AAV Gene Therapy Sequencing
Adeno-associated virus (AAV) gene therapy sequencing enables you to verify the quality and integrity of packaged AAV vectors, including inverted terminal repeat (ITR) regions, measure AAV expression after infection, monitor host response, and much more.
Whether you need to sequence a packaged AAV product, AAV plasmid, or interested in post-infection solutions, we offer custom, in-depth AAV gene therapy sequencing for your complex AAV applications. Our solutions combine next generation sequencing (NGS) using the latest technologies, such as PacBio® long-read (>10kb) or Illumina® short-read sequencing, with our proprietary QC process to provide you with reliable, accurate results and streamline your AAV gene therapy research.
Low-Pass Whole Genome Sequencing
Low-pass whole genome sequencing (also referred to as LP-WGS or shallow whole genome sequencing) is a cost-effective, high-throughput DNA sequencing technology used to detect genetic variation within the genomes of various species. Compared to genotyping arrays, this method is an affordable alternative for discovering new, rare variants with higher statistical power and increased data. LP-WGS helps to address questions related to statistical and population genetics, from complex-trait association studies to genome-wide polygenic risk score calculation.
What is imputation in low-pass genome sequencing?
Imputation is the generation of sequencing data in parallel to reference data. In low-pass whole genome sequencing, imputation is important in accurately associating and evaluating genetic markers that are not directly sequenced.
LP-WGS relies on computational methods, called imputation, to fill in the missing information. Imputation algorithms allow up to 99% accurate variant call detection as compared to genotyping arrays. The unique combination of Azenta Life Sciences, formerly GENEWIZ’s LP-WGS and imputation enables scientists to efficiently obtain analysis-ready fully-imputed VCF files in a single service. For applications that require deep sequencing coverage of specific genomic regions or variants (i.e. clinical applications), Azenta‘s LP-WGS Plus combines LP-WGS with exome or targeted sequencing – the first of its kind on the market.
Low-Pass Whole Genome Sequencing Workflow
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1. Experimental
Design -
2. Sample
Preparation -
3. Extraction
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4. Library
Preparation -
5. Sequencing
0.1x -<10x -
6. Imputation
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7. Variant
Calling
TECHNOLOGY SNAPSHOT: LOW-PASS WHOLE GENOME SEQUENCING
† WES coverage is limited to genic/exonic regions; hence, structural variants and copy number variants present only in these regions can be resolved.
DELIVERABLES
Standard Deliverables
- Sample QC (includes raw data QC & alignment metrics)
- FASTQ files
- Aligned BAM file
- Imputed VCF file
Human LP-WGS Deliverables
(In addition to standard deliverables)
- Copy number variant analysis
- Ancestry analysis
- Calculated polygenic risk scores files
Custom bioinformatics analysis and reports are available. Please contact us about how we can customize the analysis to answer your biological question.
LOW PASS WHOLE GENOME SEQUENCING PLUS
Azenta’s LP-WGS Plus combines LP-WGS with exome or targeted sequencing – the first of its kind on the market.
FEATURES & BENEFITS
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Superior Data Quality
Exceeding manufacturer’s benchmarks -
Real-Time Project Updates
Through our online system -
Ph.D.-Level Support
At every step
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Highly accurate variant calls across the genome
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10x more data than microarrays at 1/10th of the cost of standard WGS
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High-throughput, cost-efficient and scalable
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Low-Pass WGS Plus is a cost-effective solution for applications that require deep sequencing coverage of specific genomic regions or variants
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PUBLICATION
Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arraysLearn how low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼ 0.5x and higher.
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PUBLICATION
Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populationIn this study, scientists from around the world (led by a group at the Broad Institute) considered specifically the question of association studies in African populations; these population are generally under-represented in existing genomics databases. They found that, depending on cost considerations and study goals, that low-pass sequencing in the range of 0.5x to 4x coverage outperformed a wide range of genotyping arrays.
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WEBINAR
The $100 Genome: Using Low-Pass Whole Genome Sequencing as an Alternative to Genotyping ArraysIn this webinar originally presented at the ASHG 2020 Virtual Meeting, learn how low-pass WGS overcomes the inherent limitations and biases of traditional arrays, offering an inexpensive, high-throughput alternative for detecting genome-wide genetic variation and novel variants.
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WORKSHOP
Workshop & Roundtable Discussion | Exploring Bioinformatics for Whole Genome Sequencing (WGS) DataIn this recording of our WGS bioinformatics workshop & roundtable discussion led by bioinformatics scientist Zain Alvi, Ph.D., we’ll guide you through the WGS bioinformatics process to help you learn to interpret WGS bioinformatics results, as well as address common challenges and answer frequently asked questions (FAQs).
What is AAV Gene Therapy?
Adeno-associated viruses (AAV) are the optimal vehicle for, and leading viral vector used in in vivo gene therapy clinical trials due to their high efficiency and enhanced safety in humans.
NGS SOLUTIONS FOR AAV GENE THERAPY
Confirm Plasmid Sequences
Utilize Azenta’s short-read amplicon sequencing for highly-accurate confirmation of AAV plasmid inserts, or confirm full-length recombinant AAV (rAAV) vector integrity at the single-molecule level with long-read amplicon sequencing.
Validate Packaged Material
Sequence-confirm rAAV vectors and identify DNA contaminants in AAV library preparation by employing the power of Azenta’s short- and long-read whole genome sequencing solutions.
Quantify AAV Expression
Employ Azenta’s qPCR, targeted sequencing, or RNA sequencing solutions at the RUO and CLIA levels to measure AAV expression of the target gene after infection.
Monitor Host Response
Stratify and characterize host-immune response during and after infection with Azenta’s suite of RNA sequencing solutions, or use novel approaches including single-cell sequencing and spatial genomics.
Learn more about Azenta’s additional adeno-associated virus (AAV) services for your cell and gene therapy research.
AAV GENOME SEQUENCING WORKFLOW
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1. Sample
Preparation -
2. Library
Preparation -
3. Sequencing
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4. Bioinformatics
Analysis
NGS AAV FEATURES & BENEFITS
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Superior Data Quality
Exceeding manufacturer’s benchmarks -
Real-Time Project Updates
Through our online system -
Ph.D.-Level Support
At every step
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Trusted partner supporting over 150 top global pharmaceutical and biotech customers in their cell and gene therapy research
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Optimized, automated, and scalable workflows with stringent quality control producing high-quality, consistent results
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RUO and CLIA-grade, high-capacity and high-throughput sequencing for projects of virtually any size and sample type
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Customized and extensive bioinformatics solutions with interactive, hands-on analysis
AAV NEXT GENERATION SEQUENCING TECHNICAL RESOURCES
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PUBLICATION
Adeno-associated Virus Genome Population Sequencing Achieves Full Vector Genome Resolution and Reveals Human-Vector ChimerasDiscover how researchers utilized single molecule, real-time (SMRT®) sequencing to profile rAAV-packaged genomes and assess full-length integrity for rAAV quality control.
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PUBLICATION
Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation SequencingIn this study, learn how short-read sequencing technology can extensively characterize the rAAV genome while simultaneously detecting the presence of DNA contaminants.
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WEBINAR
Novel Sequencing & Synthetic Solutions for AAV-Based Gene Therapy ResearchAdeno-associated virus (AAV) vectors are an optimal vehicle for gene therapy delivery, but can present challenges for researchers. In this interview-style webinar first aired at the PacBio Global Virtual Summit 2020, Azenta presents proprietary sequencing and synthesis solutions to overcome the obstacles presented by AAV-based gene therapy.
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WORKSHOP & ROUNDTABLE DISCUSSION
A Comprehensive Guide to Using AAV Vectors in Gene TherapyWorking with AAV vectors can be challenging. In this on-demand workshop & roundtable discussion, you’ll gain a better understanding of the AAV development pipeline for gene therapy research and learn how to optimize upstream and downstream processes including AAV synthesis, sequencing, bioinformatics, and storage.
NGS PLATFORMS
For information on our NGS platforms as well as recommended configurations of your projects, please visit the NGS Platforms page. Azenta does not guarantee data output or quality for sequencing-only projects.
