We are excited to announce a beta release of our Calypso tool on the latest Phase II Undiagnosed Diseases Network (UDN) data. This is a project performed in collaboration with the UDN, and we encourage our initial set of UDN investigators to trial this release and provide any feedback, comments, questions or requests to email@example.com.
What's available in the beta launch?
This beta release includes two projects:
1. 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, Harvard Medical School, in July 2022). As an initial testing version, this beta version only provides access to some of Calypso's available features, but we will be adding more data and features to this release in the coming weeks.
2. Single family example
This project is a demonstration of how Calypso can support collaboration on data for a single patient case. This project contains HPO terms, saved gene sets, variants present only in this family, and saved analyses.
What's coming next?
Calypso has many features that we will make available moving forward. Some of these depend on data access (e.g. IGV will be available to interrogate read support for any variants in any individuals once we enable access to BAM files). Other features require incorporating additional data (e.g. newly requested variant annotations, or patient-level data). Please feel free to send feature requests to us and we will incorporate everything that we can.
Where can I find help?
The tutorials page on the Frameshift website provides descriptions of many features of the Mosaic platform. We will continue to add more tutorials as needed. If you have any specific tutorial requests, please email us at firstname.lastname@example.org, and we will try to respond to these requests as quickly as possible.
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.