TY - JOUR
T1 - PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity in Latvians, Lithuanians and Taiwanese
AU - Sjakste, Tatjana
AU - Paramonova, Natalia
AU - Wu, Lawrence Shi Shin
AU - Zemeckiene, Zivile
AU - Sitkauskiene, Brigita
AU - Sakalauskas, Raimundas
AU - Wang, Jiu Yao
AU - Sjakste, Nikolajs
N1 - Funding Information:
Costs of this work were partly covered by the following projects: Latvia–Lithuania–Taiwan Cooperation no V320100512 ; Latvian National Research Programme 2010.10.-4/VPP4 ; and ESF project No 2013/0043/1DP/1.1.1.2.0/13/APIA/VIAA/002 . The Lithuanian team acknowledges the Ministry of Education and Science and Research Council of Republic of Lithuania for financial agreements TAP 10043 , TAP-06/2011 and TAP LLT 08/2012 .
PY - 2014
Y1 - 2014
N2 - PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity was investigated in 1438 unrelated subjects from Latvia, Lithuania and Taiwan. In general, polymorphism of each individual locus showed tendencies similar to determined previously in HapMap populations.Main differences concern Taiwanese and include presence of rs2277460 rare allele A not found before in Asians and absence of rs2295827 rare alleles homozygotes TT observed in all other human populations. Observed patterns of SNPs and haplotype diversity were compatible with expectation of neutral model of evolution. Linkage disequilibrium between the rs2295826 and rs2295827 was detected to be complete in Latvians and Lithuanians (DV= 1;r2 = 1) and slightly disrupted in Taiwanese (DV= 0.978; r2 = 0.901). Population differentiation (FST statistics) was estimated from pairwise population comparisons of loci variability, five locus haplotypes and PSMA6 and PSMC6 two locus haplotypes. Latvians were significantly different from all Asians at each of 5 SNPs and from Lithuanians at the rs1048990 and PSMC6 loci. Lithuanian and Asian populations exhibited similarities at the PSMC6 loci and were different at the PSMA6 and PSMA3 SNPs. Considering five locus haplotypes all European populations were significantly different from Asian; Lithuanian population was different from both Latvian and CEU. Allele specific patterns of transcription factor binding sites and splicing signals were predicted in silico and addressed to eventual functionality of nucleotide substitutions and their potential to be involved in human genome evolution and geographical adaptation. Current study represents a novel step toward a systematic analysis of the proteasomal gene genetic diversity in human populations.
AB - PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity was investigated in 1438 unrelated subjects from Latvia, Lithuania and Taiwan. In general, polymorphism of each individual locus showed tendencies similar to determined previously in HapMap populations.Main differences concern Taiwanese and include presence of rs2277460 rare allele A not found before in Asians and absence of rs2295827 rare alleles homozygotes TT observed in all other human populations. Observed patterns of SNPs and haplotype diversity were compatible with expectation of neutral model of evolution. Linkage disequilibrium between the rs2295826 and rs2295827 was detected to be complete in Latvians and Lithuanians (DV= 1;r2 = 1) and slightly disrupted in Taiwanese (DV= 0.978; r2 = 0.901). Population differentiation (FST statistics) was estimated from pairwise population comparisons of loci variability, five locus haplotypes and PSMA6 and PSMC6 two locus haplotypes. Latvians were significantly different from all Asians at each of 5 SNPs and from Lithuanians at the rs1048990 and PSMC6 loci. Lithuanian and Asian populations exhibited similarities at the PSMC6 loci and were different at the PSMA6 and PSMA3 SNPs. Considering five locus haplotypes all European populations were significantly different from Asian; Lithuanian population was different from both Latvian and CEU. Allele specific patterns of transcription factor binding sites and splicing signals were predicted in silico and addressed to eventual functionality of nucleotide substitutions and their potential to be involved in human genome evolution and geographical adaptation. Current study represents a novel step toward a systematic analysis of the proteasomal gene genetic diversity in human populations.
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U2 - 10.1016/j.mgene.2014.03.002
DO - 10.1016/j.mgene.2014.03.002
M3 - Article
AN - SCOPUS:84901786454
SN - 2214-5400
VL - 2
SP - 283
EP - 298
JO - Meta Gene
JF - Meta Gene
IS - 1
ER -