Abstract
In order to investigate the polymorphism of Alu insertions (POALINs) in the HLA region, we genotyped ten Alu loci (AluMICB, AluTF, AluHJ, AluHG, AluHF in the HLA class I region and AluDPB2, AluDQA2, AluDQA1, AluDRB1, AluORF10 in the HLA class II region) to determine their allele frequencies and associations with the HLA-A, HLA-B, HLA-C and HLA-DRB1 genes in the Chinese Han population. Our results showed the ten-loci POALINs varied in frequency between 0.003 and 0.425. By comparing the data of the ten-loci POALIN in Chinese Han with Japanese and Caucasian data, marked differences were observed between the three ethnic groups at the allelic or haplotypic levels. Each POALIN was in significant linkage disequilibrium with a variety of HLA-A, -B, -C and -DRB1 alleles, and was associated with a variety of HLA-A, -B, -C and -DRB1 allele in Chinese Han. This comparative study of multilocus POALINs in the HLA class I and II regions of the Chinese Han population shows that POALINs alone or as haplotypes together with the HLA class I and II alleles are informative genetic markers for the identification of HLA class I and II allele and variations, such as crossing over events within the same and/or different populations.
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This work was supported by grant from Peking Union Medical College Talented Youth Project, Yunnan Provincial Science and Technology Department (2013FZ131) and National Natural Science Foundation of China (31270030).
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Communicated by S. Hohmann.
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Supplementary Fig. 1: A map of the locations of the ten POALINs with the (a) HLA class II and (b) class I regions of the MHC on chromosome 6p21.3.
Supplementary Fig. 2: The amplification products of the five Alu II-PCR assays run on 2 % agarose gels and stained with ethidiumbromide.
Supplementary Fig. 3: Example of the electrophoretic AluMICB PCR results for some of the HLA-B*13:01 heterozygotes, HLA-B*13:01 homozygotes and HLA-B*13:02 heterozygotes.
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Shi, L., Kulski, J.K., Zhang, H. et al. Association and differentiation of MHC class I and II polymorphic Alu insertions and HLA-A, -B, -C and -DRB1 alleles in the Chinese Han population. Mol Genet Genomics 289, 93–101 (2014). https://doi.org/10.1007/s00438-013-0792-2
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DOI: https://doi.org/10.1007/s00438-013-0792-2