Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence. (Q34249667)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25013183%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

title

Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence (English)

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9 March 2020

5

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9 March 2020

Ian E. Alexander

7

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9 March 2020

Claus V Hallwirth

8

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9 March 2020

author name string

Claire T Deakin

1

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9 March 2020

Jeffrey J Deakin

2

1 reference

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9 March 2020

Samantha L Ginn

3

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9 March 2020

Paul Young

4

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9 March 2020

Catherine M Suter

6

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9 March 2020

language of work or name

English

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publication date

10 July 2014

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9 March 2020

published in

Nucleic Acids Research

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9 March 2020

volume

42

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9 March 2020

issue

16

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9 March 2020

page(s)

e129

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Creative Commons Attribution-NonCommercial 3.0 Unported

9 March 2020

copyright license

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

0 references

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Multiplexing clonality: combining RGB marking and genetic barcoding.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Clonal analysis via barcoding reveals diverse growth and differentiation of transplanted mouse and human mammary stem cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Error analysis of deep sequencing of phage libraries: peptides censored in sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Analysis of the clonal growth and differentiation dynamics of primitive barcoded human cord blood cells in NSG mice

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Lentiviral hematopoietic stem cell gene therapy benefits metachromatic leukodystrophy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Lentiviral hematopoietic stem cell gene therapy in patients with Wiskott-Aldrich syndrome.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Characterizing and measuring bias in sequence data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Arrayed lentiviral barcoding for quantification analysis of hematopoietic dynamics.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Comparison of sequencing platforms for single nucleotide variant calls in a human sample

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

High efficiency restriction enzyme-free linear amplification-mediated polymerase chain reaction approach for tracking lentiviral integration sites does not abrogate retrieval bias.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Ultrafast clustering algorithms for metagenomic sequence analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Performance comparison of whole-genome sequencing platforms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Inducible apoptosis as a safety switch for adoptive cell therapy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Comparison of sequence reads obtained from three next-generation sequencing platforms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Detection and quantification of rare mutations with massively parallel sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Sequence-specific error profile of Illumina sequencers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

A method to sequence and quantify DNA integration for monitoring outcome in gene therapy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Stem-cell gene therapy for the Wiskott-Aldrich syndrome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Ultra high throughput sequencing in human DNA variation detection: a comparative study on the NDUFA3-PRPF31 region

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Efficacy of gene therapy for X-linked severe combined immunodeficiency

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Lymphomagenesis in SCID-X1 mice following lentivirus-mediated phenotype correction independent of insertional mutagenesis and gammac overexpression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Cellular barcoding tool for clonal analysis in the hematopoietic system

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Hematopoietic stem cell gene therapy with a lentiviral vector in X-linked adrenoleukodystrophy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Flanking-sequence exponential anchored-polymerase chain reaction amplification: a sensitive and highly specific method for detecting retroviral integrant-host-junction sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

UNAFold: software for nucleic acid folding and hybridization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Mapping and quantifying mammalian transcriptomes by RNA-Seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Gene therapy of human severe combined immunodeficiency (SCID)-X1 disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4176369

Gene therapy of X-linked severe combined immunodeficiency by use of a pseudotyped gammaretroviral vector

6 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

Long-term persistence of a polyclonal T cell repertoire after gene therapy for X-linked severe combined immunodeficiency

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

Correction of ADA-SCID by stem cell gene therapy combined with nonmyeloablative conditioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

Gene therapy for immunodeficiency due to adenosine deaminase deficiency.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

Hematopoietic stem cell gene therapy for adenosine deaminase-deficient severe combined immunodeficiency leads to long-term immunological recovery and metabolic correction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

Comprehensive genomic access to vector integration in clinical gene therapy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

Diverse and heritable lineage imprinting of early haematopoietic progenitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

Gene transfer by lentiviral vectors is limited by nuclear translocation and rescued by HIV-1 pol sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

Optimal enzymes for amplifying sequencing libraries.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU607

21 January 2018

Identifiers

DOI

10.1093/NAR/GKU607

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25013183%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25013183%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25013183%20AND%20SRC:MED&resulttype=core&format=json