Data from: Advanced characterization of DNA molecules in rAAV vector preparations by single-stranded virus next-generation sequencing
Data files
Aug 25, 2016 version files 19.47 GB
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Chromosomal_distribution.xls
147.46 KB
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Circos_Data.zip
1.17 MB
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ContaVect_Configuration_Files.zip
55.11 KB
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Coverage.zip
3.42 MB
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References.zip
40.64 KB
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RUN1_S1_R1.fastq.gz
551.82 MB
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RUN1_S1_R2.fastq.gz
697.74 MB
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RUN1_S2_R1.fastq.gz
638.25 MB
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RUN1_S2_R2.fastq.gz
636.79 MB
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RUN1_S3_R1.fastq.gz
728.77 MB
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RUN1_S3_R2.fastq.gz
733.08 MB
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RUN1_S4_R2.fastq.gz
777.22 MB
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RUN1_S5_R1.fastq.gz
711.13 MB
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RUN1_S5_R2.fastq.gz
707.19 MB
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RUN1_S6_R1.fastq.gz
638.30 MB
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RUN1_S6_R2.fastq.gz
639.04 MB
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RUN1_S7_R1.fastq.gz
615.34 MB
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RUN1_S7_R2.fastq.gz
622.11 MB
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RUN1_S8_R1.fastq.gz
537.62 MB
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RUN1_S8_R2.fastq.gz
549.17 MB
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RUN2_S1_R1.fastq.gz
615.50 MB
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RUN2_S1_R2.fastq.gz
649.91 MB
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RUN2_S2_R1.fastq.gz
585.04 MB
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RUN2_S2_R2.fastq.gz
612.89 MB
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RUN2_S3_R1.fastq.gz
484.60 MB
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RUN2_S3_R2.fastq.gz
512.26 MB
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RUN2_S4_R1.fastq.gz
614.60 MB
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RUN2_S4_R2.fastq.gz
644.12 MB
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RUN2_S5_R1.fastq.gz
599.60 MB
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RUN2_S5_R2.fastq.gz
629.64 MB
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RUN2_S6_R1.fastq.gz
511.56 MB
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RUN2_S6_R2.fastq.gz
535.78 MB
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RUN2_S7_R1.fastq.gz
518.34 MB
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RUN2_S7_R2.fastq.gz
543.39 MB
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RUN2_S8_R1.fastq.gz
520.69 MB
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RUN2_S8_R2.fastq.gz
547.03 MB
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Sample Corespondance.ods
15.70 KB
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Variants.zip
3.16 MB
Abstract
Recent successful clinical trials with recombinant adeno-associated viral vectors (rAAVs) have led to a renewed interest in gene therapy. However, despite extensive developments to improve vector-manufacturing processes, undesirable DNA contaminants in rAAV preparations remain a major safety concern. Indeed, the presence of DNA fragments containing antibiotic resistance genes, wild-type AAV, and packaging cell genomes has been found in previous studies using quantitative polymerase chain reaction (qPCR) analyses. However, because qPCR only provides a partial view of the DNA molecules in rAAV preparations, we developed a method based on next-generation sequencing (NGS) to extensively characterize single-stranded DNA virus preparations (SSV-Seq). In order to validate SSV-Seq, we analyzed three rAAV vector preparations produced by transient transfection of mammalian cells. Our data were consistent with qPCR results and showed a quasi-random distribution of contaminants originating from the packaging cells genome. Finally, we found single-nucleotide variants (SNVs) along the vector genome but no evidence of large deletions. Altogether, SSV-Seq could provide a characterization of DNA contaminants and a map of the rAAV genome with unprecedented resolution and exhaustiveness. We expect SSV-Seq to pave the way for a new generation of quality controls, guiding process development toward rAAV preparations of higher potency and with improved safety profiles.