Posts for the month of April 2012

Observ-OM data model published

Observ-OM and Observ-TAB, the Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information, is published in Human Mutation. Genetic and epidemiological research increasingly employs large collections of phenotypic and molecular observation data from high quality human and model organism samples. Standardization efforts have produced a few simple formats for exchange of these various data, but a lightweight and convenient data representation scheme for all data modalities does not exist, hindering successful data integration, such as assignment of mouse models to orphan diseases and phenotypic clustering for pathways. We report a unified system to integrate and compare observation data across experimental projects, disease databases, and clinical biobanks. The core object model (Observ-OM) comprises only four basic concepts to represent any kind of observation: Targets, Features, Protocols (and their Applications), and Values. An easy-to-use file format (Observ-TAB) employs Excel to represent individual and aggregate data in straightforward spreadsheets. The systems have been tested successfully on human biobank, genome-wide association studies, quantitative trait loci, model organism, and patient registry data using the MOLGENIS platform to quickly setup custom data portals. Our system will dramatically lower the barrier for future data sharing and facilitate integrated search across panels and species. All models, formats, documentation, and software are available for free and open source (LGPLv3) at

CHD7 mutation database published

We are proud with another MOLGENIS for the CHARGE syndrome using Observ-OM published in Human Mutation. CHD7 is a member of the chromodomain helicase DNA-binding (CHD) protein family that plays a role in transcription regulation by chromatin remodeling. Loss-of-function mutations in ICHD7 are known to cause CHARGE syndrome, an autosomal dominant malformation syndrome in which several organ systems, for example the central nervous system, eye, ear, nose and mediastinal organs, are variably involved. In this paper, we review all the currently described ICHD7 variants, including 184 new pathogenic mutations found by our laboratories. In total, we compiled 531 different pathogenic ICHD7 alterations from 515 previously published patients with CHARGE syndrome and 296 unpublished patients analyzed by our laboratories. The mutations are equally distributed along the coding region of ICHD7 and most are nonsense or frameshift mutations. Most mutations are unique, but we identified 96 recurrent mutations, predominantly arginine to stop codon mutations. We built a locus-specific database listing all the variants that is easily accessible at In addition, we summarize the latest data on CHD7 expression studies, animal models and functional studies, and we discuss the latest clinical insights into CHARGE syndrome.