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

Clonal Analysis via Barcoding Reveals Diverse Growth and Differentiation of Transplanted Mouse and Human Mammary Stem Cells

(2014) Long V. Nguyen et al.   Cell Stem Cell

Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling

(2014) O. V. Britanova et al.   JOURNAL OF IMMUNOLOGY

Multiplexing clonality: combining RGB marking and genetic barcoding

(2014) Kerstin Cornils et al.   NUCLEIC ACIDS RESEARCH

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

(2013) E. Verovskaya et al.   BLOOD

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

(2013) A. M. S. Cheung et al.   BLOOD

Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

(2013) Wadim L. Matochko et al.   Computational and Mathematical Methods in Medicine

Diverse and heritable lineage imprinting of early haematopoietic progenitors

(2013) Shalin H. Naik et al.   NATURE

Comparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample

(2013) Aakrosh Ratan et al.   PLoS One

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

(2013) D. I. Lou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lentiviral Hematopoietic Stem Cell Gene Therapy in Patients with Wiskott-Aldrich Syndrome

(2013) A. Aiuti et al.   SCIENCE

Lentiviral Hematopoietic Stem Cell Gene Therapy Benefits Metachromatic Leukodystrophy

(2013) A. Biffi et al.   SCIENCE

Arrayed lentiviral barcoding for quantification analysis of hematopoietic dynamics

(2013) Jeanne Grosselin et al.   STEM CELLS

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN BIOINFORMATICS

High Efficiency Restriction Enzyme–Free Linear Amplification-Mediated Polymerase Chain Reaction Approach for Tracking Lentiviral Integration Sites Does Not Abrogate Retrieval Bias

(2012) Chuanfeng Wu et al.   HUMAN GENE THERAPY

High-Throughput Sequencing Detects Minimal Residual Disease in Acute T Lymphoblastic Leukemia

(2012) D. Wu et al.   Science Translational Medicine

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

(2012) Niko Beerenwinkel et al.   Frontiers in Microbiology

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

(2011) Phuong Nguyen et al.   BMC GENOMICS

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

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Optimal enzymes for amplifying sequencing libraries

(2011) Michael A Quail et al.   NATURE METHODS

Inducible Apoptosis as a Safety Switch for Adoptive Cell Therapy

(2011) Antonio Di Stasi et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2011) Troy Brady et al.   NUCLEIC ACIDS RESEARCH

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms

(2011) Shingo Suzuki et al.   PLoS One

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

(2011) A. C. Logan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-Term Persistence of a Polyclonal T Cell Repertoire After Gene Therapy for X-Linked Severe Combined Immunodeficiency

(2011) H. B. Gaspar et al.   Science Translational Medicine

Hematopoietic Stem Cell Gene Therapy for Adenosine Deaminase-Deficient Severe Combined Immunodeficiency Leads to Long-Term Immunological Recovery and Metabolic Correction

(2011) H. B. Gaspar et al.   Science Translational Medicine

T Cells with Chimeric Antigen Receptors Have Potent Antitumor Effects and Can Establish Memory in Patients with Advanced Leukemia

(2011) M. Kalos et al.   Science Translational Medicine

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

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

(2010) G. P. Wang et al.   BLOOD

Cellular barcoding tool for clonal analysis in the hematopoietic system

(2010) A. Gerrits et al.   BLOOD

Lymphomagenesis in SCID-X1 Mice Following Lentivirus-mediated Phenotype Correction Independent of Insertional Mutagenesis and γc Overexpression

(2010) Samantha L Ginn et al.   MOLECULAR THERAPY

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

(2010) Stefan Stein et al.   NATURE MEDICINE

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

(2010) Anna Paruzynski et al.   Nature Protocols

Efficacy of Gene Therapy for X-Linked Severe Combined Immunodeficiency

(2010) Salima Hacein-Bey-Abina et al.   NEW ENGLAND JOURNAL OF MEDICINE

Stem-Cell Gene Therapy for the Wiskott–Aldrich Syndrome

(2010) Kaan Boztug et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Ultra High Throughput Sequencing in Human DNA Variation Detection: A Comparative Study on the NDUFA3-PRPF31 Region

(2010) Paola Benaglio et al.   PLoS One

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

(2009) Jacob F. Degner et al.   BIOINFORMATICS

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

(2009) W. Qu et al.   GENOME RESEARCH

Comprehensive genomic access to vector integration in clinical gene therapy

(2009) Richard Gabriel et al.   NATURE MEDICINE

Gene Therapy for Immunodeficiency Due to Adenosine Deaminase Deficiency

(2009) Alessandro Aiuti et al.   NEW ENGLAND JOURNAL OF MEDICINE

Hematopoietic Stem Cell Gene Therapy with a Lentiviral Vector in X-Linked Adrenoleukodystrophy

(2009) N. Cartier et al.   SCIENCE

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

(2009) Martin Kircher et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) M.A. Pule et al.   CYTOTHERAPY

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

(2008) Steven J. Howe et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2008) Salima Hacein-Bey-Abina et al.   JOURNAL OF CLINICAL INVESTIGATION

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

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

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH