Our group is reponsible for or centrally involved in a number of products and solutions, the most important of which are listed below. All are in active development, and many are already in active use.
ELLA is an analysis tool for clinical interpretation of genetic variants, developed with a particular focus on speed, quality and reproducibility. Core features include advanced variant filtering, flexible workflows with team worklists, presentation and structured evaluation of annotation and references, visualization of variants, and automated suggestions based on ACMG-AMP guidelines. In addition, ELLA encourages peer review of important findings and keeps a complete history of all changes, ensuring a high level of information security and patient safety.
ELLA is open source and has been live at our department since early 2018. We are continuously working to expand functionality as well as ELLA’s reach to other interested parties.
FILTUS is a stand-alone tool for working with annotated variant files, e.g. when searching for variants causing Mendelian disease. FILTUS is very flexible in terms of input file formats, and offers efficient filtering and a range of downstream utilities, including statistical analysis of gene sharing patterns, detection of de novo mutations in trios, quality control plots and autozygosity mapping. FILTUS is open source, and whole or parts of the software is in active use by numerous users in our own department and elsewhere.
Publication: Bioinformatics. 2016 May 15;32(10):1592-4.
Pharmacolyzer is a decision support system for pharmacogenomics (PGx). The system consists of three modules. The module for knowledge curation is designed to ensure coherence between PGx medication recommendations developed by the Department of Pharmacology and international knowledge databases such as the PharmGKB. The bioinformatics module provides a pipeline for genotyping of important pharmacogenes (genes involved in metabolisation, transport and uptake of drugs), some of which are not well genotyped by our standard whole genome pipeline. The decision support module assigns structured, personalized medication recommendations to the patients. We are working to integrate the personalized recommendations into the prescription module of the Electronic Health Record system of DIPS ASA.
The Pharmacolyzer is intended to be open source and published in the near future on https://www.pgx.no.
Pedtools (R packages for pedigree analysis) provides a lightweight, but comprehensive tool set for creating, manipulating and visualizing pedigrees with or without marker data. Common pedigree structures are quickly produced with tailor-made functions, while a range of utilities enable modifications like adding or removing individuals, extracting subsets, loop breaking, and merging pedigrees.
Pedtools and related packages are available on GitHub.
Many patients undergoing diagnostic sequencing are willing to share their data to help advance the quality of medical diagnostics and research, but legal barriers generally prevent data from one patient being used to help diagnose other patients, and there is no legal solution to facilitate sharing of Norwegian diagnostic sequencing data systematically at scale.
Norvariom is a planned database of DNA variants from patients that have consented to donate their sequenced genomes. The database will catalogue genetic variation in the Norwegian population and offer diagnostic personnel and researchers the ability to view variants as they co-occur in each sample. The main function of the database will be as a reference dataset, providing information about normal genetic variation.
Norvariom is being implemented as part of the BigMed project. An electronic consent solution developed by USIT in collaboration with our group will be used to collect the consents. A trusted third party (TTP) will keep a link between a pseudonymised ID and the social security number of each participant.
vcpipe is a pipeline framework for diagnostic variant calling. An automation system (named executor) takes care of monitoring a sample and analysis repository, adding new samples/analysis to the system as they appear. New analyses are launched when they are ready, storing their status, run time and logs in a database, and analyses can be monitored and controlled in an interactive web application. All components of an analysis (pipeline scripts, third-party binaries and reference data) are version controlled. vcpipe has been used in our diagnostic variant calling since 2015 and will be available as open-source in the near future.
Trusted Variant eXchange (TVX)
The Trusted Variant eXchange (TVX) is a database solution for sharing of genetic variant classifications among trusted partners. TVX is being developed by DNV GL as part of the BigMed project, with significant input from our research group.
Beacon and MatchMaker Exchange data sharing services
The Global Alliance for Genomics and Health (GA4GH) creates standard protocols for genomic data sharing. As part of the BigMed project, our group has developed an implementation of a GA4GH Beacon data sharing service. We are also implementing a MatchMaker Exchange service for finding patients with similar rare disease profiles.