Journal
JOURNAL OF VIROLOGICAL METHODS
Volume 162, Issue 1-2, Pages 280-283Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.jviromet.2009.08.002
Keywords
Single genome amplification; Quantitative real-time PCR; Population-based sequencing; Single genome sequencing; Minority variant detection
Funding
- University of California San Diego
- Center for AIDS Research Genomics Core Laboratory [5P30 A136214]
- San Diego Veterans Medical Research Foundation
- National Institutes of Health [A169432, A1043638, MH62512, MH083552, AI077304, A136214, A1047745, A174621]
- California HIV/AIDS Research Program [RN07-SD702]
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Typically, population-based sequencing of HIV does not detect minority variants present at levels below 20-30%. Single genome amplification (SGA) and sequencing improves detection, but it requires many PCRs to find the optimal terminal dilution to use. A novel method for guiding the selection of a terminal dilution was developed and compared to standard methods. A quantitative real-time PCR (qRT-PCR) protocol was developed. HIV RNA was extracted, reverse transcribed, and quantitated. A bioinformatics web-based application was created for calculating the optimal concentration of cDNA to use based on results of a trial PCR using the dilution suggested by the qRT-PCR results. This method was compared to the standard. Using the standard protocol, the mean number of PCRs giving an average of 30 (26-34, SD = 3) SGA per sample was 245 (218-266, SD = 20) after an average of 8 trial dilutions. Using this method, 135 PCRs (135-135, SD = 0) produced 30 (27-30, SD = 1) SGA using exactly two dilutions. This new method reduced turnaround time from 8 to 2 days. Standard methods of SGA sequencing can be costly and both time- and labor-intensive. By choosing a terminal dilution concentration with the proposed method, the number of PCRs required is decreased and efficiency improved. (c) 2009 Elsevier B.V. All rights reserved.
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