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Direct comparison with 454 pyrosequencing validates V3-loop based genotyping in patients eligible for Maraviroc initiation
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Reported by Jules Levin
ICAAC Sept 15 2009 San Francisco
L. Vandekerckhove1 , C. Verhofstede1, I. Vandenbroucke2, K. Van Baelen2,
C. Booth3, H. Van Marck2, AM. Geretti3, L. Stuyver2 on behalf of the Tropism Study Group
Tropism study Group: E. Demecheleer1, A. Strang3, W. Mostmans2, V. Van Eygen2, S. De Wit4, K. Kabeya4, E. Florence5, K. Fransen5, A. Van Den Heuvel5, M. Moutschen6, D.Vaira6, D.Vogelaers1, J. Plum1, Nicola Makie7, Margaret Johnson3 Nicky Perry8 and Martin Fisher8
Ghent University Hospital, Ghent, Belgium1, Virco, Mechelen, Belgium2, Royal Free Hampstead NHS Trust & UCL Medical School, London, UK3, Centre Hospitalier Universitaire Saint-Pierre, Brussels, Belgium4, Institute of Tropical Medicine, Antwerp, Belgium5, CHU Sart Tilman, Liège, Belgium6, Imperial College Healthcare NHS Trust, London7, Brighton & Sussex University Hospitals NHS Trust, Brighton8
BACKGROUND
In order to establish alternative strategies to guide initiation of maraviroc, genotypic tropism prediction obtained by population Sanger sequencing was compared to the results of 454 sequencing.
METHODS
Plasma samples were retrieved from HIV infected individuals who underwent standard Trofile testing before Maraviroc initiation in routine clinical care. Virco population phenotyping was performed and V3-loop sequences were obtained by Sanger and 454 sequencing. Tropism prediction from V3 sequences was obtained using the SVM of Geno2Pheno (G2P), PSSM and the 11/25 rule. In order to asses test concordance κ calculations were performed using SPSS.
RESULTS
Clinical decision making based on genotypic and phenotypic tests
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