Showing papers by "Jiayou Chu published in 2009"

Mapping human genetic diversity in Asia

Abstract: Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Distribution of HLA-A, -B, -Cw, and -DRB1 alleles and haplotypes in an isolated Han population in Southwest China.

Abstract: In this study, polymorphisms of human leukocyte antigen (HLA) class I (A, B, and Cw) and class II (DRB1) loci were analyzed in an isolated Han population living in Fengyandong in the Yunnan province of Southwest China (FYDH) using a high-resolution polymerase chain reaction-Luminex typing method. A total of 13 A, 26 B, 15 Cw, and 23 DRB1 alleles of HLA were found in FYDH. The frequencies of A*1101, A*0207, A*2402, B*4601, B*1502, Cw*0102, Cw*0801, DRB1*0901, and DRB1*1202 were >10%. The following haplotypes were common with frequencies >5%: three A-B, four Cw-B, two B-DRB1, two A-B-DRB1, three A-B-Cw, two B-Cw-DRB1, and two A-B-Cw-DRB1 phylogenetic tree and multidimensional scaling analysis based on HLA-A, -B, and -DRB1 allele frequencies of 18 Han populations suggested that FYDH was an isolated Han population, but the analytic result also provided a suggestion that FYDH was genetically related to Chinese Southern Han. According to the characteristics of the HLA allele and haplotype distributions and significantly reduced allelic and haplotypic diversity in FYDH, we deduced that genetic drift and/or selection and subsequent geographic isolation had influenced the distribution characteristics of the HLA gene in FYDH. In addition, significantly reduced allelic and haplotypic diversity in FYDH makes it an ideal homogenous population and very useful model for future investigations of issues related to immunogenetic diseases in the Han population.

The association between HLA-A, -B alleles and major histocompatibility complex class I polymorphic Alu insertions in four populations in China.

Abstract: The study of the association between polymorphic Alu insertions [human leukocyte antigen (HLA)-Alu] at five loci and HLA class I alleles at two loci allows for better identification of the origins and evolution of HLA class I region haplotypes in different populations. In the present study, we determined the frequencies of five HLA-Alus and their associations with HLA-A and -B alleles in Han, Wa, Maonan, and Jinuo populations. Our results showed a strong association between AluHG insertion and HLA-A*02 in all populations studied; however, the associations between AluHJ insertion and HLA-A*1101 and HLA-A*2402 and AluHF insertion and HLA-A*2601 were only observed in Han. The AluMICB insertion showed a strong association with HLA-B*5502 in Han, Maonan, and Jinuo. HLA-A*0101, HLA-A*0201, HLA-A*0203, HLA-A*1101, HLA-A*2402, HLA-A*2601, and HLA-A*3101 alleles were associated with one or more of the three different Alu elements within the alpha block as independent haplotypes, and HLA-A*0101, HLA-A*0201, HLA-A*0203, HLA-A*1101, and HLA-A*2402 alleles were associated with at least two different Alu insertions as a haplotype within the alpha block. We conclude that the HLA class I region haplotypes of the four populations were derived from different progenitor haplotypes, and relatively high rates of recombination between individuals with HLA-A alleles and different HLA-Alus occurred in this region.

[Comparison on mitochondrial ATP6, ATP8 and Cyt b genes between Chinese Tibetans in three different zones: detecting the signature of natural selection on mitochondrial genome].

Abstract: Mitochondrial DNA (mtDNA) differs from nuclear genome in many aspects such as lack of recombination, thus the investigation of mtDNA plays an essential role in human evolutionary history. We compared different sequences (approximately 2 kb) of ATP6, ATP8 and Cyt b genes in mtDNA among Tibetans in three different zones and found that the whole mtDNA sequences of the three genes, ATP6 and ATP 8 genes deviate gradually from neutral model with the increase of altitudes, yet no differences were observed. Also we found that the effect of purifying selection on Cyt b gene was elevated with the decrease of altitudes. Meanwhile, there was a possibility for the adaptive selection in ATP6 gene, which had an enhanced trend with the increase of altitudes. Thus, the geographic environment is the main determinant for selection, namely, different geographic environment has direct effect on selection.