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Rakonjac J, Gold VAM, León-Quezada RI, Davenport CH. Structure, Biology, and Applications of Filamentous Bacteriophages. Cold Spring Harb Protoc 2024; 2024:pdb.over107754. [PMID: 37460152 DOI: 10.1101/pdb.over107754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
The closely related Escherichia coli Ff filamentous phages (f1, fd, and M13) have taken a fantastic journey over the past 60 years, from the urban sewerage from which they were first isolated, to their use in high-end technologies in multiple fields. Their relatively small genome size, high titers, and the virions that tolerate fusion proteins make the Ffs an ideal system for phage display. Folding of the fusions in the oxidizing environment of the E. coli periplasm makes the Ff phages a platform that allows display of eukaryotic surface and secreted proteins, including antibodies. Resistance of the Ffs to a broad range of pH and detergents facilitates affinity screening in phage display, whereas the stability of the virions at ambient temperature makes them suitable for applications in material science and nanotechnology. Among filamentous phages, only the Ffs have been used in phage display technology, because of the most advanced state of knowledge about their biology and the various tools developed for E. coli as a cloning host for them. Filamentous phages have been thought to be a rather small group, infecting mostly Gram-negative bacteria. A recent discovery of more than 10 thousand diverse filamentous phages in bacteria and archaea, however, opens a fascinating prospect for novel applications. The main aim of this review is to give detailed biological and structural information to researchers embarking on phage display projects. The secondary aim is to discuss the yet-unresolved puzzles, as well as recent developments in filamentous phage biology, from a viewpoint of their impact on current and future applications.
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Affiliation(s)
- Jasna Rakonjac
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
| | - Vicki A M Gold
- Living Systems Institute University of Exeter, Exeter, EX4 4QD, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, United Kingdom
| | - Rayén I León-Quezada
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
| | - Catherine H Davenport
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
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2
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Pashova S, Balabanski L, Elmadjian G, Savov A, Stoyanova E, Shivarov V, Petrov P, Pashov A. Restriction of the Global IgM Repertoire in Antiphospholipid Syndrome. Front Immunol 2022; 13:865232. [PMID: 35493489 PMCID: PMC9043687 DOI: 10.3389/fimmu.2022.865232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
The typical anti-phospholipid antibodies (APLA) in the anti-phospholipid syndrome (APS) are reactive with the phospholipid-binding protein β2GPI as well as a growing list of other protein targets. The relation of APLA to natural antibodies and the fuzzy set of autoantigens involved provoked us to study the changes in the IgM repertoire in APS. To this end, peptides selected by serum IgM from a 7-residue linear peptide phage display library (PDL) were deep sequenced. The analysis was aided by a novel formal representation of the Igome (the mimotope set reflecting the IgM specificities) in the form of a sequence graph. The study involved women with APLA and habitual abortions (n=24) compared to age-matched clinically healthy pregnant women (n=20). Their pooled Igomes (297 028 mimotope sequences) were compared also to the global public repertoire Igome of pooled donor plasma IgM (n=2 796 484) and a set of 7-mer sequences found in the J regions of human immunoglobulins (n=4 433 252). The pooled Igome was represented as a graph connecting the sequences as similar as the mimotopes of the same monoclonal antibody. The criterion was based on previously published data. In the resulting graph, identifiable clusters of vertices were considered related to the footprints of overlapping antibody cross-reactivities. A subgraph based on the clusters with a significant differential expression of APS patients' mimotopes contained predominantly specificities underrepresented in APS. The differentially expressed IgM footprints showed also an increased cross-reactivity with immunoglobulin J regions. The specificities underexpressed in APS had a higher correlation with public specificities than those overexpressed. The APS associated specificities were strongly related also to the human peptidome with 1 072 mimotope sequences found in 7 519 human proteins. These regions were characterized by low complexity. Thus, the IgM repertoire of the APS patients was found to be characterized by a significant reduction of certain public specificities found in the healthy controls with targets representing low complexity linear self-epitopes homologous to human antibody J regions.
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Affiliation(s)
- Shina Pashova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Lubomir Balabanski
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
- Genomics Laboratory, Hospital “Malinov”, Sofia, Bulgaria
| | - Gabriel Elmadjian
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Alexey Savov
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Elena Stoyanova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Peter Petrov
- Institute Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Anastas Pashov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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3
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Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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4
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Derda R, Ng S. Genetically encoded fragment-based discovery. Curr Opin Chem Biol 2019; 50:128-137. [DOI: 10.1016/j.cbpa.2019.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/09/2019] [Accepted: 03/12/2019] [Indexed: 12/30/2022]
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He B, Tjhung KF, Bennett NJ, Chou Y, Rau A, Huang J, Derda R. Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing. Sci Rep 2018; 8:1214. [PMID: 29352178 PMCID: PMC5775325 DOI: 10.1038/s41598-018-19439-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/02/2018] [Indexed: 01/09/2023] Open
Abstract
Understanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed on the M13KE platform, which are produced via trinucleotide cassette synthesis (19 codons) and NNK-randomized codon. Differential enrichment of synthetic DNA {S}, ligated vector {L} (extension and ligation of synthetic DNA into the vector), naïve libraries {N} (transformation of the ligated vector into the bacteria followed by expression of the library for 4.5 hours to yield a "naïve" library), and libraries chemically modified by aldehyde ligation and cysteine macrocyclization {M} characterized by paired-end deep sequencing, detected a significant drop in diversity in {L} → {N}, but only a minor compositional difference in {S} → {L} and {N} → {M}. Libraries expressed at the N-terminus of phage protein pIII censored positively charged amino acids Arg and Lys; libraries expressed between pIII domains N1 and N2 overcame Arg/Lys-censorship but introduced new bias towards Gly and Ser. Interrogation of biases arising from cPTM by aldehyde ligation and cysteine macrocyclization unveiled censorship of sequences with Ser/Phe. Analogous analysis can be used to explore library diversity in new display platforms and optimize cPTM of these libraries.
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Affiliation(s)
- Bifang He
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Katrina F Tjhung
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
- The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
- The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Nicholas J Bennett
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ying Chou
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Andrea Rau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jian Huang
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Center for Information in Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Ratmir Derda
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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Zade HM, Keshavarz R, Shekarabi HSZ, Bakhshinejad B. Biased selection of propagation-related TUPs from phage display peptide libraries. Amino Acids 2017; 49:1293-1308. [DOI: 10.1007/s00726-017-2452-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/09/2017] [Indexed: 10/19/2022]
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Rakonjac J, Russel M, Khanum S, Brooke SJ, Rajič M. Filamentous Phage: Structure and Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1053:1-20. [PMID: 29549632 DOI: 10.1007/978-3-319-72077-7_1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ff filamentous phage (fd, M13 and f1) of Escherichia coli have been the workhorse of phage display technology for the past 30 years. Dominance of Ff over other bacteriophage in display technology stems from the titres that are about 100-fold higher than any other known phage, efficacious transformation ensuring large library size and superior stability of the virion at high temperatures, detergents and pH extremes, allowing broad range of biopanning conditions in screening phage display libraries. Due to the excellent understanding of infection and assembly requirements, Ff phage have also been at the core of phage-assisted continual protein evolution strategies (PACE). This chapter will give an overview of the Ff filamentous phage structure and biology, emphasizing those properties of the Ff phage life cycle and virion that are pertinent to phage display applications.
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Affiliation(s)
- Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | | | - Sofia Khanum
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Sam J Brooke
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Marina Rajič
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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Phage display biopanning and isolation of target-unrelated peptides: in search of nonspecific binders hidden in a combinatorial library. Amino Acids 2016; 48:2699-2716. [DOI: 10.1007/s00726-016-2329-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/08/2016] [Indexed: 12/22/2022]
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Brinton LT, Bauknight DK, Dasa SSK, Kelly KA. PHASTpep: Analysis Software for Discovery of Cell-Selective Peptides via Phage Display and Next-Generation Sequencing. PLoS One 2016; 11:e0155244. [PMID: 27186887 PMCID: PMC4871350 DOI: 10.1371/journal.pone.0155244] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/26/2016] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing has enhanced the phage display process, allowing for the quantification of millions of sequences resulting from the biopanning process. In response, many valuable analysis programs focused on specificity and finding targeted motifs or consensus sequences were developed. For targeted drug delivery and molecular imaging, it is also necessary to find peptides that are selective—targeting only the cell type or tissue of interest. We present a new analysis strategy and accompanying software, PHage Analysis for Selective Targeted PEPtides (PHASTpep), which identifies highly specific and selective peptides. Using this process, we discovered and validated, both in vitro and in vivo in mice, two sequences (HTTIPKV and APPIMSV) targeted to pancreatic cancer-associated fibroblasts that escaped identification using previously existing software. Our selectivity analysis makes it possible to discover peptides that target a specific cell type and avoid other cell types, enhancing clinical translatability by circumventing complications with systemic use.
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Affiliation(s)
- Lindsey T. Brinton
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, 22908, United States of America
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, 22908, United States of America
| | - Dustin K. Bauknight
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, 22908, United States of America
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, 22908, United States of America
| | - Siva Sai Krishna Dasa
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, 22908, United States of America
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, 22908, United States of America
| | - Kimberly A. Kelly
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, 22908, United States of America
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, 22908, United States of America
- * E-mail:
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Facile, high quality sequencing of bacterial genomes from small amounts of DNA. Int J Genomics 2014; 2014:434575. [PMID: 25478564 PMCID: PMC4247979 DOI: 10.1155/2014/434575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/02/2014] [Indexed: 11/26/2022] Open
Abstract
Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing and de novo assembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing and de novo assembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderia spp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing and de novo assembly is not decreased when only 10 ng of input genomic DNA is used.
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11
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Rentero Rebollo I, Sabisz M, Baeriswyl V, Heinis C. Identification of target-binding peptide motifs by high-throughput sequencing of phage-selected peptides. Nucleic Acids Res 2014; 42:e169. [PMID: 25348396 PMCID: PMC4267670 DOI: 10.1093/nar/gku940] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
High-throughput sequencing was previously applied to phage-selected peptides in order to gain insight into the abundance and diversity of isolated peptides. Herein we developed a procedure to efficiently compare the sequences of large numbers of phage-selected peptides for the purpose of identifying target-binding peptide motifs. We applied the procedure to analyze bicyclic peptides isolated against five different protein targets: sortase A, urokinase-type plasminogen activator, coagulation factor XII, plasma kallikrein and streptavidin. We optimized sequence data filters to reduce biases originating from the sequencing method and developed sequence correction algorithms to prevent identification of false consensus motifs. With our strategy, we were able to identify rare target-binding peptide motifs, as well as to define more precisely consensus sequences and sub-groups of consensus sequences. This information is valuable to choose peptide leads for drug development and it facilitates identification of epitopes. We furthermore show that binding motifs can be identified after a single round of phage selection. Such a selection regimen reduces propagation-related bias and may facilitate application of phage display in non-specialized laboratories, as procedures such as bacterial infection, phage propagation and purification are not required.
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Affiliation(s)
- Inmaculada Rentero Rebollo
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Michal Sabisz
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Vanessa Baeriswyl
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Deakin CT, Deakin JJ, Ginn SL, Young P, Humphreys D, Suter CM, Alexander IE, Hallwirth CV. Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence. Nucleic Acids Res 2014; 42:e129. [PMID: 25013183 PMCID: PMC4176369 DOI: 10.1093/nar/gku607] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Barcoded vectors are promising tools for investigating clonal diversity and dynamics in hematopoietic gene therapy. Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown. This is an inherently challenging application, and the feasibility of using contemporary next-generation sequencing technologies is unresolved. To explore this potential application empirically, without prior assumptions, we sequenced barcode libraries of known complexity. Libraries containing 1, 10 and 100 Sanger-sequenced barcodes were sequenced using an Illumina platform, with a 100-barcode library also sequenced using a SOLiD platform. Libraries containing 1 and 10 barcodes were distinguished from false barcodes generated by sequencing error by a several log-fold difference in abundance. In 100-barcode libraries, however, expected and false barcodes overlapped and could not be resolved by bioinformatic filtering and clustering strategies. In independent sequencing runs multiple false-positive barcodes appeared to be represented at higher abundance than known barcodes, despite their confirmed absence from the original library. Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be fully resolved.
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Affiliation(s)
- Claire T Deakin
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Jeffrey J Deakin
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Paul Young
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, New South Wales 2010, Australia
| | - David Humphreys
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, New South Wales 2010, Australia
| | - Catherine M Suter
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, New South Wales 2010, Australia Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia Discipline of Paediatrics and Child Health, The Children's Hospital at Westmead Clinical School, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
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