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The immune defense against extracellular pathogens is largely dependent on antibody production. Class switch recombination and somatic hypermutation shape the secondary antibody repertoire in peripheral lymphoid tissue. In the past few years, a series of primary immune deficiencies characterized by defects in these processes and collectively referred to as hyper-IgM syndromes, have been described. Careful investigation of these rare “experiments of nature” has enabled to identify novel genes and molecular events that drive terminal B-cell differentiation. Abnormalities in these genes are likely involved also in lymphoid tumorigenesis and autoimmunity.