Advances in DNA sequencing technologies have increased attention on genetic variation in somatic tissues. Although long known to cause neoplastic diseases, somatic variation is now being investigated as a pathogenetic mechanism for other diseases. Somatic changes are genomic DNA variations that were not inherited but arise in tissues throughout life. In this issue of the JCI, Magerus-Chatinet et al. explore somatic changes in patients with autoimmune lymphoproliferative syndrome (ALPS), a congenital disease of defective apoptosis and autoimmunity that is usually associated with germline heterozygous mutations in the gene encoding the Fas death receptor. They explain why certain individuals have severe disease manifestations by documenting somatic alterations in the germline normal FAS allele in an unusual population of "double-negative" T cells found in ALPS. Thus, the oncological concept of somatic loss of heterozygosity leading to selected cell expansion also applies to autoimmune diseases.
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