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Detection of minor drug-resistant populations by parallel allele-specific sequencing

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A Corrigendum to this article was published on 01 February 2007

This article has been updated

Abstract

We developed a highly sensitive parallel allele-specific sequencing (PASS) assay to simultaneously analyze a large number of viral genomes and detect minor drug-resistant populations at ∼0.1–0.01% levels. Using this assay on samples from individuals infected with human immunodeficiency viruses (HIV), we successfully detected and quantified minor populations of drug-resistant viruses and performed linkage analysis of multiple-drug resistance mutations. This assay may serve as a useful tool to study drug resistance in HIV and other infectious agents.

NOTE: In the supplementary information initially published online to accompany this article, the image for patient 200371 in Supplementary Figure 6 was incorrect. This panel was replaced. The error has been corrected online.

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Figure 1: Detection of minor drug-resistance populations by PASS.
Figure 2: Detection of drug-resistance mutations in patient plasma samples by PASS.

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Change history

  • 18 January 2007

    In the supplementary information initially published online to accompany this article, the image for patient 200371 in Supplementary Figure 6 was incorrect. This panel was replaced. The error has been corrected online.

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Acknowledgements

We thank Z. Camacho, A. Meade, B. Fee and X. Cao for their excellent technical assistance, J. Kirchherr for artwork, K. McGee for help in obtaining samples and clinical data, and B. Haynes for critical reading of the manuscript. This work was supported by grants from the US National Institutes of Health (RO1 GM 065057 to F.G. and K24 AI 01744 to J.A.B.), AIDS Clinical Trials Group (AI 136156 to J.A.B.), International Studies of AIDS-associated Co-infections (U01 AI062563 to J.A.B.), and Center for AIDS Research (P30 AI64518 to J.A.B. and F.G.).

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Author notes

  1. Fangping Cai and Haifeng Chen: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Fangping Cai, Haifeng Chen & Feng Gao

  2. Division of Infectious disease, Department of Medicine, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Charles B Hicks & John A Bartlett

  3. Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Jun Zhu

  4. Department of Cell Biology, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Jun Zhu

Authors
  1. Fangping Cai
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  2. Haifeng Chen
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  3. Charles B Hicks
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  4. John A Bartlett
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  5. Jun Zhu
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  6. Feng Gao
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Contributions

F.C. and H.C. performed experiments and analyzed data; C.B.H. and J.A.B. provided samples, analyzed data and prepared the manuscript; J.Z. designed experiments and prepared the manuscript; F.G. conceived the project and prepared the manuscript.

Corresponding author

Correspondence to Feng Gao.

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Competing interests

A patent application has been filed in the US for the parallel allele-specific sequencing (PASS) assay (inventors, F.G. and J.Z.).

Supplementary information

Supplementary Fig. 1

Schematic presentation of the parallel allele-specific sequencing (PASS) assay.

Supplementary Fig. 2

Detection of minor drug-resistance mutations by PASS.

Supplementary Fig. 3

Determination of primary drug-resistance mutations in the same viral genome by sequential PASS assays.

Supplementary Fig. 4

Detection of single base mutations among diverse HIV-1 subtypes and recombinants.

Supplementary Fig. 5

Determination of sensitivity of the PASS assay.

Supplementary Fig. 6

Detection of multiple drug-resistance mutations in a patient plasma sample.

Supplementary Table 1

Detection of the A to G mutation in the M184V codon.

Supplementary Methods

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Cai, F., Chen, H., Hicks, C. et al. Detection of minor drug-resistant populations by parallel allele-specific sequencing. Nat Methods 4, 123–125 (2007). https://doi.org/10.1038/nmeth995

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