Journal article
Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy
JZ Li, B Chapman, P Charlebois, O Hofmann, B Weiner, AJ Porter, R Samuel, S Vardhanabhuti, L Zheng, J Eron, B Taiwo, MC Zody, MR Henn, DR Kuritzkes, W Hide, RM Matining, CC Wilson, BI Berzins, EP Acosta, B Bastow Show all
Plos One | PUBLIC LIBRARY SCIENCE | Published : 2014
Abstract
Background: The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs. Methods: A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naïve patients. Pre-treatment plasma was obtained from 5 participants with raltegravir resistance at the time of virologic failure. A control library was created by pooling integrase clones at predefined proportions. Multiplexed sequencing was performed with Illumina and 454 platforms ..
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Grants
Awarded by National Institute of Allergy and Infectious Diseases
Funding Acknowledgements
This work was supported in part by National Institutes of Health (NIH) grants K08 AI100699 (to Dr. Li), U01 AI068634 (Statistical and Data Management Center of the AIDS Clinical Trials Group), U01 AI068636 (AIDS Clinical Trials Group), U01 AI068634 (ACTG Statistical and Data Management Center), and a subcontract from U01 AI068636 to the Harvard Virology Support Laboratory (to Dr. Kuritzkes). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The TopCoder crowdsourcing competition was funded by the Harvard Clinical and Translational Science Center (UL1 RR 025758 and financial contributions from participating institutions).