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Background  There is increasing evidence of the importance of copy number variants (CNV) in genetic diversity among individuals and populations, as well as in some common genetic diseases. We previously characterized a common 32-kb insertion/deletion variant of the  PSORS4  locus at chromosome 1q21 that harbours the  LCE3C  and  LCE3B  genes. This variant allele  (LCE3C_LCE3B-del)  is common in patients with psoriasis and other autoimmune disorders from certain ethnic groups.    Results  Using array-CGH (Agilent 244 K) in samples from the HapMap and Human Genome Diversity Panel (HGDP) collections, we identified 54 regions showing population differences in comparison to Africans. We provided here a comprehensive population-genetic analysis of one of these regions, which involves the 32-kb deletion of the  PSORS4  locus. By a PCR-based genotyping assay we characterised the profiles of the  LCE3C_LCE3B-del  and the linkage disequilibrium (LD) pattern between the variant allele and the tag SNP rs4112788. Our results show that most populations tend to have a higher frequency of the deleted allele than Sub-Saharan Africans. Furthermore, we found strong LD between rs4112788 G  and  LCE3C_LCE3B-del  in most non-African populations (r2 >0.8), in contrast to the low concordance between loci (r2 <0.3) in the African populations.    Conclusions  These results are another example of population variability in terms of biomedical interesting CNV. The frequency distribution of the  LCE3C_LCE3B-del  allele and the LD pattern across populations suggest that the differences between ethnic groups might not be due to natural selection, but the consequence of genetic drift caused by the strong bottleneck that occurred during “out of Africa” expansion.

Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders