• Lancet 2015: Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

  • Furness 2017: Bridging the Gap: the need for genomic and clinical -omics data integration and standardization in overcoming the bottleneck of variant interpretation

  • Steward et al. 2017: Genome Annotation for Clinical Genomic Diagnostics: Strengths & Weaknesses




Congenica is HIPAA self-certified and underwent a rigorous self-certification process with an external HIPAA consultancy (HITRUST), who specialise in the field of healthcare regulation and legislation compliance. Congenica uses a HIPAA-compliant cloud platform for storage (AWS Platform).  Please contact for more details on our HIPAA compliance.


All genetic problems caused by one or more abnormalities in the genome, provided that it is present from birth (congenital), including well known conditions such as Cystic Fibrosis, Duchenne Muscular Dystrophy, haemophilia and sickle cell disease. Our approach encompasses most rare diseases and orphan diseases, and also inherited cancers.

We can accept sequence data in either FastQ, BAM and VCF formats for analysis in Sapientia. We can also upload gene lists and BED files describing genomic regions for analysis. To standardise phenotypic annotation, users have a Human Phenotype Ontology interface to click and drag terms to generate a list of phenotypes for the patient.

Yes. As well as using the structured HPO (Human Phenotype Ontology) terms in Sapientia, users can also add their own descriptions in free text.

When you start working with Congenica, we can set up the fields you require in your default project settings and these can also be carried through to the clinical reports generated on your patients.

After analysing the patient’s data in Sapientia, clinicians can review their filtered, annotated data, add annotations of their own using integrated tools linking to literature sources, and assign the pathogeneicity of each variant and its likelihood of contributing to the disease.

Yes. You can provide Congenica with the VCF file containing the variants called within your own pipeline, and we can run that file through Sapientia. However, if you also wish to view the variants in the context of the aligned data, we would also require a BAM file.

The person setting up a project is the default administrator. The administrator of a project has control over who can access the samples in that project. They can choose to share access with collaborators or co-workers by granting them either read-only, read/write, or administrator access. Information about each variant is shared anonymously, so other users of Sapientia working on the exact same variant would know it has already been observed.

Congenica has an internally used template, but if you provide us with a report template that you would prefer to use and the data you wish to include, we can create these templates for use in all your projects on Sapientia.

Security is paramount when we handle customer data. We have a range of accreditations and certifications associated with our security – a brief overview can be found in our recent Security and compliance Update white paper.

None. Congenica only works with anonymised data provided by clinicians and researchers, so we do not store any personal patient data. The primary sequence data is stored at Congenica for analysis, and only Congenica and the provider of that sequence have access to this data.

Genetic testing has already moved from single gene tests to small panels of genes in which variants were known to identify disease. However, if the gene involved is not in the small panel of genes, changes in the gene would not be detected. Today, labs are starting to use exomes (the part of the genome that codes for proteins) or whole genomes to try and examine all genes in one single test, speeding up diagnosis for patients. Find more about Genomics Medicine by watching this interview of Professor Graeme Black, Strategic Director of the Center for Genomic Medicine in Manchester (UK).