Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance Export

@article{wang2007, abstract = {10.1101/gr.6468307 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.}, author = {Wang, Chunlin and Mitsuya, Yumi and Gharizadeh, Baback and Ronaghi, Mostafa and Shafer, Robert W.}, citeulike-article-id = {1534080}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.6468307}, citeulike-linkout-1 = {http://genome.cshlp.org/content/early/2007/06/28/gr.6468307.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/early/2007/06/28/gr.6468307.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/17/8/1195}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/17600086}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=17600086}, doi = {10.1101/gr.6468307}, journal = {Genome Research}, keywords = {hiv, snp, srs, srs-deep}, month = {August}, number = {8}, pages = {1195--1201}, posted-at = {2009-06-29 11:03:16}, priority = {0}, title = {Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance}, url = {http://dx.doi.org/10.1101/gr.6468307}, volume = {17}, year = {2007} }

TY - JOUR ID - wang2007 L3 - citeulike-article-id:1534080 N2 - 10.1101/gr.6468307 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. IS - 8 JF - Genome Research EP - 1201 TI - Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance VL - 17 SP - 1195 KW - hiv KW - snp KW - srs KW - srs-deep AU - Wang, Chunlin AU - Mitsuya, Yumi AU - Gharizadeh, Baback AU - Ronaghi, Mostafa AU - Shafer, Robert PY - 2007/08/01/ UR - http://dx.doi.org/10.1101/gr.6468307 ER -