A high-throughput system for snp-analysis in population/case control studies of complex traits and diseases

The analysis of subtle differences in genomic DNA frequently occurring in the population (DNA polymorphisms) has become a major focus of research in Medical Sciences with potentially far-reaching clinical consequences. DNA polymorphisms are thought to underly individual variations in risk of disease, differences in response to environmental factors (e.g. diet), and differences in response-to-treatment with medication. For explaining inter-individual variability in particular, it has become clear that rather than analysing individual SNPs (e.g., to predict response-to-treatement or risk-of-disease), it will be necesary to analyse and genotype all relevant polymorphisms in multiple genes involved in particular biological pathways. The Human Genome Project has identified millions of polymorphisms (Single Nucleotide Polymorphisms; SNPs, as well as other types of DNA variations) and the most relevant of these should now be tested in clinically oriented settings for their relevance for the major complex diseases such as diabetes, osteoporosis, cancer, Alzheimer's dementia, Parkinson' s disease, and cardiovascular disease. In addition, they will provide more fundamental biological insight into inter-individual differences with respect to growth and development and the ageing process. Testing such DNA polymorphisms is usually done in large population-based epidemiological cohort studies and in clinical case/control series of patients and involves determining the genotype of hundreds of polymorphisms in thousands of DNA samples. High throughput genotyping is therefore an important activity to identify the polymorphisms "that matter". The present proposal is a joined initiative of several departments within the Erasmus MC, requesting NWO support for the acquisition of a very novel high through-put system for SNP genotyping. The equipment requested (ABI 7900HT) and the service program provided by the manufacturer ("Assay-on-Demand" and Assay-by-Design"), has been released very recently (August 2002). Applied BIosystems (ABI), the largest firm world-wide in the area of genetic analysis equipment, introduced this novel genotyping program in which the 5'nuclease method for genotyping has been optimized and where they now offer, through a collaboration with Celera, a set of 200.000 SNPs (spread over the genome but focussed on genes) for which ready-to-go assays are available ("Assay-on-Demand"). In addition, they offer a service to design tests for a particular SNP of interest, based on customer-provided sequence information ("Assay-by-Design"). This has resulted in high accessibility by taking away the time-consuming assay design/optimization step in the genotyping process. Most importantly, together with this genotyping format a novel (real-time PCR) machine was introduced (ABI 7900HT) offering 384-well format, bar-code plate-identification, and robotic loading. This allows high througput, optimized data-handling, and unattended 24-hr operation for reliable and cost-effective large volume genotyping. Because of the large volume of data generated and the fact that there are multiple users of the SNP genotyping system within the Eramus MC at different locations, there is a strong need for a Laboratory Information Management System (LIMS) for efficient data-storage, -analysis, and -transfer between the genotyping facility and end-users. For this particular purpose ABI has recently introduced the SQL-GT and -GDT packages which form an optimal LIMS for this genotyping format. Erasmus MC has an outstanding track record in the fields of research mentioned above because of several strong research groups and availibility of large, well-characterized population studies and patient collections which have received world-wide acclaim. Because of the size of these collections (currently >40.000 DNA samples) and the expected growth in applying SNP analysis, a facility for high throughput genotyping is necessary. The proposed system will be a crucial part of the infrastructure for genetic epidemiological research of complex diseases and traits at the Erasmus MC.