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Genome-scale variant analysis for individual patients, families and cohorts.

Secure web portal provides tool for exploring variant annotations
Optional summary report
for each patient
Support from saphetor’s network of molecular geneticists

Saphetor Services at a Glance

Our complete genome-scale NGS bioinformatics solution

saphetor service

Data Intergration

Saphetor has developed proprietary algorithms and is employing trade secret know-how to clean and integrate data from a growing number of databases.

Data integrated from a growing number of sources

To date Saphetor has aggregated more than 30 leading databases, representing over 33 billion variant annotations, and our collection keeps growing.

Variant discovery and genotyping using our software

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

Annotations, confidence and pathogenicity scores

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: ClinVar, gnomAD, COSMIC1000 Genomes, dbSNP, Mutation Taster, Sift, CGD, Pubmed, RefSeq, Unigene, DGI, Clinical Trials, HPO, Orphanet, ICGC, CIViCIARC TP53 somatic and germline, etc…

and external links: DECIPHER, Genecards, KEGG, BioGPS, Reactome, Genetests, HGNC, Wikigenes, Uniprot, Ensembl, Vega, UCSC.

Value added reports from saphetor’s network of molecular geneticists

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