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

Laia Bassaganyas, Eva Riveira-Muñoz, Manel García-Aragonés, Juan R. González, Mario Cáceres, Lluís Armengol, Xavier P. Estivill

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish
Article number261
JournalBMC Genomics
Volume14
Issue number1
DOIs
Publication statusPublished - 17 Apr 2013
Externally publishedYes

Fingerprint

Psoriasis
Demography
Linkage Disequilibrium
Population
Alleles
Ethnic Groups
HapMap Project
Genetic Drift
Inborn Genetic Diseases
Genetic Selection
Population Genetics
Human Genome
Gene Frequency
Single Nucleotide Polymorphism
Chromosomes
Polymerase Chain Reaction
Genes

Keywords

  • Autoimmune disorders
  • Copy number variants
  • Genetic drift
  • Genetic variation
  • Human populations
  • LCE3C_LCE3B-del
  • Psoriasis

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Bassaganyas, L., Riveira-Muñoz, E., García-Aragonés, M., González, J. R., Cáceres, M., Armengol, L., & Estivill, X. P. (2013). Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders. BMC Genomics, 14(1), [261]. https://doi.org/10.1186/1471-2164-14-261

Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders. / Bassaganyas, Laia; Riveira-Muñoz, Eva; García-Aragonés, Manel; González, Juan R.; Cáceres, Mario; Armengol, Lluís; Estivill, Xavier P.

In: BMC Genomics, Vol. 14, No. 1, 261, 17.04.2013.

Research output: Contribution to journalArticle

Bassaganyas, L, Riveira-Muñoz, E, García-Aragonés, M, González, JR, Cáceres, M, Armengol, L & Estivill, XP 2013, 'Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders', BMC Genomics, vol. 14, no. 1, 261. https://doi.org/10.1186/1471-2164-14-261
Bassaganyas L, Riveira-Muñoz E, García-Aragonés M, González JR, Cáceres M, Armengol L et al. Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders. BMC Genomics. 2013 Apr 17;14(1). 261. https://doi.org/10.1186/1471-2164-14-261
Bassaganyas, Laia ; Riveira-Muñoz, Eva ; García-Aragonés, Manel ; González, Juan R. ; Cáceres, Mario ; Armengol, Lluís ; Estivill, Xavier P. / Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders. In: BMC Genomics. 2013 ; Vol. 14, No. 1.
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