Calypso Released to UDN

IMPORTANT: Calypso should not contain any PHI. If working in Calypso and adding information, please ensure that you do not include any PHI in any of the projects. Only UDN members have access to Calypso, however, this is to be used with de-identified data only.

We made a beta release of Calypso to a limited number of UDN users in 2022. Based on invaluable feedback from these early users, we have made improvements to Calypso and are now providing a beta release to the full network. The purpose of this release is to familiarise all UDN users with Calypso and give them the opportunity to provide feedback to ensure Calypso effectively serves everyone in the network.

This is a beta release of a tool still under development. Not all data is currently available in Calypso and features will likely need to be added or amended. This release will help us identify requirements and address them. All critical comments of Calypso are extremely valuable, regardless of how simple they may appear to be. So please send any comments to info@frameshit.io.

Accessing Calypso

After logging into UDN Gateway, there will be a link in the left menu to Calypso. When you log into Calypso, you will be prompted to update your name and username. Please update these as they are used to allow UDN members to communicate within Calypso, and so having accurate names is important.

Where can I find help?

We would be delighted to assist anyone in getting up to speed with all of the features available in Calypso and will happily set up as many demo sessions as required. If you would like to have a demo, please contact us at info@frameshift.io.

The tutorials page on the Frameshift website provides descriptions of many features of the Mosaic platform on which Calypso is based. We will continue to add more tutorials as needed. If you have any specific tutorial requests, please email us at info@frameshift.io, and we will try to respond to these requests as quickly as possible.

What's available in the beta launch?

All users should have access to the following data, described in more detail below:

1. A project for every accepted UDN participant (the project names will be the UDN ID of the proband)
2. A project comprising SNVs and short indels from the UDN Phase II jointly called whole genome dataset (completed by Shilpa Kobren and team at HMS in Jult 2022)
3. A collection of all UDN projects
4. Collections of all UDN projects from each clinical site

1. Projects for every UDN case

Every accepted case in the UDN has a project in Calypso. Information about the case (e.g. the assigned clinical site, age of onset, diagnostic status, HPO terms etc) has been imported from Gateway. In addition, some of the cases have had variants imported for querying. See the following tutorials For information on how to use predefined filters, advanced filters, get detailed information about variants, or update the information available in the variant table.

LIMITATIONS: We have currently only populated some projects with variant data, but can update others on request. Variants in these projects are limited to rare (<0.01 gnomAD popmax allele frequency) variants that are present in the proband. If you have any requests, suggestions on variants, variant annotations or anything else please let us know.

2. UDN Cohort Phase II - July 2022

This project comprises SNV and short indel variants from the UDN Phase II jointly called whole genome dataset (completed by Shilpa Kobren and team at Harvard Medical School in July 2022). The tutorials listed above will provide some help on how to query these variants, but please contact us to arrange a demo session if you want to learn about all available features.

LIMITATIONS: As with the patient projects, this beta release does not contain all variants, but is limited to rare (<0.01 gnomAD popmax allele frequency) variants. Please contact us if there are specific queries that you want to run and you want to be sure that the variants you want will be available.

3. Collection of all UDN projects (UDN Full Cohort)

A collection allows us to collect cohorts of projects into a single organizational unit. Within collections, you can see a table of all attributes associated with all projects in the collection see here, investigate HPO data across all projects, as well as chart all of this information. See here and here for tutorials on working with charts.

4. Collections for each clinical site

Each clinical site has a collection with all the same features as above. These collections are named e.g. NIH Cohort and will only contain those cases assigned to the specific clinical site.

What are Calypso and Mosaic?

Calypso refers to the collaboration between Frameshift Genomics, which provides the Mosaic platform, and the laboratory of Professor Gabor Marth at the University of Utah. The goal of Calypso is to build a longitudinal genomic data management and analysis platform to support team-based, collaborative genomic analysis. Calypso is comprised of three complementary components: (i) bioinformatics pipelines to analyse, annotate, and re-analyse genomic data; (ii) Frameshift's Mosaic platform to provide secure data access, management, intuitive analytics and a fast, queryable variant warehouse, and; (iii) diagnostic workflows to support clinical teams powered by iobio tools. This is an ongoing development that will continue to develop in the coming years.