The ultimate relevance of a component of the innate immune system in human physiology is uncovered by the consequence of mutations in the associated gene. We have integrated systems genomics tools to mine, uncover and pathway-map primary deficiencies with high efficiency. Primary immunodeficiency disorders involving innate immunity are characterized by recurrent and life-threatening infections. ImmunoCore profits from an exquisite combination of access to a large collection of informative pedigrees, high throughput genetics/genomics such as high-resolution SNP arrays and deep sequencing as well as functional proteomics of protein complexes. This discovery engine is complemented by biochemical, immunological and imaging technologies to obtain molecular gene-to-phenotype relationships for potentially dozens of components. The initial focus of the work will be on phagocyte deficiencies such as congenital neutropenia syndromes, for which we have very recently identified two novel genetic defects.The proposed investigations are expected to contribute significantly to our understanding of the molecular processes that structure our innate immune system. These studies will not only enable a more comprehensive molecular classification system of primary immunodeficiency disorders, but also improve patient care by enabling molecular diagnosis and classification. Our investigations may serve as the basis for future development of more specific therapies targeting affected signaling cascades.