To date Saphetor has aggregated more than 20 leading databases, representing over 18 billion variant annotations, and our collection keeps growing.
Saphetor Services at a Glance
Saphetor has developed proprietary algorithms and is employing trade secret know-how to clean and integrate data from a growing number of databases.
Saphetor software provides an automated identification and ranking of potentially pathogenic variants, with confidence scores to support decisions.
Saphetor has developed pipelines which integrate a variety of variant discovery tools to yield validated optimal results. In order to provide an excellent decision support system, our pipelines have been designed to achieve high quality standards, such as flexibility, reproducibility, sensitivity and precision:
Works with any capture kit or gene panel reproducibly
- Sensitivity*: 99.9 % for SNPs and 95.8% for INDELS
- Precision*: 99.9 % for SNPs and 99.7 % for INDELS
*Genome in a Bottle validation datasets
Saphetor’s platform annotates variants using its vast database, linking them to known disease associations, population statistics, treatment options, clinical trials, scientific literature and a number of pathogenicity metrics, including our own score, in order to support diagnosis and treatment strategy options.
Automation of the annotation process, ensures a comprehensive understanding of variant significance and implication to disease. Saphetor pipeline integrates data from 20 databases (public and licensed), and annotates each variant with:
- Gene and functional position
- Protein functional impact
- Population allele frequencies
- Pathogenicity prediction scores
Each variant is classified by our algorithm using the 5-class score suggested by the ACGS guidelines
Real-time update of the following databases: HGMD, ClinVar, ExAC, 1000 Genomes, dbSNP, Mutation Taster, Sift, CGD, Pubmed, RefSeq, Unigene, DGI, Clinical Trials, HPO, Orphanet, ICGC , IARC TP53 somatic and germline, etc…
Our experts’ identification of likely causal variants, along with a summary of available therapeutic options, supports clinical decisions.
You can visualise the results on our highly configurable and intuitive web portal. Data can also be exported to a variety of formats for further processing. Each user can customize the view of sample analysis according to 30 different modules (Chromosome position, Variant seq, Variant type, pathogenicity class, RSID, Zygosity, CGD Inheritance, Gene ID, coding impact, allelic balance, etc…)
The Saphetor portal gives you access to modular and tailor-made reports:
- Table with the variants, classification and most relevant annotations
- Common variants shared within all your samples
- Genome browser and gene/exon coverage visualisation
- Biological context
- Direct links to other external databases
- Complete quality and coverage reports