Clinical Laboratories Meeting Minimum Requirements for Data Sharing to Support Quality Assurance

ClinGen considers the sharing of variant classifications 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 clinical laboratories who meet a minimum standard of data sharing. The minimum requirements were updated January 1, 2020.

  • Laboratory is a CLIA certified laboratory (USA) or meets an equivalent standard in another country
  • A complete list of the laboratory’s test offerings are publicly available either through a registry such as Genetic Test Registry (GTR) or Orphanet or on the laboratory’s website 
  • Laboratory submissions are registered in ClinVar as ‘Single Submitter, Assertion criteria provided’ (single star) 
  • Laboratory submits at least once per year, adding new variants and updating reclassified variants as necessary 
  • Laboratory has submitted at least 100 variants
  • Laboratory submits all categories of variants reported to patients (labs are also encouraged to share B/LB variants and VUS if not reported)
  • Laboratory has attested to submitting at least 95% of all sequence and/or copy number variants reported in the past two years 
    • Note: The intent of the 95% rule is to ask that labs submit all reported variants with some exceptions for those variants where there may be challenges to sharing in ClinVar. If a lab has concern over whether they meet the 95% rule and would like to discuss exceptions, please contact ClinGen at clingen@clinicalgenome.org.
  • All pathogenic/likely pathogenic submissions reported in the last year have supporting evidence, defined as an evidence description containing enough information to follow how you arrived at your classification (for example, this could include a descriptive summary, and/or submitting ACMG/AMP criteria codes and PMIDs)

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

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


Laboratory 

Meets

Requirements

Additional Achievements
>95% from past 5 years1

Discrepancy resolution2

Consenting mechanism3

Ambry

ARUP

 

Athena Diagnostics Inc.

 

 

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

 

 

Color Genomics, Inc.

GeneDx

 

GeneKor MSA

Illumina

Integrated Genetics/Laboratory Corporation of America

Invitae

Myriad Women's Health

Partners Laboratory for Molecular Medicine

Quest Diagnostics Nichols Institute San Juan Capistrano

 

 

University of Chicago


Some requirements and additional achievements based on self-reported data by laboratory

*Most recent submission pending ClinVar processing
1>75% of classified sequence and/or copy number variants from past 5 years submitted
2Actively working to resolve interlab interpretation differences
3Laboratory actively supports use of a consenting mechanism to enable patients to directly consent to share detailed, individual-level clinical data (e.g., an internal patient registry made available for collaborative research, or report language highlighting external registries such as GenomeConnect)

 

Frequently Asked Questions

  • How were the updated requirements that went into effect in January 2020 determined?
  • How does a laboratory maintain status on the list?
    • Laboratories apply to be on the list by taking a survey to attest to minimum requirements
    • An annual announcement regarding requirements for the following year (Jan-Dec) are posted by July 1st of the current year for major changes or October 1st for minor changes. If no changes are planned, laboratories much attest to the existing requirements. Compliance must be achieved by December 31st to be included in the following year’s list. If laboratories do not meet requirements by Dec 31st, they will be removed from the list. However, labs can be added back to the list as soon as requirements are complete and new labs can be added at any time based on achieving compliance. 
  • My laboratory is based outside of the United States. Do I still need to be registered within the Genetic Testing Registry (GTR) to qualify for inclusion?
    • No, in February 2019 this requirement was modified. Now, a laboratory must have publicly available a complete list of test offerings either through a registry such as GTR or Orphanet or on the laboratory’s website.
  • Do the requirements to be on this list pertain to sequence or copy number variants?
    • Clinical laboratories that perform both sequence and structural variant testing are encouraged to submit both types of information to ClinVar.
  • What kind of “consenting mechanism” is required to achieve a badge? 
    • We assign ‘consent achievement badges’ to clinical laboratories that have a means for patients to directly consent to share detailed, individual-level clinical data. Examples of this include:
      • Lab-specific patient registries for patients to share data in collaborative research
      • Language in clinical reports describing external ways for patients to share their data (e.g., highlighting the existence of direct patient data sharing initiatives like GenomeConnect: www.genomeconnect.org/)
      • Consent mechanism allowing patient to permit laboratory to share individual-level data directly with ClinVar. Template consent resources from ClinGen can be found here: www.clinicalgenome.org/share
    • If you are interested in including GenomeConnect language on your consent forms, sample wording can be found here: https://www.clinicalgenome.org/genomeconnect/for-patients-genomeconnect/documents/
    • If you have any questions about whether or not you meet this requirement, please contact us.
  • What kind of “discrepancy resolution” efforts are required to achieve a badge?
    • This badge is given to laboratories that attest to “actively engaging in variant interpretation discrepancy resolution activities with other submitters in ClinVar.”
    • An example of discrepancy resolution efforts, performed by four clinical laboratories as a part of ClinGen, is described by Harrison et al. in Genetics in Medicine (PMID: 28301460).
    • The ClinGen Sequence Variant Inter-Laboratory Discrepancy Resolution team, led by Steven Harrison (Broad Institute) and Jill Dolinsky (Ambry), is actively working to resolve discrepancies within ClinVar and to identify persistent interpretation differences due to varying application of ACMG/AMP rules.  If you are interested in participating in this group, please reach out to Steven Harrison (steven@broadinstitute.org). To participate in discrepancy resolution efforts focused on copy number variants, please contact Erin Riggs (eriggs@geisinger.edu).
  • If my laboratory 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 laboratories 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.
  • Can a lab be removed from the list?
    • Yes, labs will need to fill out the survey annually and will be removed if criteria are not met in the future.
  • Does this list apply to somatic testing?
    • Yes, laboratories performing somatic cancer testing can submit to ClinVar and will be listed if they meet the data sharing criteria.