Background: Copy number variants (CNVs) account for a significant proportion of normal phenotypic variation and may have an important role in human pathological variation. The α-defensin cluster on human chromosome 8p23.1 is one of the better-characterized CNVs, in which high copy number variability affecting the DEFA1 and DEFA3 genes has been reported. Moreover, the DEFA3 gene has been found to be absent in a significant proportion of control population subjects. CNVs involving immune genes, such as α-defensins, are possibly contributing to innate immunity differences observed between individuals and influence predisposition and susceptibility to disease. Results: We have tested the DEFA3 absence in 697 samples from different human populations. The proportion of subjects lacking DEFA3 has been found to vary from 10% to 37%, depending on the population tested, suggesting differences in innate immune function between populations. Absence of DEFA3 was correlated with the region's haplotype block structure. African samples showed a higher intra-populational variability together with the highest proportion of subjects without DEFA3 (37%). Association analysis of DEFA3 absence with 136 SNPs from a 100-kb region identified a conserved haplotype in the Caucasian population, extending for the whole region. Conclusion: Complexity and variability are essential genomic features of the α-defensin cluster at the 8p23.1 region. The identification of population differences in subjects lacking the DEFA3 gene may be suggestive of population-specific selective pressures with potential impact on human health.

This work was financially supported by Fundació La Marató de TV3 (993610), Instituto de Salud Carlos III, FIS-ISCIII (G03/203, PI052347 and CIBER-CB06/02/0058) and Departament d'Universitats i Societat de la Informació, Generalitat de Catalunya (2005SGR00008). The Spanish National Genotyping Center (CeGen) is founded by Genoma España. EB is recipient of a FI fellowship from Departament d'Universitats i Societat de la Informació, Generalitat de Catalunya (2003FI00066). NB is a recipient of a BEFI fellowship from Instituto de Salud Carlos III FIS-ISCIII.

http://dx.doi.org/10.1186/1471-2164-8-14