The Evolution of Genomic Interpretation

Cypher Genomics is leading the shift from manual genomic interpretation to one that’s shaped by technology, helping clinical labs and pharmaceutical companies tap into the enormous potential of high throughput genome sequencing. Yet technology alone cannot solve the challenge of interpreting vast amounts of data to pinpoint variants of interest. It is the application of Cypher’s deep biological expertise that drives development of the unique algorithms that enable more accurate, rapid discovery of variant classifications for germline and somatic variants.


Comprehensive content enables research and clinical applications.


90+ annotations per variant for each transcript enables highly accurate classification and prioritization.


Modular annotation system maintains content relevance and acceptability to multiple applications.


Annotation content for targeted panels, whole exome or whole genome sequencing data.

Quality Controls

Sophisticated technical, functional and biological controls identify relevant variants with greater speed, precision and confidence.

Warning flags highlight low confidence variants due to potential errors in the variant calling process and/or false positives found in the literature of reported pathogenic variants.

Scripps Wellderly Cohort

Only Cypher’s biological filtering includes data from the proprietary Scripps Wellderly Genome Resource, a study of whole genome data for nearly 700 healthy individuals over the age of 80, which serves as an ideal control population.

Cypher Synthesis

The Cypher Synthesis is used to provide meaningful reported and predicted interpretation of genomic variants for both coding and non-coding variants.

After individual annotations are calculated and compiled, these annotations are synthesized into a final ranking modeled after the American College of Medical Genetics (ACMG) guidelines for molecular diagnostics for each variant (Cypher Syntheses).
Three different scores are produced:
1) Cypher Functional Synthesis: disease agnostic score
2) Cypher Clinical Synthesis: rare disease score
3) Cypher Cancer Synthesis: cancer specific score


Expert analytical algorithms derived from biological principles.

Cypher’s unique, automated algorithm is interpretation that goes beyond simple feature-based classifications to include proprietary data and specialized knowledge, evaluating the holistic impact of each variant. Accuracy is validated in multiple in silico and clinical concordance studies.

Technology Founded on Strong Science

Security & Privacy

Cypher maintains the highest standards to insure complete data security and patient privacy.

Our base architecture is designed to control sensitive data access at every step, and maintain HIPAA compliance. Distributed encryption, rigorous maintenance and around-the-clock onsite monitoring provide maximum security, while still allowing for seamless client access to Cypher services.


Our cloud-based, scalable infrastructure supports big data and bioinformatic analytics, while strict data management and governance framework ensure quality and compliance.

Advanced Analytics

Cypher has developed proprietary, robust commercial architecture and storage methods that reduce costs, increase speed and allow for efficient data mining from large sets of annotated genomes.


Our automated process supports ongoing, versioned updates and backwards compatibility.


Access cloud technology instantly or deploy locally.