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Open Access Research article

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

Laia Bassaganyas1234, Eva Riveira-Muñoz12346, Manel García-Aragonés12347, Juan R González345, Mario Cáceres123489, Lluís Armengol12347 and Xavier Estivill1234*

Author Affiliations

1 Genetic Causes of Disease Group, Centre for Genomic Regulation (CRG), Barcelona, E-08003, Spain

2 Universitat Pompeu Fabra (UPF), Barcelona, E-08003, Spain

3 Hospital del Mar Medical Research Institute (IMIM), Barcelona, E-08003, Spain

4 Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, E-08003, Spain

5 Centre de Recerca en Epidemiologia Ambiental (CREAL), Barcelona, E-08003, Spain

6 Laboratori de Retrovirología, IrsiCaixa, Hospital Germans Trias i Pujol, Barcelona, Badalona, 08916, Spain

7 qGenomics Laboratories, Barcelona, E-08003, Spain

8 Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, E-08193, Spain

9 Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, E-08010, Spain

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BMC Genomics 2013, 14:261  doi:10.1186/1471-2164-14-261

Published: 17 April 2013

Abstract

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 rs4112788G 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.

Keywords:
Copy number variants; Psoriasis; Autoimmune disorders; LCE3C_LCE3B-del; Genetic variation; Genetic drift; Human populations