Rapid deep sequencing of patient-derived HIV with ion semiconductor technology

Max W. Chang; Glenn Oliveira; Jinyun Yuan; Jason F. Okulicz; Samuel Levy; Bruce E. Torbett

doi:10.1016/j.jviromet.2013.01.019

Rapid deep sequencing of patient-derived HIV with ion semiconductor technology

Max W. Chang, Glenn Oliveira, Jinyun Yuan, Jason F. Okulicz, Samuel Levy, Bruce E. Torbett^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Abstract

The development of next-generation sequencing technologies has facilitated the study of HIV drug resistance evolution. However, the high capacity and per-run cost of many sequencers is not ideal for viral sequencing unless many samples are analyzed simultaneously. Ion semiconductor sequencing has recently emerged as a flexible, lower-cost alternative with short runtime. This paper describes the use of Ion Torrent devices for deep sequencing of drug resistant HIV samples. High levels of sequencing coverage were obtained in HIV Gag and protease, allowing the detection of mutations at low frequencies.

Original language	English
Pages (from-to)	232-234
Number of pages	3
Journal	Journal of Virological Methods
Volume	189
Issue number	1
DOIs	https://doi.org/10.1016/j.jviromet.2013.01.019
State	Published - Apr 2013
Externally published	Yes

Keywords

Deep sequencing
HIV Gag
HIV protease
HIV-1 drug resistance
Ion Torrent

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10.1016/j.jviromet.2013.01.019

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title = "Rapid deep sequencing of patient-derived HIV with ion semiconductor technology",

abstract = "The development of next-generation sequencing technologies has facilitated the study of HIV drug resistance evolution. However, the high capacity and per-run cost of many sequencers is not ideal for viral sequencing unless many samples are analyzed simultaneously. Ion semiconductor sequencing has recently emerged as a flexible, lower-cost alternative with short runtime. This paper describes the use of Ion Torrent devices for deep sequencing of drug resistant HIV samples. High levels of sequencing coverage were obtained in HIV Gag and protease, allowing the detection of mutations at low frequencies.",

keywords = "Deep sequencing, HIV Gag, HIV protease, HIV-1 drug resistance, Ion Torrent",

author = "Chang, {Max W.} and Glenn Oliveira and Jinyun Yuan and Okulicz, {Jason F.} and Samuel Levy and Torbett, {Bruce E.}",

note = "Funding Information: This work was supported by NIH/NCRR UL1 RR025774 , NIH P01 GM083658 , and 1P50 GM103368 . MWC was supported by NIH T32AI007354 . Patient specimens were obtained from the U.S. Military HIV Natural History Study (IDCRP-000-03) as part of the Infectious Disease Clinical Research Program (IDCRP) funded in part by the National Institute of Allergy and Infectious Diseases , NIH under Inter-Agency Agreement Y1-AI-5072 . This is manuscript 21964 from The Scripps Research Institute.",

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doi = "10.1016/j.jviromet.2013.01.019",

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AU - Oliveira, Glenn

AU - Yuan, Jinyun

AU - Okulicz, Jason F.

AU - Levy, Samuel

AU - Torbett, Bruce E.

N1 - Funding Information: This work was supported by NIH/NCRR UL1 RR025774 , NIH P01 GM083658 , and 1P50 GM103368 . MWC was supported by NIH T32AI007354 . Patient specimens were obtained from the U.S. Military HIV Natural History Study (IDCRP-000-03) as part of the Infectious Disease Clinical Research Program (IDCRP) funded in part by the National Institute of Allergy and Infectious Diseases , NIH under Inter-Agency Agreement Y1-AI-5072 . This is manuscript 21964 from The Scripps Research Institute.

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KW - Deep sequencing

KW - HIV Gag

KW - HIV protease

KW - HIV-1 drug resistance

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Rapid deep sequencing of patient-derived HIV with ion semiconductor technology

Abstract

Keywords

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