Application of whole exome sequencing to identify the genetic defect in hereditary connective tissue disorders

With the completion of the human genome project in 2003 and its ambitious goal of sequencing the entire human genome, the field of genetic medicine has benefited from the development of resources and technology that has accelerated genetic analysis tremendously. In addition, the better understanding of the structure and the function of the human genome has lead to the development of new tools and findings that can be applied to human health and disease. This genetic revolution has opened opportunities for a personalized genomic medicine in which genetic information is used for better diagnosis, treatment and prevention of disease.In the past, the identification of disease genes was a time- and money-consuming and labor-intensive process that often took advantage of the study of large families with multiple affected individuals. By a process called positional cloning, genomic regions were identified through the analysis of the linkage of genetic markers and the disease phenotype within families. Subsequently, it often took years to identify the causal genetic variant (called mutation) in those genomic regions. Only after the identification of mutations, research of the mechanism by which mutations lead to disease could be started with the ultimate hope to find new therapeutic options.Over the last couple of years, the development of new innovative sequencing technologies, has significantly reduced the cost and increased the speed of DNA sequencing. With these next generation sequencing technologies, it has become feasible to sequence the whole genome of single individuals. In this project, we want to apply next generation sequencing technology to perform whole exome sequencing (WES). By applying the latter technique we focus the sequencing effort on the coding part of the genome (the exome) which represents approximately 1% of the human genome but is estimated to harbor about 85% of all disease causing mutations. We plan to apply this new powerful technology to accelerate the process of disease gene/mutation identification in order to enable further pathogenetic studies and to fasten the translation to clinical care.In the initial phase, we will use this strategy to study two disease groups for which the (co)promoters have a strong research record, namely aneurysmal disease and skeletal dysplasias. The strategies that we develop for these disease groups serve as a paradigm for the study of other cardiovascular diseases (such as rhythm disorders and cardiomyopathies) or more common disorders such as osteo-arthrosis and osteoporosis. Moreover, the workflow and the bio-informatics tools developed during the course of this project can be extrapolated to any human condition with a (partly) genetic basis. We will focus on three objectives. One objective aims to combine traditional linkage analysis with WES in order to identify new disease genes. Secondly, we will apply WES to facilitate the molecular screening process to identify mutations in conditions that can be caused by multiple genes. This will significantly decrease the time required for molecular confirmation of a clinical diagnosis. Thirdly, we will use WES to search the genetic cause in sporadic patients with disorders for which no obvious causal genes exist or in patients in whom all known genes were excluded.Ultimately, this project will generate the basis for further functional studies allowing a better understanding of the disease causing mechanism and will deliver a platform that can be used by other researchers to unravel the genetic basis of other diseases.

Keywords:GENE IDENTIFICATION, CARDIOVASCULAR DISORDERS, EXOME SEQUENCING, SKELETAL DISORDERS

Disciplines:Scientific computing, Bioinformatics and computational biology, Genetics, Systems biology, Molecular and cell biology, Public health care, Public health services