Genevieve

Genevieve is end of life. If it breaks, it's likely I won't fix it. For future genomic analyses, I'm hoping to play with our notebooks system in Open Humans. – Mad

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Connect an Open Humans account to enable Genevieve to automatically create reports from the genetic data you've added to Open Humans.

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About Genevieve

Genevieve is a tool that invites you to explore your genome. Your genome data is matched against ClinVar, a public database that aggregates information about genetic variants. To help improve our shared understanding, Genevieve also invites users to contribute to shared, public, wiki-style notes that elaborate on genetic variant information.

Specifically, Genevieve mainly does two things:

Genevieve matches your genome data against the ClinVar database.

ClinVar is a public database of genetic variants and their reported effects on disease, health, and biological traits.

Genevieve also draws on allele frequency data from the Exome Aggregate Consortium (ExAC). ClinVar and ExAC data are retrieved from MyVariant.info API, an open source server hosting variant information from various databases.
Genevieve allows users to add and edit shared notes.

User-generated notes can help clarify and expand on the information contained in ClinVar. You can contribute to this shared understanding! Genevieve's notes are public domain (CC0), and are publicly available via the GenNotes server API.

Genevieve does not provide ancestry reports. Also, Genevieve does not attempt to assess any combined effects arising from a combination of different genetic variants.

Genevieve reports are dynamic. The shared notes on Genevieve are constantly subject to change, and the databases Genevieve uses are regularly updated. Changes and revisions to the databases are expected and a normal part of the scientific process.

Genevieve is for personal exploration and education.

I believe access and discussion of knowledge is a right and necessity for informed citizenry in the age of genomics. Thus, I want to facilitate personal exploration and education with access to published claims regarding the effects of variants in an individual genome, and enable discussion and consensus understanding of these claims.

Genevieve is NOT intended to be used as a clinical device for diagnosis or detection of disease. If you find information in Genevieve that appears to indicate something clinically important, you should work with a health care provider (e.g. genetic counselor) that can review, verify, and determine if clinical action is warranted.

Genevieve reports will have errors.

The Genevieve community strives to do a better job at understanding variants. However, user-contributed notes are not reviewed. Users could potentially contribute misleading or incorrect information, and there is no screening of user contributions.

In addition, many published reports of variant effects are wrong. The ClinVar database is an amazing resource that aggregates reports, but those reports are often incorrect – even if they were published as scientific papers! Science is a process that requires testing and reproducibility, and many initial findings are later discovered to be spurious or flawed.

Also, Genevieve may fail to highlight variant information that you or others believe is noteworthy. Scientific knowledge is incomplete, the databases or algorithms may fail to return published information about a variant, and user notes may incorrectly dismiss a reported variant effect.

Your raw genetic data may be incomplete. Genotyping data sources (e.g. 23andMe or AncestryDNA) cover a very limited subset of your genome. Even if you have an "imputed" version of this data, these are unlikely to contain information about rare and unusual variants in your genome.

Finally, your raw genetic data may contain errors. Depending on where your data came from, the data provider may have systemic or sporadic errors in generating that data. Genevieve's accuracy is limited by the underlying accuracy of the data it's analyzing.

Who runs Genevieve?

Genevieve is primarily written and maintained by Mad Price Ball, one of the co-founders of Open Humans. Although it uses data from Open Humans, it is a personal project. Mad's work is supported by their funding from the Shuttleworth Foundation.

Genevieve is open source.

Genevieve's source code is shared on GitHub with an MIT (Expat) license.

In addition, notes contributed via Genevieve are public domain (CC0) . Notes are stored in the GenNotes database as public domain material (CC0) and are available via the GenNotes API. The GenNotes server is operated by Open Humans, and the source code for this is also available.)

If Open Humans data is public, it will make the corresponding report public.

Data is private by default on Open Humans, but members can opt in to publicly sharing their data if they've enrolled in the Public Data Sharing study. Participants in that study can turn on (and off) public sharing for each data source.

Are you publicly sharing genetic data on Open Humans? Thank you! By publicly sharing your genetic data you're gifting the world with a great resource for shared understanding.

To further that shared understanding, Genevieve will make the corresponding variant reports publicly available as well. If you make genetic data public after a report has been generated, Genevieve tries to detect this and make the corresponding report public. Also, if you change your mind and remove public status to your genome data on Open Humans, Genevieve attempts to honor that on this site as well.

Example reports

See the public reports for some examples of reports produced by Genevieve.

Deleting and deauthorizing Genevieve

You can go to the account management page to to delete your account from this site, as well as associated genome reports. While this website will no longer retain authorizations for accessing Open Humans, your authorizations will still be available within Open Humans itself. To remove these, you should deauthorize the project in Open Humans. (Do this after deleting the account here!)

Can I contribute notes without connecting Open Humans?

Even if you aren't interested in generating a report from your own genetic data, I hope you consider connecting via Open Humans. It's a fun community, and you're also welcome to join our community Slack to chat!

But if joining as an Open Humans member isn't an option, you can log in directly with an authorized GenNotes account. Create a GenNotes account if you don't already have one. Then use the button below to authorize notes submissions and log in to Genevieve.