AAV Data Dictionary

The provided definitions can be highly advantageous for professionals who are associated with or working in the field of adeno-associated virus (AAV) gene therapy research and development. AAV has become one of the most promising and widely used vectors for gene therapy due to its non-pathogenic nature, and these definitions will assist in better understanding the fundamentals of AAV gene therapy R&D.

Category
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File Formats/Terms

Type
Alternate Terms
Subtype
Definition with references
BAM / uBAM
Read, alignment, mapped reads, read set
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BED
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CRAM
Read, alignment, mapped reads, read set
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CSV
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Demultiplexing
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FastA
Sequencing reads
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FastQ
(Demultiplexed) sequencing reads
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GFF
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GTF
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HiFi
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JSON
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Library Preparation
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MAP
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PDB
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PED
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Primary Analysis
Demultiplexing, bcl2fastq, data prep
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Reads
Sequencing reads
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SAM
Alignment Reads
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Secondary Analysis
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Sequencing Machine
Sequencing instrument, sequencer
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Subreads
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Tertiary Analysis
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VCF
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VCF
Variant calls
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PacBio AAV Sequencing

Type
Alternate Terms
Subtype
Definition with references
AAV-Mode
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Flip/Flop
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Recall Adapters
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chimeric
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host
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pRepCap
Repcap plasmid
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phelper
Helper plasmid
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scAAV
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scAAV
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scAAV
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scAAV
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scAAV
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scAAV
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ssAAV
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ssAAV
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ssAAV
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ssAAV
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ssAAV
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ssAAV
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unknown/other
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Viral Physiology & Molecular Biology

Type
Alternate Terms
Subtype
Definition with references
2° structure
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3° structure
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Adeno Associated Virus
NA
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Adenovirus
NA
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Allogenic
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Autologous
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Capsid
NA
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Capsid Fill Rate
Encapsidation rate
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Empty Capsid
NA
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Endosomal escape
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Full Capsid
NA
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GOI plasmid
Transfer plasmid, vector, construct
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ITR
NA
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Lox sites
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MCS
NA
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Non-empty capsids
NA
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Nuclear transfection efficiency
Nuclear delivery efficiency
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Nuclear uptake
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Payload
GOI, vector genome
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Post-translational elements
Post-translational modifications
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Probability 2°/3° structure
NA
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Producer Cell line
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Recombinant Adeno-Associated Viral Vectors
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SV40
NA
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Transfection efficiency
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Transfection rate
Transfection effieciency rate
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Truncated Capsid
NA
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Unlabeled Region
NA
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WPRE
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enhancer
NA
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intron
NA
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non-B DNA
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non-coding region
NA
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pLannotate
NA
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polyA tail
NA
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promoter
NA
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regulatory elements
NA
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transgene
GOI, CDS
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truncation propensity
NA
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viral vector
construct, plasmid
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