Introduction

Genome sequencing (WGS) is rapidly becoming routine in clinical practice and in everyday life. Processing and interpretation of genomic data requires more computational power and storage than any other task which an ordinary person is likely to come across in their life. One could assume that it should lead to a massive software development effort, however, today, most genomics platforms are either proprietary or academically developed and maintained. We have started building a community of clinicians, researchers and professional software developers from different countries and backgrounds to create the first community-built and fully open-source genomic analysis software platform - Forome.

Two important goals of the Forome Genomics Platform are to support both clinical and research workflows for all flavors of genetic data and to build into the platform an integrated development environment for clinical rules, providing the ability to seamlessly transform research workflows into clinical guidelines, thus facilitating the adoption of genome sequencing into clinical practice.

Forome includes a Variant Curation Tool Anfisa which is based on three simple ideas: using OLAP for genetic data, using curated decision trees for clinical rules, and crowdsourcing of the most difficult cases

From a technical point of view, Forome Anfisa is based on the realization that genetic analysis belongs to the same class of analytical problems as data warehousing and business intelligence, when relatively static data are processed. This is where OnLine Analytical Processing (OLAP) is valuable. Traditional Database Management Systems (DBMS) try to balance efficient modification of data with fast access to it, while OLAP tools specifically focus on achieving the maximum performance for data querying and information retrieval. The OLAP approach is proven with other verticals like financial analysis, sales forecasting, etc., but to the best of our knowledge has never been applied to the big data in genetics.

Forome Anfisa is being actively used in three diverse and complementary projects: SEQaBOO (SEQuencing a Baby for an Optimal Outcome), Brigham Genomic Medicine (BGM)/Harvard Undiagnosed Disease Network Clinical Site and research cohort analysis of purpura fulminans (PF) patients.