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Service: Genoxus Annotation™
Optimized Genomic Variant Annotation
Version 1.0 | Live Now on AWS Open Data Registry (ClinVar)
Enhanced Variant Annotation
Genoxus Annotation™ is a harmonized collection of human genetic variant databases designed for accurate, scalable variant annotation. As sequencing technologies generate ever-larger volumes of genomic data, well-structured annotation resources are essential for translating raw variant calls into clinically meaningful insights.
Genoxus Annotation makes this resource freely available to the research community—hosted on AWS, optimized for programmatic access (V1.0 supports ClinVar; more datasets to come), and ready to integrate into your existing bioinformatics workflow.
Genoxus Annotation™ Instructions – Download [PDF]
Current Challenge: ClinVar is Comprehensive.
But It Wasn’t Built for Scale.
The NCBI ClinVar database is the gold standard for clinical variant interpretation. However, its standard interface creates significant bottlenecks for high-throughput research:
- One variant at a time – No batch queries. Researchers manually enter thousands of variants individually.
- No API – Impossible to integrate ClinVar into automated analysis pipelines.
- Slow queries (unoptimized data structure) – The raw data structure isn’t optimized for large-scale searches.
- Workflow breaks – Manual copy-paste between systems wastes time and introduces errors.
Genoxus Solution: Same Trusted ClinVar Data.
Optimized for Speed & Scale.
We took the authoritative ClinVar dataset and restructured it for the way modern research actually works.
| What You Get from Genoxus Annotation: | Why it Matters: |
|---|---|
| Complete ClinVar (V1.0 supports ClinVar; more datasets to come) | All variant types: SNVs, INDELs, CNVs, SVs, and more |
| Programmatic Access | Query via SQL, Python, Spark—no web interface required |
| Batch Queries | Annotate thousands of variants in a single request |
| Partitioned Parquet Files | Fast performance, targeted queries—read only what you need |
| AWS S3 Hosting | No infrastructure to manage. Direct, global access. |
| Free to All | No cost. No account. No restrictions. Get started today! |
Who Is This For?
| User Type: | How They Benefit: |
|---|---|
| Bioinformatics Teams | Integrate optimized ClinVar data directly into custom pipelines |
| Sequencing Companies | Batch-annotate thousands of variants without manual intervention |
| Research Institutes | Run large-scale association studies with programmatic access |
| Software Developers | Build applications on a reliable, well-structured genomic foundation |
| Academic Labs | Access comprehensive variant data for hypothesis generation—at no cost |
Genoxus Annotation v1.0: Data Sources (Roadmap)
By harmonizing variant representations, standardizing disease terminology, and consolidating evidence across sources, Genoxus Annotation provides a unified framework that streamlines variant interpretation for research and clinical applications.
| Source: | Coverage: | Status: |
|---|---|---|
| NCBI ClinVar | All variant types (SNVs, INDELs, CNVs, SVs) with clinical significance assertions | Included Full ClinVar Dataset |
| GWAS Catalog | SNVs associated with complex traits and diseases via genome-wide studies | Planned for v2.0 (Q3 2026) |
| GnomAD | Population frequency data for variant filtering | Planned for V3.0 (Q1 2027) |
| OMIM | Gene-disease relationships and inheritance patterns | Under evaluation |
| COSMIC | Somatic variants in cancer | Under evaluation |
FAQ
Q: Is this the same ClinVar data from NCBI?
A: Yes. We restructured the authoritative NCBI ClinVar dataset for programmatic access and optimized query performance.
Q: Do I need an AWS account?
A: No. The data is publicly accessible via S3 without authentication.
Q: Can I use this commercially?
A: Yes. The free dataset is available for any use—academic, commercial, or personal.
Q: How often is the free dataset updated?
A: The Open Data version is a snapshot from March 2026. For monthly updates, contact us about the paid subscription tier.
Q: What tools can I use?
A: Any tool that supports Parquet: DuckDB, Apache Spark, Pandas (pyarrow), AWS Athena, and more.
Q: When will GWAS and GnomAD be added?
A: GWAS is planned for v2.0 (Q3 2026) and GnomAD for v3.0 (Q1 2027).
A: Yes. We restructured the authoritative NCBI ClinVar dataset for programmatic access and optimized query performance.
Q: Do I need an AWS account?
A: No. The data is publicly accessible via S3 without authentication.
Q: Can I use this commercially?
A: Yes. The free dataset is available for any use—academic, commercial, or personal.
Q: How often is the free dataset updated?
A: The Open Data version is a snapshot from March 2026. For monthly updates, contact us about the paid subscription tier.
Q: What tools can I use?
A: Any tool that supports Parquet: DuckDB, Apache Spark, Pandas (pyarrow), AWS Athena, and more.
Q: When will GWAS and GnomAD be added?
A: GWAS is planned for v2.0 (Q3 2026) and GnomAD for v3.0 (Q1 2027).
Paid Tier (Coming Soon)
For users requiring continuous monthly updates synchronized with NCBI ClinVar releases, a subscription option, Genoxus Annotation Plus™, will be available. This paid tier provides:
- Monthly refreshed data (aligned with ClinVar release schedule)
- Same optimized Parquet format and partitioning structure
- Direct access via private S3 bucket or AWS Marketplace
Contact Genoxus for pricing details: info@genoxuslabs.com.
Disclaimer: Genoxus materials, reports, analyses, and platform outputs are provided for research, educational, and informational purposes only. They are not intended to serve as clinical, diagnostic, or medical advice and have not been validated or approved for use in medical decision-making. Any insights or interpretations generated by Genoxus are exploratory in nature and are intended to support research, evaluation, and collaborative learning. These materials should not be used as the sole basis for diagnosis, treatment, patient management, or healthcare decisions. All medical or clinical decisions should be made in consultation with qualified healthcare professionals and supported by appropriately validated clinical testing.
Join Us on the Journey
We collaborate with clinicians, researchers, healthcare organizations, and strategic partners who share our commitment to advancing precision medicine.