Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders
Bassaganyas, Laia (Centre de Regulació Genòmica)
Riveira Muñoz, Eva (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa)
García Aragonés, Manel (Centre de Regulació Genòmica)
González, Juan Ramón (Institut Hospital del Mar d'Investigacions Mèdiques)
Cáceres Aguilar, Mario (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Armengol, Lluís (Centre de Regulació Genòmica)
Estivill, Xavier (Centre de Regulació Genòmica)

Date:	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.
Grants:	European Commission 201413 Ministerio de Economía y Competitividad SAF2008-00357 Agència de Gestió d'Ajuts Universitaris i de Recerca 2009/SGR-0008
Note:	Altres ajuts: the study was supported by grants from European Commission (AnEuploidy -LSHG-CT-2006-037627)
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Copy number variants ; Psoriasis ; Autoimmune disorders ; LCE3C_LCE3B-del ; Genetic variation ; Genetic drift ; Human populatio
Published in:	BMC genomics, Vol. 14 (2013) , art. 261, ISSN 1471-2164

DOI: 10.1186/1471-2164-14-261
PMID: 23594316

11 p, 754.8 KB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut d'Investigació en Ciencies de la Salut Germans Trias i Pujol (IGTP)
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Biotecnologia i de Biomedicina (IBB)
Articles > Research articles
Articles > Published articles