Applications
HIV Sequencing
Overview
Characterize and quantify the viral population within an infected individual with Ultra-Deep 454 Sequencing. The Genome Sequencer FLX System enables accurate and quantitative assessment of HIV quasi-species through the sequencing of target genes (ex. protease and reverse transcriptase genes). Sequencing hundreds of thousands of individual DNA molecules simultaneously, the GS FLX System detects rare genetic variants constituting as little as 1% of the population, levels far deeper than those of traditional sequencing methods. Furthermore, long reads elucidate haplotypes within each amplicon.
Publications
- Wang et al. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Research 17: 1195-201. August 2007.
- Hoffmann et al. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Research 35: e19. 2007.
- Wang et al. HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Research ePub June 1, 2007
- Mitsuya et al. Minority HIV-1 Variants in Antiretroviral Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations. Journal of Virology ePub August 20, 2008.
Click here to see all HIV Sequencing publications.
Data Analysis tools:
GS Amplicon Variant Analyzer Software
How it works:
Ultra Deep 454 Sequencing
Targeted amplicon sequencing on amplicons derived from cDNA fragments, amplified with lucus specific primers covering the major variant positions in desired genes.
