. "RIV/61388963:_____/12:00383618!RIV13-AV0-61388963" . . "Weber, Jan" . . . "Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism"@en . "1932-6203" . . "P(LK11207), Z(AV0Z40550506)" . "Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism" . . . "Gibson, R." . "HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile (TM), Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454 (TM) Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454 (TM), PacBio (R) RS (Pacific Biosciences), Illumina (R), and Ion Torrent (TM) (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile (TM) and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage."@en . "Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism"@en . "176351" . "7" . "Arts, E. J." . "[DBE7DCBCA4C4]" . . "US - Spojen\u00E9 st\u00E1ty americk\u00E9" . "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049602" . "Archer, J." . "HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile (TM), Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454 (TM) Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454 (TM), PacBio (R) RS (Pacific Biosciences), Illumina (R), and Ion Torrent (TM) (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile (TM) and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage." . . . . . . "17"^^ . "Lee, L." . "PLoS ONE" . "11"^^ . "Quinones-Mateu, M. E." . "000311151900171" . . "Mimms, L." . . "Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism" . . "Winner, D." . "1"^^ . "HIV-1 tropism; V3 region; deep sequencing"@en . "Robertson, D. L." . "Paxinos, E." . "11" . . "RIV/61388963:_____/12:00383618" . . "10.1371/journal.pone.0049602" . "Henry, K." .