@article{Wang01082007,
author = {Wang, Chunlin and Mitsuya, Yumi and Gharizadeh, Baback and Ronaghi, Mostafa and Shafer, Robert W.}, 
title = {Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance},
volume = {17}, 
number = {8}, 
pages = {1195-1201}, 
year = {2007}, 
doi = {10.1101/gr.6468307}, 
abstract ={The detection of mutant spectra within a population of microorganisms is critical for the management of drug-resistant infections. We performed ultra-deep pyrosequencing to detect minor sequence variants in HIV-1 protease and reverse transcriptase (RT) genes from clinical plasma samples. We estimated empirical error rates from four HIV-1 plasmid clones and used them to develop a statistical approach to distinguish authentic minor variants from sequencing errors in eight clinical samples. Ultra-deep pyrosequencing detected an average of 58 variants per sample compared with an average of eight variants per sample detected by conventional direct-PCR dideoxynucleotide sequencing. In the clinical sample with the largest number of minor sequence variants, all 60 variants present in ≥3% of genomes and 20 of 35 variants present in <3% of genomes were confirmed by limiting dilution sequencing. With appropriate analysis, ultra-deep pyrosequencing is a promising method for characterizing genetic diversity and detecting minor yet clinically relevant variants in biological samples with complex genetic populations.}, 
URL = {http://genome.cshlp.org/content/17/8/1195.abstract}, 
eprint = {http://genome.cshlp.org/content/17/8/1195.full.pdf+html}, 
journal = {Genome Research} 
}