruses such as human immunodeficiency virus (HIV) or hepatitis C virus (HCV). In contrast to Sanger sequencing, next-generation sequencing (NGS) can detect resistance mutations in minority populations. Thus, genotypic resistance testing based on NGS data can offer novel, treatment-relevant insights. Since existing web services for analyzing resistance in NGS samples are subject to long processing times and follow strictly rules-based approaches, we developed geno2pheno[ngs-freq], a web service for rapidly identifying drug resistance in HIV-1 and HCV samples. By relying on frequency files that provide the read counts of nucleotides or codons along a viral genome, the time-intensive step of processing raw NGS data is eliminated. Once a frequency file has been uploaded, consensus sequences are generated for a set of user-defined prevalence cutoffs, such that the constructed sequences contain only those nucleotides whose codon prevalence exceeds a given cutoff. After locally aligning the sequences to a set of references, resistance is predicted using the well-established approaches of geno2pheno[resistance] and geno2pheno[hcv]. geno2pheno[ngs-freq] can assist clinical decision making by enabling users to explore resistance in viral populations with different abundances and is freely available at http://ngs.geno2pheno.org.

Highlights

Drug resistance mutations can emerge rapidly in patients infected with pathogens such as human immunodeficiency virus type 1 (HIV-1) or hepatitis C virus (HCV)
The levels of resistance that were predicted with geno2pheno[ngs-freq] and geno2pheno[hcv] for the default consensus sequences had an agreement of 99.7%
While non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations at low abundances are associated with virological failure [14,28,29,30], it is still generally unclear how minority resistant variants influence the treatment outcomes of HIV1 infected persons [31,32,33,34,35,36]

Summary

Introduction

Drug resistance mutations can emerge rapidly in patients infected with pathogens such as human immunodeficiency virus type 1 (HIV-1) or hepatitis C virus (HCV). Since viral resistance can severely impact the success of antiretroviral therapy, genotypic resistance testing is performed when treatment is initiated or in case of treatment failure. Genotypic resistance tests consist of two steps: sequencing the relevant segments of the viral genome followed by the interpretation of drug resistance based on the amino-acid sequence [1]. There exist two approaches for interpreting drug resistance: rules-based interpretation systems and algorithmdriven interpretation systems. While rules-based interpretation systems rely on the knowledge of expert panels, algorithm-driven systems are based on statistical models that are trained on clinical or virological data using machine learning algorithms. Algorithm-driven approaches differ among each other with respect to the applied machine learning algorithms and the data sets that are used for training the models. Geno2pheno[resistance] [4,5,6,7] uses support vector regression and classification, while the more recent SHIVA software [8] employs random forests

Methods

Results

Discussion

Conclusion