PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data (Q30657886)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

title

PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

1 reference

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

5

Thomas Leitner

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

7

Jan Albert

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Charlotte Hedskog

3

0 references

author name string

Johanna Brodin

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Mattias Mild

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Ellen Sherwood

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

language of work or name

English

0 references

publication date

23 July 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

volume

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

page(s)

e70388

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons CC0 License

6 March 2020

copyright license

start time

23 July 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Systematic exploration of error sources in pyrosequencing flowgram data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: a systematic review and pooled analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Removing noise from pyrosequenced amplicons

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Next-generation DNA sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Accuracy and quality of massively parallel DNA pyrosequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Persistence of nevirapine-resistant HIV-1 in women after single-dose nevirapine therapy for prevention of maternal-to-fetal HIV-1 transmission

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Genome sequencing in microfabricated high-density picolitre reactors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Quality assessment program for genotypic antiretroviral testing improves detection of drug resistance mutations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

The Bioperl toolkit: Perl modules for the life sciences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

EMBOSS: the European Molecular Biology Open Software Suite

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Errors in the polymerase chain reaction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

DNA polymerase fidelity and the polymerase chain reaction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3720931

Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0070388

Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applications

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0070388

Predominant mutations induced by the Thermococcus litoralis, vent DNA polymerase during DNA amplification in vitro

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23894647

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Analysis of heterogeneous viral populations by direct DNA sequencing

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23894647

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0070388

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

PubMed publication ID

23894647

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23894647%20AND%20SRC:MED&resulttype=core&format=json