Accurate and Rapid Sequence Analysis of Adeno-Associated Virus Plasmids by Illumina Next-Generation Sequencing

Human Gene Therapy Methods

Volumn 29, Issue 5, 2018, Pages 201-211

  Saveliev, Alexei ^a   Liu, Juan ^a   Li, Mingyao ^a   Hirata, Lee ^a   Latshaw, Caitlin ^a   Zhang, Jia ^a   Wilson, James M ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

AAV; AAV plasmids; ITR; MiSeq; NGS

Indexed keywords

PLASMID DNA;

ADENO ASSOCIATED VIRUS; ARTICLE; COMPARATIVE STUDY; DNA LIBRARY; DNA SUPERCOILING; FREQUENCY; GEL ELECTROPHORESIS; GENETIC TRANSFECTION; INDEL MUTATION; INVERTED TERMINAL REPEAT; NEXT GENERATION SEQUENCING; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; QUALITY CONTROL; SANGER SEQUENCING; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; VIRAL GENE THERAPY; ANIMAL; CHEMISTRY; DEPENDOPARVOVIRUS; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; REPRODUCIBILITY; STANDARDS;

ANIMALS; DEPENDOVIRUS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PLASMIDS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 85055072777     PISSN: 19466536     EISSN: 19466544     Source Type: Journal    
DOI: 10.1089/hgtb.2018.037     Document Type: Article

References (26)

1. Srivastava A, Lusby EW, Berns KI. Nucleotide sequence and organization of the adeno-associated virus 2 genome. J Virol 1983;45:555-564.
2. Gaj T, Epstein BE, Schaffer DV. Genome engineering using adeno-associated virus: basic and clinical research applications. Mol Ther 2016;24:458-464.
3. Naso MF, Tomkowicz B, Perry WL 3rd, et al. Adeno-associated virus (AAV) as a vector for gene therapy. BioDrugs 2017;31:317-334.
4. Zhang F, Gradinaru V, Adamantidis AR, et al. Optogenetic interrogation of neural circuits: Technology for probing mammalian brain structures. Nat Protoc 2010;5:439-456.
5. Nussinovitch U, Gepstein L. Optogenetics for in vivo cardiac pacing and resynchronization therapies. Nat Biotechnol 2015;33:750-754.
6. Food and Drug Administration. FDA approves novel gene therapy to treat patients with a rare form of inherited vision loss, 2017. Available at: https://www .fda.gov/newsevents/newsroom/pressannounce ments/ucm589467.html
7. Clement N, Grieger JC. Manufacturing of recombinant adeno-associated viral vectors for clinical trials. Mol Ther Methods Clin Dev 2016;3:16002.
8. Lock M, Alvira M, Vandenberghe LH, et al. Rapid, simple, and versatile manufacturing of recombinant adeno-associated viral vectors at scale. Hum Gene Ther 2010;21:1259-1271.
9. Wang XS, Ponnazhagan S, Srivastava A. Rescue and replication of adeno-associated virus type 2 aswell as vector DNA sequences from recombinant plasmids containing deletions in the viral inverted terminal repeats: selective encapsidation of viral genomes in progeny virions. J Virol 1996;70:1668-1677.
10. Julien L, Chassagne J, Peccate C, et al. RFX1 and RFX3 transcription factors interact with the D sequence of adeno-associated virus inverted terminal repeat and regulate AAV transduction. Sci Rep 2018;8:210.
11. Savy A, Dickx Y, Nauwynck L, et al. Impact of inverted terminal repeat integrity on rAAV8 production using the baculovirus/Sf9 cells system. Hum Gene Ther Methods 2017;28:277-289.
12. Jungmann A, Leuchs B, Rommelaere J, et al. Protocol for efficient generation and characterization of adeno-associated viral vectors. Hum Gene Ther Methods 2017;28:235-246.
13. Daya S, Berns KI. Gene therapy using adenoassociated virus vectors. Clin Microbiol Rev 2008; 21:583-593.
14. Kieleczawa J. Fundamentals of sequencing of difficult templates-an overview. J Biomol Tech 2006;17:207-217.
15. Bzymek M, Lovett ST. Instability of repetitive DNA sequences: The role of replication in multiple mechanisms. Proc Natl Acad Sci U S A 2001;98:8319-8325.
16. Petri K, Fronza R, Gabriel R, et al. Comparative next-generation sequencing of adeno-associated virus inverted terminal repeats. Biotechniques 2014;56:269-273.
17. Shapland EB, Holmes V, Reeves CD, et al. Lowcost, high-throughput sequencing of DNA assemblies using a highly multiplexed Nextera process. ACS Synth Biol 2015;4:860-866.
18. Lecomte E, Tournaire B, Cogne B, et al. Advanced characterization of DNA molecules in rAAV vector preparations by single-stranded virus next-generation sequencing. Mol Ther Nucleic Acids 2015;4:e260.
19. Penaud-Budloo M, Lecomte E, Guy-Duche A, et al. Accurate identification and quantification of DNA species by next-generation sequencing in adenoassociated viral vectors produced in insect cells. Hum Gene Ther Methods 2017;28:148-162.
20. Tai PWL, Xie J, Fong K, et al. Adeno-associated virus genome population sequencing achieves full vector genome resolution and reveals human-vector chimeras. Mol Ther Methods Clin Dev 2018;9:130-141.
21. Bushnell B, Rood J, Singer E. BBMerge-accurate paired shotgun read merging via overlap. PLoS One 2017;12:e0185056.
22. Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 2017;45:e18.
23. Schirmer M, Ijaz UZ, D'Amore R, et al. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res 2015;43:e37.
24. Potapov V, Ong JL. Examining sources of error in PCR by single-molecule sequencing. PLoS One 2017;12:e0169774.
25. Illumina. Effects of index misassignment on multiplexing and downstream analysis. 2017;770-2017-004-D.
26. Illumina. Index Adapters Pooling Guide. Document # 1000000041074 v02 2018.