Supporting translational research on inherited cardiomyopathies through information technology.

OBJECTIVES: The INHERITANCE project, funded by the European Commission, is aimed at studying genetic or inherited Dilated cardiomyopathies (DCM) and at understanding the impact and management of the disease within families that suffer from heart conditions that are caused by DCMs. The biomedical informatics research activity of the project aims at implementing information technology solutions to support the project team in the different phases of their research, in particular in genes screening prioritization and new gene-disease association discovery. METHODS: In order to manage the huge quantity of scientific, clinical and patient data generated by the project several advanced biomedical informatics tools have been developed. The paper describes a layer of software instruments to support translation of the results of the project in clinical practice as well as to support the scientific discovery process. This layer includes data warehousing, intelligent querying of the phenotype data, integrated search of biological data and knowledge repositories, text mining of the relevant literature, and case based reasoning. RESULTS: At the moment, a set of 1,394 patients and 9,784 observations has been stored into the INHERITANCE data warehouse. The literature database contains more than 1,100,000 articles retrieved from the Pubmed and generically related to cardiac diseases, already analyzed for extracting medical concepts and genes. CONCLUSIONS: After two years of project the data warehouse has been completely set up and the text mining tools for automatic literature analysis have been implemented and tested. A first prototype of the decision support tool for knowledge discovery and gene prioritization is available, but a more complete release is still under development.

Familial dilated cardiomyopathy. Clinical and genetic characteristics.

Familial dilated cardiomyopathy (F-DCM) describes a clinically and genetically heterogeneous group of diseases, mostly inherited as autosomal dominant traits, having idiopathic left ventricular dilatation and dysfunction as a common phenotype. The age of onset, rate of progression, disease complications, as well as overall prognosis and outcome vary both amongst and within families. Clinical traits, both cardiac and extracardiac, may recur in association with the DCM phenotype. The former include conduction defects, structural abnormalities such as left ventricular noncompaction, of right ventricular involvement, and recurrence of atrial or ventricular arrhythmias; the latter commonly affect the musculoskeletal (myopathies/dystrophies, both clinically overt and subclinical), ocular, auditory, nervous, and integument systems. These traits may help guide genetic testing. In parallel to the clinical heterogeneity, F-DCM also shows genetic heterogeneity: more than 40 genes have been causally linked to F-DCM, with mutations recurring more commonly in a few known genes, and less frequently in rare, less commonly known genes. Based on the known prevalence of mutations in disease genes, more than 50% of F-DCM cases can be regarded as still genetically orphan, implying that further disease genes have to be discovered. Family screening and genetic testing are now established as the gold standard for diagnosis, care, and prevention in F-DCM. Diagnostic tests are performed using Sanger-based sequencing. Furthermore, new biotechnology tools, based on next-generation sequencing, are now being implemented in the research setting and will dramatically modify the future of the nosology of F-DCM.