“Deep” Sequencing Accuracy and Reproducibility Using Roche/454 Technology for Inferring Co-Receptor Usage in HIV-1

David J H F Knapp, Rachel A McGovern, Art F Y Poon, Xiaoyin Zhong, Dennison Chan, Luke C Swenson, Winnie Dong and P Richard Harrigan

PLOS ONE, 2014, vol. 9, issue 6, 1-10

Abstract: Next generation, “deep”, sequencing has increasing applications both clinically and in disparate fields of research. This study investigates the accuracy and reproducibility of “deep” sequencing as applied to co-receptor prediction using the V3 loop of Human Immunodeficiency Virus-1. Despite increasing use in HIV co-receptor prediction, the accuracy and reproducibility of deep sequencing technology, and the factors which can affect it, have received only a limited level of investigation. To accomplish this, repeated deep sequencing results were generated using the Roche GS-FLX (454) from a number of sources including a non-homogeneous clinical sample (N = 47 replicates over 18 deep sequencing runs), and a large clinical cohort from the MOTIVATE and A400129 studies (N = 1521). For repeated measurements of a non-homogeneous clinical sample, increasing input copy number both decreased variance in the measured proportion of non-R5 using virus (p

Date: 2014
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0099508

DOI: 10.1371/journal.pone.0099508

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