development of a low bias method for characterizing viral populations using next generation sequencing technology开发低偏压的方法描述病毒人群使用下一代测序技术.pdfVIP

Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology 1. ´ 2. 3 4 2 Stephanie M. Willerth , Helder A. M. Pedro , Lior Pachter , Laurent M. Humeau , Adam P. Arkin *, David V. Schaffer1,2* 1 Department of Chemical Engineering and the Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America, 2 Department of Bioengineering, University of California, Berkeley, California, United States of America, 3 Department of Mathematics and Molecular and Cell Biology, University of California, Berkeley, California, United States of America, 4 VIRxSYS Corporation, Gaithersburg, Maryland, United States of America Abstract Background: With an estimated 38 million people worldwide currently infected with human immunodeficiency virus (HIV), and an additional 4.1 million people becoming infected each year, it is important to understand how this virus mutates and develops resistance in order to design successful therapies. Methodology/Principal Findings: We report a novel experimental method for amplifying full-length HIV genomes without the use of sequence-specific primers for high throughput DNA sequencing, followed by assembly of full length viral genome sequences from the resulting large dataset. Illumina was chosen for sequencing due to its ability to provide greater coverage of the HIV genome compared to prior methods, allowing for more comprehensive characterization of the heterogeneity present in the HIV samples analyzed. Our novel amplification method in combination with Illumina sequencing was used to analyze two HIV populations: a ho