Gene Therapy CRO Services
At Cyagen, we streamline your gene therapy pipeline—from AI-driven target discovery and AAV vector design to disease model generation and in vivo efficacy testing. Our integrated platform empowers translational research with speed, precision, and scientific confidence.
Visualize Your Path to Gene Therapy Success
Navigate every stage of your gene therapy program with clarity and confidence. Our
integrated workflow guides you from target discovery through vector engineering, model generation, and efficacy
validation—ensuring scientific continuity at every step.
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Predict. Validate. Accelerate.
AI-enabled discovery of therapeutic targets and pathogenic mutations.
Cyagen integrates advanced AI modeling with our proprietary rare disease database
(RDDC) to predict pathogenic gene mutations, design relevant models, and validate therapeutic
targets. Our platform bridges bioinformatics and wet-lab validation to de-risk and fast-track gene
therapy pipelines.
AI-Based Variant Prediction
Predict high-risk pathogenic variants using deep learning.
Model-Based Target Validation
Validate targets via custom cellular and animal models.
Rare Disease Data Center (RDDC)
Access curated mutation-disease databases for therapy design.
Integrated Screening Tools
Visualize mutation effects and explore RNA splicing outcomes.
AI-Based Variant Prediction
Uncover Disease-Causing Mutations with Predictive Precision
Evaluate the pathogenic potential and splicing consequences of genetic
variants using our AI-powered tools – Pathogenicity Predictor and RNA Splicer.
Case study：AI-Assisted Prediction of DMD
Clinical Features
DMD is an X-linked recessive disorder caused by DMD gene mutations.
While in-frame mutations typically cause BMD, frameshift mutations lead to DMD. WGS
identified a hemizygous splice-site mutation, c.4675-2A>G, in this patient.
| Project Type | Detailed Information |
|---|---|
| Gene | DMD |
| Chromosomal Location | chrX:32398799 |
| Transcript / Exon | NM_004006;Exon34 |
| Nucleotide / Amino Acid | c.4675-2A>G |
| Homozygous / Heterozygous | Heterozygote |
| Allele Frequency | - |
| ACMG-Based Pathogenicity Assessment | Pathogenic |
| Associated Disease / Phenotype | Duchenne Muscular Dystroph（XLR），Becker Muscular Dystrophy（XLR），Dilated Cardiomyopathy, Type 3B（XL） |
| Variant Origin | Spontaneous |
AI-Based Prediction Results
The Pathogenicity Predictor yielded a pathogenicity estimate that is
consistent with the patient’s observed clinical phenotype.
| Probability | Prediction | Gene Name | Chromosome X | Coordinate | PHRED | Gene ID | Consequence |
|---|---|---|---|---|---|---|---|
| 0.84 | Pathogenic | DMD | X | 32380682 | 35 | 1756 | Canonical splice |
Cyagen’s RNA Splicer tool showing splicing impact prediction of a
pathogenic DMD variant.
Validation Results
A mutation at the same site has also been reported in DMD carriers,
where it generates a novel splice acceptor site (Hofstra et al., 2004). These published
findings are consistent with the results displayed on the tool page.
Model-Based Target Validation
Validate Functional Impact Using Custom Cell and Animal Models
Translate predicted targets into experimental systems. Cyagen offers
KO, KI, and overexpression models—available in both rodent and cellular platforms—to confirm
variant pathogenicity and assess gene therapy responsiveness in vivo and in vitro.
Rare Disease Data Center (RDDC)
A Curated AI-Ready Database for Rare Disease Research
RDDC is a centralized hub for rare disease discovery, integrating
gene-disease associations, variant annotation, epidemiological data, and model repositories.
Researchers can identify targetable mutations and associated models for over 3,000 rare
conditions—all with AI-powered filters.
Integrated Screening Tools
Visualize Genotype-Phenotype Linkages in Seconds
Interact with gene, mutation, and model data via our visual dashboards
and natural language tools. From variant prioritization to model recommendation, our
screening platform simplifies early-stage decision-making for gene therapy programs.
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Design. Deliver. Transform.
AI-enhanced AAV vector engineering, high-titer packaging, and in vivo
validation—all in one place.
Cyagen’s AAV service platform supports the full cycle of vector development—from
AI-optimized capsid selection and cloning to customized packaging, purification, and QC validation.
Our inventory includes both off-the-shelf AAV serotypes and proprietary capsid variants for brain,
eye, and systemic delivery. Backed by validated in vivo and in vitro data, we ensure reliable
performance in your gene therapy research.
AI-Assisted AAV Capsid Design
Customize AAV serotype and cassette for your target tissue.
Custom AAV Packaging Services
Accelerating your timeline from vector design to functional
validation.
Ready-to-Ship AAVs
Access validated AAVs for common gene therapy applications –
shipped globally.
In Vitro & In Vivo Validation
Ensure precise delivery into target tissues with expert-guided
stereotaxic or systemic injection.
AI-Assisted AAV Capsid Design
Customize Capsids for Precise Targeting and Tissue Penetration
Cyagen has developed predictive AI models powered by deep learning to
efficiently identify AAV mutants suitable for multi‐target gene therapy applications. These
models enable in silico prediction of tissue tropism—including brain targeting, pan-ocular
expression, and ocular penetrance—across multiple anatomical regions.
Leverage our AI-trained models to design capsids with enhanced
targeting for CNS, ocular, or hepatic delivery. Our proprietary variants (e.g., PN168,
PN218) demonstrate superior infectivity and organ selectivity—validated by in vivo data in
cynomolgus monkeys.
Figure 1. PN168-hGRK1-GUCY2D-FLAG was delivered via
intravitreal injection. Immunofluorescence staining for FLAG revealed that PN168
effectively transduced cynomolgus monkey rod photoreceptor cells (Injection dose:
5E11 vg/eye; Tissue harvest: 4 weeks post-injection)
Figure 2. PN218-CAG-EGFP was delivered via cisterna
magna injection. Immunofluorescence staining for EGFP revealed that PN218
effectively transduced cynomolgus monkey astrocytes and a small population of
neurons (Injection dose: 1.8E13vg; Tissue harvest: 3 weeks post-injection).
Custom AAV Packaging Services
Rigorous quality control and high-quality AAV variants
Cyagen provides purified AAV suitable for use in cultured cells and in
vivo animal studies, supporting multiple modalities including overexpression, knockdown, and
knockout. From AAV design and construction to viral packaging, purification, expression
analysis, and functional validation, we deliver an end-to-end workflow that minimizes
experimental turnaround time for researchers.
AAV delivery standards
Ready-to-Ship AAVs
Validated AAV Serotypes and AI-Optimized Variants
Utilizing triple-plasmid co-transfection and advanced purification
processes, our available in-stock AAV vectors include EGFP (covering standard and variant
serotypes, proprietary mutants, and tissue-specific promoters), mCherry and Luciferase
fluorescent proteins, and genetic tools (Cre recombinase, GCaMP6f calcium indicators,
chemogenetics, and optogenetics).
Figure 3. AAV9-cTNT-Cre was administered via tail vein
injection to Rosa-LSL-tdTomato mice. Examination of mCherry fluorescence in tissue
sections demonstrated that AAV9 efficiently transduced cardiomyocytes and that the
cTNT promoter exhibited high cardiac specificity (Injection dose: 1E12 vg; Harvest
timepoint: 4 weeks).
In Vitro & In Vivo Validation
Verify Expression Before Preclinical Evaluation
In vivo transduction efficiency: Demonstration of AAV transduction across
various tissues.
Figure 4. AAV transduction efficiency In vivo
In vitro transduction efficiency: Demonstration of AAV-EGFP
transduction in 293T cells.
Figure 5. AAV transduction efficiency In
vitro
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Build. Validate. Translate.
Custom cellular and animal models for functional validation of gene therapy
targets.
Cyagen’s model generation platform empowers researchers to evaluate therapeutic
candidates in biologically relevant systems—from in vitro transduction assays to
disease-representative rodent models. We offer precise genome engineering for KO, KI, and
overexpression models, paired with comprehensive histological and biomarker validation to ensure
translational relevance for preclinical studies.
In Vitro Functional Assays
Validate gene function and transduction efficiency in cellular
systems.
Rodent Model Generation
Create disease-relevant KO, KI, and overexpression models for
preclinical research.
Histology & Biomarker Analysis
Confirm tissue-level changes and biomarker profiles with
precision.
In Vitro Functional Assays
Test Transgene Effects in a Controlled Cellular Environment
Use our optimized cell-based platforms to evaluate AAV-mediated
transduction efficiency, protein expression, and cell viability. Ideal for early-stage
screening before in vivo validation.
Rodent Model Generation
Validate Gene Function and Therapeutic Potential In Vivo
Establish knockout, knockin, or overexpression mouse models tailored
to
your gene of interest. Available on immunodeficient, humanized, or tissue-specific
backgrounds.
Histology & Biomarker Analysis
Uncover Biological Impact at the Tissue and Molecular Level
Perform detailed pathological analysis, including H&E, IHC/IF, and
biomarker profiling (e.g., dystrophin, inflammation, fibrosis markers) to confirm
therapeutic response.
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Deliver with Precision. Validate with Confidence.
Expert-guided CNS drug delivery to support gene therapy research.
Cyagen’s preclinical pharmacology team offers in vivo drug delivery services
tailored for CNS-targeted gene therapy research. From stereotactic injections into precise brain
regions to systemic administration methods, our experts ensure accuracy and reproducibility through
standardized procedures and post-delivery validation. Backed by imaging and biomarker readouts, we
help researchers confirm delivery success and downstream therapeutic effects.
Stereotactic Brain Injection
High-precision delivery to defined brain regions using 3D
coordinate systems.
Intrathecal Injection
Direct administration into cerebrospinal fluid (CSF) via lumbar
puncture or cisterna magna.
Intravenous (IV) Injection
Systemic delivery allowing broader biodistribution and tissue
transduction.
Additional Routes
Intramuscular, subcutaneous, intranasal, intraperitoneal, and more
– based on research goals.
Case Highlight
Example 1 – Precise Brain Targeting via Stereotactic
Injection
- Substance: AAV5-CAG-EGFP, AAV9-CAG-EGFP, PM228-CAG-EGFP
- Method: Stereotactic injection
- Target Site: Bilateral striatum
- Validation: EGFP expression observed 4 weeks post-injection via native fluorescence imaging, confirming successful localized brain transduction.
Figure 6. Representative coronal brain sections from mice
stereotactically injected with AAV5, AAV9, or PM228 vectors targeting the striatum. EGFP
signal (green) shows transgene expression; DAPI (blue) labels nuclei. Merge images
highlight co-localization. Brain atlas reference indicates targeting region.
Example 2 – Systemic Administration for Brain-Wide Gene
Delivery
- Substance: AAV9, AAV-PHP.eB, PM228
- Method: Intravenous injection via tail vein
- Validation: Robust, brain-wide GFP signal detected via immunofluorescence 3 weeks after administration, confirming efficient transduction across brain tissues.
Figure 7. Sagittal brain sections showing widespread EGFP
expression following intravenous delivery of AAV9 WT, PHP.eB, and PM228 vectors. Green:
EGFP signal; Blue: DAPI-stained nuclei. Merge panels show broad transgene distribution
throughout brain parenchyma.
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Measure. Analyze. Optimize.
Multi-tiered in vivo and in vitro assessments to quantify therapeutic
efficacy.
Cyagen delivers a full suite of efficacy evaluation services to support gene
therapy development. Whether assessing vector performance, biomarker expression, immune response, or
behavioral outcomes, our platform ensures scientific rigor and translational relevance. Testing is
conducted in validated models using standardized assays across molecular, cellular, tissue, and
systemic levels.
Molecular & Cellular Assays
qPCR, western blot, ELISA, and IF to quantify transgene expression
and protein function.
Functional Cell Readouts
Assays for proliferation, apoptosis, migration, and cellular
response to therapy.
Behavioral Studies
Water maze, open field, and gait analysis to evaluate CNS recovery
or degeneration.
Ocular Phenotyping
Retinal flat mount, ERG, and fundus imaging for evaluating ocular
gene therapy.
Case Highlight
Example – ASO-Mediated SMN Restoration in SMA Model
- Model: B6-hSMN2 mouse
- Assay: Western blot and IHC (ChAT staining)
- Outcome: ASO-10-27 treatment led to increased SMN protein levels and significantly higher numbers of spinal motor neurons, indicating effective target engagement and phenotypic improvement in the SMA model.
Figure 8. Western blot analyses confirm increased SMN
protein levels in B6-hSMN2 mice after ASO-10-27 administration, indicating successful
gene regulation. Immunohistochemistry (ChAT staining) further shows an increased number
of spinal motor neurons following treatment.
Our Unique Advantages
One Partner, Full Pipeline
Streamline your entire gene therapy workflow—target discovery, AAV design, model generation, and validation—all in one place.
AI-Powered Discovery
Accelerate progress with AI-guided variant prediction, splicing analysis, and capsid optimization from our proprietary RDDC platform.
Human-Relevant Models
Access validated humanized and disease-specific models, including HUGO-GT™ mice tailored for gene therapy research.
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