Learn how to use the RD-Connect platform and how it can help you to analyse your sequencing data. The video will guide you through the process of genome sequencing data analysis to identify a disease-causing genetic variant in a patient.
May 2016: The RD-Connect genomic analysis platform has been registered in the Spanish Agency for Data Protection, which makes it possible for additional projects to securely share their data with RD-Connect. The platform already includes the exomes and phenomes of over 500 donors and expects around 2000 individuals to be included by the end of the Summer 2016. Thanks to feedback from NeurOmics beta-testers, the platform has included new functionality for genetic variant discovery, including compound-heterozygosis, effect prediction metrics, population frequencies, genotype:phenotype queries and links to external resources, such as ExAC, HGMD and many more. To enable simple external queries to find out whether a particular variant is present or absent in the RD-Connect dataset, the platform has implemented the GA4GH Beacon API and has joined the Beacon Network, for more sophisticated queries enabling clinicians to assess similarity between cases and perform genotype or phenotype matching.
June 2015: The RD-Connect genomic analysis platform is now ready to be opened up for beta-testing by our first partner projects, NeurOmics and EURenOmics. The platform was presented at the meeting of the European Society of Human Genetics in Glasgow, June 2015.
See the slides of the Glasgow presentation.
The genomics side of the platform already includes over 360 exomes (generated by next generation sequencing) linked to detailed phenotypes stored in PhenoTips using the Human Phenotype Ontology. Exomes have been processed with version one of the RD-Connect standard analysis pipeline for genomics, which exceeds 99% precision and sensitivity when compared to the National Institute of Standards and Technology (NIST) reference set of calls for NA12878. The platform runs on a Hadoop cluster and uses technologies such as ElasticSearch, Postgres, Scala and Angular.js, making it highly configurable and efficient. The exomes can be combined in a very flexible manner and variants can be filtered and prioritized through the user-friendly front-end using the most common quality, genomic location, effect, pathogenicity and population frequency annotations, including CADD and ExAC. Moreover, additional tools can be integrated at the database level or at the interface through API queries. To date, UMD Predictor, DiseaseCard, Alamut Functional Annotation (ALFA) and gene-disease relationships in nanopublication format have been integrated.
The online genomics analysis interface is currently open to beta-testers only, but we look forward to welcoming additional users. Further information about how to contribute data to the platform can here found here.
Please email to register for updates on the platform or further information.