Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

scientific article published on 13 February 2013

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA. is …
instance of (P31):
scholarly articleQ13442814

External links are
P6179Dimensions Publication ID1047479213
P356DOI10.1186/1742-4690-10-18
P932PMC publication ID3599717
P698PubMed publication ID23402264
P5875ResearchGate publication ID235602548

P50authorJohn CoffinQ6226532
Mary KearneyQ55274692
John W MellorsQ89850095
Frank MaldarelliQ90433858
Valerie BoltzQ106272718
Wei ShaoQ115278688
Jonathan SpindlerQ115278933
P2093author name stringRobert M Stephens
Claudia Stewart
Alexander Levitsky
Natalia Volfovsky
P2860cites workArchived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent.Q51775877
Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy.Q54622397
The impact of PCR-generated recombination on diversity estimation of mixed viral populations by deep sequencingQ61440990
The development and impact of 454 sequencingQ82255359
Removing noise from pyrosequenced ampliconsQ21284335
Selective excision of AZTMP by drug-resistant human immunodeficiency virus reverse transcriptaseQ24529111
Genome sequencing in microfabricated high-density picolitre reactorsQ24544260
Viral population estimation using pyrosequencingQ28472641
Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencingQ28474783
Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral useQ28475651
Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesisQ28763524
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR ampliconsQ29614292
Accuracy and quality of massively parallel DNA pyrosequencingQ29622857
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing.Q30501204
454 sequencing put to the test using the complex genome of barleyQ33261654
Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivoQ33455862
Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.Q33517082
Monitoring resistance to human immunodeficiency virus type 1 protease inhibitors by pyrosequencingQ33971117
Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variationQ33974966
Role of low-frequency HIV-1 variants in failure of nevirapine-containing antiviral therapy in women previously exposed to single-dose nevirapineQ35021860
Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer IDQ35647691
Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistanceQ35914785
Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations.Q36949610
Pyrosequencing for discovery and analysis of DNA sequence variationsQ36989849
Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populationsQ37139125
Massively parallel pyrosequencing in HIV researchQ37211581
Stimulation and suppression of PCR-mediated recombinationQ39723457
DNA recombination during PCR.Q40515497
Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysisQ41694742
Frequent in vitro recombination in internal transcribed spacers 1 and 2 during genotyping of Pneumocystis jiroveciiQ42090155
Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomesQ43889383
Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applicationsQ44479431
P275copyright licenseCreative Commons Attribution 2.0 GenericQ19125117
P6216copyright statuscopyrightedQ50423863
P407language of work or nameEnglishQ1860
P921main subjectdrug resistanceQ12147416
P304page(s)18
P577publication date2013-02-13
P1433published inRetrovirologyQ15793508
P1476titleAnalysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.
P478volume10

Reverse relations

cites work (P2860)
Q50056309A Survey of Virus Recombination Uncovers Canonical Features of Artificial Chimeras Generated During Deep Sequencing Library Preparation
Q35494993A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library.
Q33758777A high-throughput assay for quantitative measurement of PCR errors
Q42009781Aligning coding sequences with frameshift extension penalties.
Q28554999An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies
Q36293268An Improved Barcoded Oligonucleotide Primers-based Next-generation Sequencing Approach for Direct Identification of Viral Pathogens in Clinical Specimens
Q55316660An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer.
Q33659736Analysis of plant microbe interactions in the era of next generation sequencing technologies
Q34594027Analysis of the evolution and structure of a complex intrahost viral population in chronic hepatitis C virus mapped by ultradeep pyrosequencing
Q38977086Artifact-Free Quantification and Sequencing of Rare Recombinant Viruses by Using Drop-Based Microfluidics
Q38259889Beyond the whole genome consensus: unravelling of PRRSV phylogenomics using next generation sequencing technologies
Q35571990Challenges with using primer IDs to improve accuracy of next generation sequencing
Q35676193ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3'-Azido cDNAs
Q28550310Comparison of 454 Ultra-Deep Sequencing and Allele-Specific Real-Time PCR with Regard to the Detection of Emerging Drug-Resistant Minor HIV-1 Variants after Antiretroviral Prophylaxis for Vertical Transmission
Q35759184Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection
Q89802441Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak
Q34997577Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq
Q39063756Deep sequencing in the management of hepatitis virus infections.
Q38226696Deep sequencing: becoming a critical tool in clinical virology
Q46277779Diversity and dynamics of lactic acid bacteria in Atole agrio, a traditional maize-based fermented beverage from South-Eastern Mexico, analysed by high throughput sequencing and culturing
Q39049381Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing
Q35247825Extensive recombination due to heteroduplexes generates large amounts of artificial gene fragments during PCR
Q28650499Frameshift alignment: statistics and post-genomic applications
Q36871866Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs
Q37518900Genome sequencing accuracy by RCA-seq versus long PCR template cloning and sequencing in identification of human papillomavirus type 58.
Q47548221HIV evolution and diversity in ART-treated patients
Q39835202HIV-1 Protease, Reverse Transcriptase, and Integrase Variation
Q35657974High-Throughput, Amplicon-Based Sequencing of the CREBBP Gene as a Tool to Develop a Universal Platform-Independent Assay
Q47551736Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection.
Q28709205Identification of diverse full-length endogenous betaretroviruses in megabats and microbats
Q27321390Identifying selection in the within-host evolution of influenza using viral sequence data
Q30658257Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data
Q37707249Large-scale development of gene-associated single-nucleotide polymorphism markers for molluscan population genomic, comparative genomic, and genome-wide association studies
Q48165950Lower pre-ART intra-participant HIV-1 pol diversity may not be associated with virologic failure in adults
Q33642719MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.
Q55192719MERIT reveals the impact of genomic context on sequencing error rate in ultra-deep applications.
Q30652082Nautilus: a bioinformatics package for the analysis of HIV type 1 targeted deep sequencing data
Q36181660New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome
Q42234370Next-Generation Sequencing to Help Monitor Patients Infected with HIV: Ready for Clinical Use?
Q39041843Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database
Q34994579Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination
Q33925806Oligotyping analysis of the human oral microbiome
Q49852632Organellar genome assembly methods and comparative analysis of horticultural plants.
Q30788601PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data
Q30657886PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data
Q90440311PacBio Amplicon Sequencing Method To Measure Pilin Antigenic Variation Frequencies of Neisseria gonorrhoeae
Q58768677Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus
Q92903815Proliferative memory SAMHD1low CD4+ T cells harbour high levels of HIV-1 with compartmentalized viral populations
Q39043678Promises and pitfalls of Illumina sequencing for HIV resistance genotyping
Q36507279Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing
Q28539563Residual viremia in an RT-SHIV rhesus macaque HAART model marked by the presence of a predominant plasma clone and a lack of viral evolution
Q35737495Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation
Q33622927Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism.
Q35237036Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations
Q40732189Similarities between Human Immunodeficiency Virus Type 1 and Hepatitis C Virus Genetic and Phenotypic Protease Quasispecies Diversity
Q45979839Size, Composition, and Evolution of HIV DNA Populations during Early Antiretroviral Therapy and Intensification with Maraviroc.
Q34451254Targeted deep sequencing of HIV-1 using the IonTorrentPGM platform
Q34193087The antibody genetics of multiple sclerosis: comparing next-generation sequencing to sanger sequencing
Q50027000Transcriptional-Readthrough RNAs Reflect the Phenomenon of "A Gene Contains Gene(s)" or "Gene(s) within a Gene" in the Human Genome, and Thus Are Not Chimeric RNAs.
Q38751410Ultra-Deep Sequencing Analysis on HIV Drug-Resistance-Associated Mutations Among HIV-Infected Individuals: First Report from the Philippines.
Q36229772Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA.
Q33899918Validation of an oligonucleotide ligation assay for quantification of human immunodeficiency virus type 1 drug-resistant mutants by use of massively parallel sequencing
Q41436712Virus characterization and discovery in formalin-fixed paraffin-embedded tissues

Search more.