Journal article

HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay

Sara Sunshine, Rory Kirchner, Sami S Amr, Leandra Mansur, Rimma Shakhbatyan, Michelle Kim, Alberto Bosque, Robert F Siliciano, Vicente Planelles, Oliver Hofmann, Shannan Ho Sui, Jonathan Z Li

Journal of Virology | AMER SOC MICROBIOLOGY | Published : 2016

Abstract

UNLABELLED: Antiretroviral therapy (ART) is successful in the suppression of HIV but cannot target and eradicate the latent proviral reservoir. The location of retroviral integration into the human genome is thought to play a role in the clonal expansion of infected cells and HIV persistence. We developed a high-throughput targeted sequence capture assay that uses a pool of HIV-specific probes to enrich Illumina libraries prior to deep sequencing. Using an expanded clonal population of ACH-2 cells, we demonstrate that this sequence capture assay has an extremely low false-positive rate. This assay assessed four cellular models commonly used to study HIV latency and latency-reversing agents: ..

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University of Melbourne Researchers

Grants

Awarded by National Institutes of Health


Awarded by Harvard Catalyst, The Harvard Clinical and Translational Science Center (National Center for Advancing Translational Sciences, National Institutes of Health)


Awarded by NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES


Awarded by NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES


Funding Acknowledgements

This work was supported in part by National Institutes of Health grant K08 AI100699 (to Jonathan Z. Li); funding from the Harvard Catalyst, The Harvard Clinical and Translational Science Center (National Center for Research Resources and National Center for Advancing Translational Sciences, National Institutes of Health, award UL1 TR001102); and financial contributions from Harvard University and its affiliated academic health care centers.