Doering, Matthias, Buech, Joachim, Friedrich, Georg, Pironti, Alejandro, Kalaghatgi, Prabhav, Knops, Elena, Heger, Eva, Obermeier, Martin, Daeumer, Martin, Thielen, Alexander, Kaiser, Rolf, Lengauer, Thomas ORCID: 0000-0003-3801-2640 and Pfeifer, Nico (2018). geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data. Nucleic Acids Res., 46 (W1). S. W271 - 7. OXFORD: OXFORD UNIV PRESS. ISSN 1362-4962

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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 rulesbased 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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Doering, MatthiasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Buech, JoachimUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Friedrich, GeorgUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pironti, AlejandroUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kalaghatgi, PrabhavUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Knops, ElenaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Heger, EvaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Obermeier, MartinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Daeumer, MartinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thielen, AlexanderUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kaiser, RolfUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lengauer, ThomasUNSPECIFIEDorcid.org/0000-0003-3801-2640UNSPECIFIED
Pfeifer, NicoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-180078
DOI: 10.1093/nar/gky349
Journal or Publication Title: Nucleic Acids Res.
Volume: 46
Number: W1
Page Range: S. W271 - 7
Date: 2018
Publisher: OXFORD UNIV PRESS
Place of Publication: OXFORD
ISSN: 1362-4962
Language: English
Faculty: Faculty of Mathematics and Natural Sciences
Divisions: Faculty of Mathematics and Natural Sciences > Department of Mathematics and Computer Science > Institute of Computer Science
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
HEPATITIS-C; VARIANT DETECTION; CORECEPTOR USAGE; HIV-1; VIRUS; LAMIVUDINE; THERAPY; KRAS; TRANSMISSION; MUTATIONSMultiple languages
Biochemistry & Molecular BiologyMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/18007

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