{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:43:25Z","timestamp":1778636605089,"version":"3.51.4"},"reference-count":29,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2012,3,15]],"date-time":"2012-03-15T00:00:00Z","timestamp":1331769600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002417","type":"journal-article","created":{"date-parts":[[2012,3,15]],"date-time":"2012-03-15T21:49:35Z","timestamp":1331848175000},"page":"e1002417","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":103,"title":["Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data"],"prefix":"10.1371","volume":"8","author":[{"given":"Alexander R.","family":"Macalalad","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael C.","family":"Zody","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Charlebois","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niall J.","family":"Lennon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruchi M.","family":"Newman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine M.","family":"Malboeuf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth M.","family":"Ryan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian L.","family":"Boutwell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karen A.","family":"Power","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Doug E.","family":"Brackney","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kendra N.","family":"Pesko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joshua Z.","family":"Levin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gregory D.","family":"Ebel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Todd M.","family":"Allen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruce W.","family":"Birren","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew R.","family":"Henn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2012,3,15]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1089\/aid.1998.14.869","article-title":"Comparative performance of high-density oligonucleotide sequencing and dideoxynucleotide sequencing of HIV type 1 pol from clinical samples.","volume":"14","author":"HF Gunthard","year":"1998","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1126\/science.8356453","article-title":"Genotypic and Phenotypic Characterization of HIV-1 in Patients with Primary Infection.","volume":"261","author":"T Zhu","year":"1993","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1128\/JCM.43.1.406-413.2005","article-title":"Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experienced Patients Are Missed by Standard Genotype Analysis.","volume":"43","author":"S Palmer","year":"2005","journal-title":"J Clin Microbiol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1097\/00002030-199106000-00006","article-title":"Detection, quantification and sequencing of HIV-1 from the plasma of seropositive individuals and from factor VIII concentrates.","volume":"5","author":"LQ Zhang","year":"1991","journal-title":"AIDS"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"3952","DOI":"10.1128\/JVI.02660-07","article-title":"Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing.","volume":"82","author":"JF Salazar-Gonzalez","year":"2008","journal-title":"J Virol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","article-title":"Genome sequencing in microfabricated high-density picolitre reactors.","volume":"437","author":"M Margulies","year":"2005","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature07517","article-title":"Accurate whole human genome sequencing using reversible terminator chemistry.","volume":"456","author":"DR Bentley","year":"2008","journal-title":"Nature"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1101\/gr.6468307","article-title":"Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance.","volume":"17","author":"C Wang","year":"2007","journal-title":"Genome Res"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"e1000074","DOI":"10.1371\/journal.pcbi.1000074","article-title":"Viral Population Estimation Using Pyrosequencing.","volume":"4","author":"N Eriksson","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"ref10","first-page":"417","article-title":"Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. J Comput.","volume":"17","author":"O Zagordi","year":"2010","journal-title":"Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"7400","DOI":"10.1093\/nar\/gkq655","article-title":"Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies.","volume":"38","author":"O Zagordi","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-12-119","article-title":"ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.","volume":"12","author":"O Zagordi","year":"2011","journal-title":"BMC Bioinf"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1093\/bioinformatics\/btr627","article-title":"QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.","volume":"28","author":"MCF Prosperi","year":"2012","journal-title":"Bioinformatics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1101\/gr.070227.107","article-title":"Quality scores and SNP detection in sequencing-by-synthesis systems.","volume":"18","author":"W Brockman","year":"2008","journal-title":"Genome Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","article-title":"Mapping short DNA sequencing reads and calling variants using mapping quality scores.","volume":"18","author":"H Li","year":"2008","journal-title":"Genome Res"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1101\/gr.088013.108","article-title":"SNP detection for massively parallel whole-genome resequencing.","volume":"19","author":"R Li","year":"2009","journal-title":"Genome Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A Framework for Variation Discovery and Genotyping Using Next-Generation DNA Sequencing Data.","volume":"43","author":"MA DePristo","year":"2011","journal-title":"Nat Genet"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1093\/bioinformatics\/btq040","article-title":"SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.","volume":"26","author":"R Goya","year":"2010","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1093\/bioinformatics\/btn565","article-title":"Slider\u2013maximum use of probability information for alignment of short sequence reads and SNP detection.","volume":"25","author":"N Malhis","year":"2009","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e91","DOI":"10.1093\/nar\/gkm435","article-title":"DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.","volume":"35","author":"C Hoffmann","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e1001022","DOI":"10.1371\/journal.pcbi.1001022","article-title":"The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR<sub>4<\/sub> Using Variants through Time - An Ultra-Deep Approach.","volume":"6","author":"J Archer","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/1742-4690-6-15","article-title":"Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations.","volume":"6","author":"G Rozera","year":"2009","journal-title":"Retrovirology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1471-2105-12-38","article-title":"Removing noise from pyrosequenced amplicons.","volume":"12","author":"C Quince","year":"2011","journal-title":"BMC Bioinf"},{"key":"ref24","article-title":"Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection.","volume":"8","author":"MR Henn","year":"2011","journal-title":"PLoS Pathog"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1471-2105-12-S6-S1","article-title":"Inferring viral quasispecies spectra from 454 pyrosequencing reads.","volume":"12","author":"I Astrovskaya","year":"2011","journal-title":"BMC Bioinf"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.jviromet.2009.11.025","article-title":"Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design.","volume":"164","author":"VF Boltz","year":"2010","journal-title":"J Virol Methods"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1101\/gr.6468307","article-title":"Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance.","volume":"17","author":"C Wang","year":"2007","journal-title":"Genome Res"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e11345","DOI":"10.1371\/journal.pone.0011345","article-title":"Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing.","volume":"5","author":"C Hedskog","year":"2010","journal-title":"PLoS ONE"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1038\/35035083","article-title":"An SNP map of the human genome generated by reduced representation shotgun sequencing.","volume":"407","author":"D Altshuler","year":"2000","journal-title":"Nature"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002417","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T15:40:51Z","timestamp":1589038851000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002417"}},"subtitle":[],"editor":[{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2012,3,15]]},"references-count":29,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2012,3,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002417","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,3,15]]}}}