Genomic Analysis Software Platforms Meeting Minimum Requirements for Data Sharing to Support Quality Assurance

ClinGen considers the sharing of variant interpretations essential for supporting genomic medicine and a critical part of quality assurance for accurate genetic and genomic testing. Open and transparent sharing allows peer-review and knowledge dissemination to ensure the highest quality care of patients. 

Here, we identify genomic analysis software platforms that meet a minimum standard to support data sharing.

  • Variant centric database, searchable and manageable at the variant-level (e.g. ability to create and update classifications and add evidence over time, independent of case interpretation)
  • Support export of variant-level data meeting all required elements for submission to ClinVar (e.g. variants with classifications with respect to a disease and with accompanying evidence)
  • Include to HGVS nomenclature
  • Platform supports application of ACMG/AMP classification terms (Pathogenic to Benign) and criteria codes (e.g. BS1, PS3_Moderate, etc)
  • Documentation of evidence for variant classification (PubMed IDs, ACMG/AMP codes, text-based evidence summaries)

To apply for status, or to update your status, software platforms can apply here.

Questions about the criteria? Visit our Frequently Asked Questions below or contact clingen@clinicalgenome.org.


Software Company 
(Platform name)

Meets
Requirements

Additional Achievements

Structured clinical data1

Exports de-identified phenotype data2

Supports use of Phenopackets3

Agilent Technologies
(Alissa Interpret)

 

Emedgene

 

Genoox
(Franklin)

 

Golden Helix
(VarSeq & VSClinical)

Illumina
(TruSight Software Suite)

   

Sunquest Information Systems
(Sunquest Mitogen Genetics)

 

Some requirements and additional achievements are based on self-reporting by software company, verified by at least one client reference.
Platform supports the intake of clinical data in a structured way (e.g. HPO terms, disease diagnoses using MONDO ontology), either through manual entry or electronic interfaces.
Enable export of de-identified phenotypic data (e.g. HPO terms, disease diagnoses using MONDO ontology)
Support use of the GA4GH phenopackets standard for exporting case level data (http://phenopackets.org/)

Frequently Asked Questions

  • If my software platform does not meet requirements now, but does so in the future, how do I get added to the list?  How often do you update this list?
    • We continually update the list of genomic analysis software platforms posted on our website, so a lab can be added at any time. If you have recently completed the survey, and believe you qualify but do not see your lab represented online, please reach out to us at clingen@clinicalgenome.org.
  • Will criteria for inclusion on this list change over time? Can a software be removed from the list?
    • Yes, we foresee changes to the inclusion criteria over time
    • Yes, labs will need to fill out the survey each year and will be removed if criteria are not met in the future.