TY  - JOUR
A1  - Wang, Chunlin
A1  - Mitsuya, Yumi
A1  - Gharizadeh, Baback
A1  - Ronaghi, Mostafa
A1  - Shafer, Robert W.
T1  - Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
Y1  - 2007/08/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1195 
EP  - 1201 
DO  - 10.1101/gr.6468307 
VL  - 17 
IS  - 8 
UR  - http://genome.cshlp.org/content/17/8/1195.abstract 
N2  - 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. 
ER  -