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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
medicine
Comparison of a high-resolution melting assay to next-generation sequencing for analysis of HIV diversity
Journal of Clinical Microbiology, Volume 50, No. 9, Year 2012
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Description
Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV gag and env from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (n = 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both gag and env (P < 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (P < 0.001 for all measures except for percent complexity in gag), and similar amounts of diversification were observed with both methods (P < 0.001 for all measures except for percent complexity in gag). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution. Copyright © 2012, American Society for Microbiology. All Rights Reserved.
Authors & Co-Authors
Cousins, Matthew M.
United States, Baltimore
Johns Hopkins School of Medicine
Ou, Sansan
United States, Seattle
Fred Hutchinson Cancer Research Center
Wawer, Maria J.
United States, Baltimore
Johns Hopkins Bloomberg School of Public Health
Munshaw, Supriya
United States, Baltimore
Johns Hopkins School of Medicine
Swan, David
United States, Seattle
Fred Hutchinson Cancer Research Center
Magaret, Craig A.
United States, Seattle
Fred Hutchinson Cancer Research Center
Mullis, Caroline E.
United States, Baltimore
Johns Hopkins School of Medicine
Serwadda, David Musoke
Uganda, Kalisizo
Rakai Health Sciences Program
Uganda, Kampala
Makerere University
Porcella, Stephen F.
United States, Hamilton
Niaid Rocky Mountain Laboratories
Gray, Ronald H.
United States, Baltimore
Johns Hopkins Bloomberg School of Public Health
Quinn, Thomas Charles
United States, Baltimore
Johns Hopkins School of Medicine
United States, Bethesda
National Institute of Allergy and Infectious Diseases Niaid
Donnell, Deborah J.
United States, Seattle
Fred Hutchinson Cancer Research Center
Eshleman, Susan H.
United States, Baltimore
Johns Hopkins School of Medicine
Redd, Andrew D.
United States, Bethesda
National Institute of Allergy and Infectious Diseases Niaid
Statistics
Citations: 51
Authors: 14
Affiliations: 7
Identifiers
Doi:
10.1128/JCM.01460-12
ISSN:
00951137
e-ISSN:
1098660X
Research Areas
Genetics And Genomics
Infectious Diseases
Study Locations
Uganda