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New: We encourage participants to get a head start on the data before the weekend starts! You can start working on this case as soon as you have received an invitation to participate and we have you set up in Google Cloud.


Our objectives are exploratory and investigative. We’re seeking to:

  1. Accelerate research.

  2. Generate ideas for diagnosis.

  3. Explore treatment options.

  4. Better manage symptoms.

  5. Reduce hospital visits.

  6. Eliminate unnecessary care.


Suggested problem tracks: Provided as guidance, please do not limit your analysis to these suggestions.

  1. Exploration of disease pathology and current development efforts/ongoing clinical trials.

  2. Identifying off-label therapeutics through mutational homogeneity.

  3. Interpretation of candidate mutations that have not been previously reported or validated (variants of unknown significance (VUS).

  4. Variant validation through confirmation in independent patients with similar clinical characteristics and/or population frequency determination.

  5. Structuring, cleaning, and deposition of data in clinical structural variant databases/rare disease databases.

  6. Phenotype-based gene prioritization using semantic similarity and human phenotype ontology.


QIAGEN has generously made two tool suites available for advanced teams participating in Undiagnosed-1. We have setup and provisioned access through SVAI email addressed. Ryan Leung (Ryan on Slack) is helping teams get setup with QIAGEN tools. Be sure to catch Jen P.’s presentation on these tools on Saturday at 11.00am! All participants using QIAGEN tools must complete the QIAGEN End User License Agreement.

  1. Ingenuity Variant Analysis

  2. QIAGEN Clinical Insight Interpret



Parliament2: Access on Github. Authors: Samantha Zarate and Andrew Carroll

Introduction on DNAnexus blog: Fast Structural Variant Calling Using Optimized Combinations of Callers.

Published on Biorxiv.

From Chai: “We generated the structural variant (SV) call from WGS of the undiagnosed patient of this Hackathon using the Parliament2 tool. SV is harder to detect than SNVs and largely underexplored, yet there are lots of research over the last decade demonstrate their implication in human diseases. We think this would be particularly interesting in this patient case.
Parliament2 runs several structural variant callers underneath and generates ensemble call. The tool is recently developed by Samantha and Andrew from DNAnexus and several researchers at Baylor College of Medicine.”


We'd like to see submissions follow the standard format of academic research. There are three potential products for submission for this research case. At minimum, check your work into our Github to save your project as a reference for this case. Second: most teams will present their results at the event or via video. If you are participating online, please submit a link to a 2 min. video talking about your work. Lastly we will be inviting leading teams to publish their results in our F1000 Research collection. All submissions should include: Introduction, Purpose, Approach, Methods, Results.

  1. Github ↗

  2. General Presentation Submissions & Video Link ↗

  3. F1000 Research Publication: Submissions due no later than Friday June 21st. Featured articles and will be selected by our evaluation panel.

    F1000 has two templates available: software tool template, and research article template.

  • Short article: Submit an article 1000 words or under. Here’s a nice additional template for short articles.

  • Medium article: Submit an article 1000-2500 words.

  • Long article: Awesome! Please let us know in advance if you plan on submitting an article more than 2500 words.


Final in-person presentations: Each team or individual will have 5 Minutes to present what they worked on. Presentations will be fast! But don't worry, we will link submissions here afterwards so you can get a closer look at what everyone worked on.

Online participant presentations: To best represent your work at the event and streamline logistics, please submit a short 2 Minute video covering your research results. Submission link will be up soon.


Evaluation will happen in 2 phases:

  1. During Event: Following the Sunday presentations and video submissions, our panel of evaluators will select five leading results. These results will be highlighted on SVAI’s website social channels.

  2. Publication Deadline: After our June 21st publication submission deadline, we will be conducting an in-depth review of submissions for inclusion in our F1000 Research collection.


Each presentation will be evaluated on the following criteria weighted in this order:

  1. How well does the solution lead to positive outcomes for the patient?

  2. How novel is the approach to finding a solution?

  3. Quality and depth of the problem analysis.

  4. Team dynamics, diversity, and intersectionality including cross discipline and specialization collaboration.


Hari Singhal is helping integrate our online participants with the in person event. In addition to being Knowledge support and Reviewer, Hari will be dedicated to support for online participation during the event weekend.


All of the submitted results for this research case will remain accessible to the community. Leading results will be featured on SVAI’s website and promoted more extensively to our community.