The Programme for Medical Genome Research is a successor to the large funding initiatives of the BMBF in human genome research in Germany, the German Human Genome Project (DHGP, 1995-2004) and two phases of the National Genome Research Network. The latter has been supported with over 300 million euros in the years 2001 to 2008. In the programme, researchers in more than 60 locations throughout Germany cooperate in interdisciplinarily organised research consortia that connect large research institutes, universities, clinics, and small and medium-sized enterprises. Efficient utilisation of research capacities on the highest scientific level and of the latest technologies allows the investigation of the molecular cause of diseases with a high incidence and special importance in health policy. These diseases include cancer, cardiovascular diseases, diseases of the nervous system, infection and inflammation, and diseases linked to environmental factors. Application-oriented Alliances focus on the fast transfer of research results into medical and economical exploitation. High-throughput sequencing, the implementation of prognostic and diagnostic gene signatures, and the development of innovative molecular tools are examples.

The scientists cooperate in investigating the function of genes and proteins in the development of hitherto incurable diseases. The aim is to promote the development of innovative methods for prevention, diagnosis, and therapy. The large repertoire of technologies includes methods of functional and structural genomics, proteomics, epigenetics, systems biology, bioinformatics, genetic epidemiology, genotyping, (next-generation) sequencing and proof-of-principle approaches such as animal models. The technology development projects focus on innovative solutions in such fields as chip technology and material production. Standardisation and quality control are benchmark procedures in all areas. In the NGFNtransfer sub-programme, approaches with high and direct potential for added value are developed to the maturity and attractiveness required for industrial exploitation.

The output of the NGFN until 2008 includes over 80 patent applications, 2,400 scientific publications, and cooperation in 60 EU projects. The gain in insight into cause and process of disease development through the identification of molecular target structures can lead to a direct transfer of the results into development and optimisation of diagnostics and therapeutics. A portfolio of results is ready for in-licensing or collaboration partnerships for further development. The scientists succeeded in discovering genetic variations with implications for Alzheimer's disease, epilepsy, depression, Parkinson’s disease, cancer, susceptibility to allergies, adipositas, coronary heart disease, heart failure and enteritis. They developed DNA chips and identified gene signatures for neuroblastoma, Parkinson's disease, prostate cancer and heart failure that constitute a substantial advance in prognosis and diagnosis. They developed tools against autoimmune diseases, established systematic proof-of-principle approaches such as animal models and cell-based assays, used active semiconductor chips to develop highly complex peptide arrays and optimised micro-endoscopes for brain analysis. In one of the world's largest projects for the analysis of disease-causing genetic variations, the genetic information of up to 25,000 patients and controls is currently being examined with the help of DNA chips.