A HPC and Grid enabling framework for genetic linkage analysis of SNPs

Understanding the structure, function and development of the human genome is a key factor to improve the quality of life. In order to achieve this goal developing and using a modern ICT infrastructure is essential, and can exploit next, generation High Performance Computing (HPC) systems beyond the Petaflop scale in a collaborative and efficient way. The genetic linkage analysis of Single Nucleotide Polymorphism (SNP) markers has recently become a very popular for genetic epidemiology and population studies, aiming to discover the genetic correlation in complex diseases. The high computational cost and memory requirements of the major algorithms proposed in the literature make analyses of medium/large data sets very hard on a single CPU. A Grid based facility has hence been set up upon a high-performance infrastructure, the EGEE Grid, in order to create a tool for achieving whole-genome linkage analysis.