Analysis of HIV Using a High Resolution Melting (HRM) Diversity Assay: Automation of HRM Data Analysis Enhances the Utility of the Assay for Analysis of HIV Incidence

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Cousins, Matthew M ^a   Swan, David ^b   Magaret, Craig A ^b   Hoover, Donald R ^c   Eshleman, Susan H ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; DNA DENATURATION; DNA DETERMINATION; HIGH RESOLUTION MELTING ANALYSIS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INTERMETHOD COMPARISON; LARGE SCALE PRODUCTION; MAJOR CLINICAL STUDY; MATHEMATICAL COMPUTING; MELTING POINT; MICROBIAL DIVERSITY; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; REPRODUCIBILITY; VIRUS IDENTIFICATION;

BIOLOGICAL MARKERS; GENETIC VARIATION; HIV; HIV INFECTIONS; HUMANS; NUCLEIC ACID DENATURATION;

EID: 84871174586     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051359     Document Type: Article

References (18)

1. Brookmeyer R, (2010) Measuring the HIV/AIDS epidemic: approaches and challenges. Epidemiol Rev 32: 26-37.
2. Dobbs T, Kennedy S, Pau CP, McDougal JS, Parekh BS, (2004) Performance characteristics of the immunoglobulin G-capture BED-enzyme immunoassay, an assay to detect recent human immunodeficiency virus type 1 seroconversion. J Clin Microbiol 42: 2623-2628.
3. Murphy G, Parry JV (2008) Assays for the detection of recent infections with human immunodeficiency virus type 1. Euro Surveill 13.
4. Guy R, Gold J, Calleja JM, Kim AA, Parekh B, et al. (2009) Accuracy of serological assays for detection of recent infection with HIV and estimation of population incidence: a systematic review. The Lancet Infectious Diseases 9: 747-759.
5. Cousins MM, Laeyendecker O, Beauchamp G, Brookmeyer R, Towler WI, et al. (2011) Use of a high resolution melting (HRM) assay to compare gag, pol, and env diversity in adults with different stages of HIV infection. PloS ONE 6: e27211.
6. Kouyos RD, von Wyl V, Yerly S, Boni J, Rieder P, et al. (2011) Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection. Clinical Infectious Diseases 52: 532-539.
7. Towler WI, James MM, Ray SC, Wang L, Donnell D, et al. (2010) Analysis of HIV diversity using a high-resolution melting assay. AIDS Res Hum Retroviruses 26: 913-918.
8. Cousins MM, Ou SS, Wawer MJ, Munshaw S, Swan D, et al. (2012) Comparison of a high resolution melting (HRM) assay to next generation sequencing for analysis of HIV diversity. J Clin Microbiol 50: 3054-3059.
9. Montgomery JL, Sanford LN, Wittwer CT, (2010) High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 10: 219-240.
10. James MM, Wang L, Musoke P, Donnell D, Fogel J, et al. (2011) Association of HIV diversity and survival in HIV-infected Ugandan infants. PLoS ONE 6: e18642.
11. Cleveland WS, (1979) Robust locally weighted regression and smoothing scatterplots. Journal of the American Statistical Association 74: 829-836.
12. Cleveland WS, Devlin SJ, (1988) Locally weighted regression- an approach to regression-analysis by local fitting. Journal of the American Statistical Association 83: 596-610.
13. Tibshirani R, (1996) Regression shrinkage and selection via the Lasso. Journal of the Royal Statistical Society Series B-Methodological 58: 267-288.
14. Wittwer C, Kusukawa N (2004) Real-time PCR. In: Pershing D, Versalovic J, al e, editors. Diagnostic Molecular Microbiology: Principles and Applications. Washington DC: ASM Press. 71-84.
15. Erali M, Palais B, Wittwer C (2007) SNP genotyping by unlabeled probe melting analysis. In: Marx A, Seitz O, editors. Molecular Beacons: Signaling Nucleic Acid Probes. Totowa, NJ: Humana Press.
16. Ihaka R, Gentleman R, (1996) R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics 5: 299-314.
17. James MM, Wang L, Donnell D, Cousins MM, Barlow-Mosha L, et al. (2012) Use of a high resolution melting assay to analyze HIV diversity in HIV-infected Ugandan children. Pediatr Infect Dis J.
18. Cousins MM, Donnell D, Eshleman SH (2012) Impact of mutation type and amplicon characteristics on genetic diversity measures generated using a high resolution melting diversity assay. Journal of Molecular Diagnostics. In Press.