Japanese In Tokyo Research Articles

Playback interviews as a method for research on language ideologies: Citationality, reflexivity, and rapport in interdiscursive encounters

Abstract This contribution deals with the use of playback interviews in interactional sociolinguistics, a method wherein participants review audio or video recordings of their conversations and provide retrospective commentary. I first outline a brief history of the development of the playback method and how it was incorporated into the interactional sociolinguistic research agenda. As theoretical frameworks for playback interviews and their application to research on language ideologies remain underexplored, this article introduces three concepts from linguistic anthropology—citationality, reflexivity, and interdiscursivity—to theorize playback interviews from a semiotic perspective. Departing from these theories, playback interviews are contextualized within broader social dynamics, including participation frames, power, and rapport that are inherent in the interviewing process. Drawing on source recordings from interactions between L1 and European L2 users of Japanese in Tokyo, and playback sessions with the L2 users, I illustrate how playback interviews contribute to language-ideological inquiries, for example, perceptions of style and code-switching. The analysis showcases the method’s potential to unveil participants’ metapragmatic awareness and explore the intersection of linguistic structure, practice, and ideology. Playback interviews are positioned as a valuable tool for investigating language ideologies, offering new methodological perspectives through retrospection and reflection on communication.

The landscape of very important pharmacogenes variants and potential clinical relevance in the Chinese Jingpo population: a comparative study with worldwide populations.

Pharmacogenomics is a facet of personalized medicine that explores how genetic variants affect drug metabolism and adverse drug reactions. Therefore, this study aims to detect distinct pharmacogenomic variations among the Jingpo population and explore their clinical correlation with drug metabolism and toxicity. Agena MassARRAY Assay was used to genotype 57 VIP variants in 28 genes from 159 unrelated Jingpo participants. Subsequently, the chi-squared test and Bonferroni's statistical tests were utilized to conduct a comparative analysis of genotypes and allele frequencies between the Jingpo population and the other 26 populations from the 1000 Genome Project. We discovered that the KHV (Kinh in Ho ChiMinh City, Vietnam), CHS (Southern Han Chi-nese, China) and JPT (Japanese in Tokyo, Japan) exhibited the smallest differences from the Jingpo with only 4 variants, while ESN (Esan in Nigeria) exhibited the largest differences with 30 variants. Besides, a total of six considerably different loci (rs4291 in ACE, rs20417 in PTGS2, rs1801280 and rs1799929 in NAT2, rs2115819 in ALOX5, rs1065852 in CYP2D6, p < 3.37 × 10-5) were identified in this study. According to PharmGKB, rs20417 (PTGS2), rs4291 (ACE), rs2115819 (ALOX5) and rs1065852 (CYP2D6) were found to be associated with the metabolism efficiency of non-steroidal anti-inflammatory drugs (NSAIDs), aspirin, montelukast and tamoxifen, respectively. Meanwhile, rs1801280 and rs1799929 (NAT2) were found to be related to drug poisoning with slow acetylation. Our study unveils distinct pharmacogenomic variants in the Jingpo population and discovers their association with the metabolic efficiency of NSAIDs, montelukast, and tamoxifen.

AI-SNPs screening based on the whole genome data and research on genetic structure differences of subcontinent populations.

The genetic structure differences in population is one of the key elements in medical research involving multi-population samples. A set of ancestry-informative single nucleotide polymorphisms (AI-SNPs) can be utilized to analyze genetic component of a population, infer ancestral origin of individuals and pre-filter samples to reduce the impact of population genetic structure differences on medical research. However, most of the published studies were focused on revealing the differences between populations of continents or regions of a continent. In this paper, AI-SNPs were screened by calculating FST value in each pair of five East Asian populations: Japanese in Tokyo (JPT), Han Chinese in Beijing (CHB), Southern Han Chinese (CHS), Chinese Dai in Xishuangbanna (CDX) and Kinh in Ho Chi Minh City (KHV) in the 1000 Genomes Project phase 3 (GRCh37.p13) to analyze differences in subcontinent populations. The results demonstrate that the five East Asian populations in our study were assigned to three clusters: JPT, CHB and CHS, CDX and KHV. A set of AI-SNPs can be used for analysis of individual genetic composition and selection of representative individuals. Individuals with over 80% population representative genetic components have good representativeness of a population. This paper demonstrated the practical value of the method, which was performed to verify the ancestral composition and select representative samples with a panel of screened AI-SNPs by FST value, thereby reducing the influence of genetic structure differences in subcontinent populations on population-related medical research.

Genetic polymorphisms of interluekin-17A gene in Black-clothes Zhuang population in Guangxi

Objective To explore the distribution characteristics of rs3819024 and rs2275913 polymorphisms of interleukin-17A (IL-17A) gene in Black-clothes Zhuang population in Guangxi and the polymorphism different among ethnic populations. Methods The polymorphisms of rs3819024 and rs2275913 of IL-17A gene in 115 Black-clothes Zhuang subjects were genotyped by SNaPshot technique. And used statistical methods to compare the differences in the distribution of these polymorphisms across sexes and populations. Results There were AA, AG and GG genotypes at rs3819024 and rs2275913 of IL-17A gene of Black-clothes Zhuang population in Guangxi, and AG genotype was the most common genotype in both loci. The frequencies of AA, AG and GG genotypes at rs3819024 were 15.6%, 54.8% and 29.6%, respectively, and the frequencies of AA, AG and GG genotypes at rs2275913 were 27.8%, 51.3% and 20.9%, respectively. G and A alleles were commonly found at rs3819024 and rs2275913, respectively, and their distribution frequencies were 57.0% and 53.5%, respectively. The genotype and allele frequency of rs3819024 and rs2275913 had no significant difference between male and female ( P>0.05). The genotype and allele of rs3819024 were significantly different from Japanese in Tokyo, Japan (JPT), Yoruba in Ibadan, Nigeria (YRI), Gujarati Indians in Houston (GIH) and Utah residents with Northern and Western European ancestry from the CEPH collection (CEU) populations published by the 1000 Genome Project (all P<0.05). There was no statistically significant different from Han Chinese in Beijing, China (CHB) population ( P>0.05)。The distribution frequency of each genotype and allele at rs2275913 site were significantly different from YRI, GIH and CEU ( P<0.05), and there was no statistically significant different from HCB ( P>0.05). Compared with JPT, the difference in genotype distribution frequency was not statistically significant ( P<0.05), but the difference in allele distribution frequency was statistically significant ( P<0.05). Conclusion The locus polymorphisms of rs3819024 and rs2275913 of IL-17A gene have difference among different races and regions. 摘要： 目的 探讨广西黑衣壮人群白细胞介素 17A 基因 ( IL-17A) rs3819024、rs2275913 位点的多态性分布特点和 不同人群间的多态性差异。 方法 采取多重单碱基延伸法 (SNaPshot) 方法对 115 例广西黑衣壮人群 IL-17A 基因 rs3819024、rs2275913 位点进行基因分型检测, 并比较不同性别及人群分布差异。 结果 广西黑衣壮人群 IL-17A 基因 rs3819024 和 rs2275913 位点均存在 AA、AG、GG 3 种基因型, 两位点基因型分布均以 AG 基因型多见, 其中 rs3819024 位 点 AA、AG、GG 基因型的分布频率分别为 15.6%、54.8%、29.6%; rs2275913 位点 AA、AG、GG 基因型的分布频率分别为 27.8%、51.3%、20.9%。rs3819024 和 rs2275913 位点分别以 G 和 A 等位基因多见, 分布频率分别为 57.0% 和 53.5%。rs3819024 和 rs2275913 两位点基因型及等位基因频率在广西黑衣壮人群男女性别间比较, 差异无统计学意义 ( P>0.05)。rs3819024 位点基因型及等位基因频率与千人基因组计划 (1000 Genomes) 数据库公布的日本人群 (JPT)、非洲 尼日利亚人群 (YRI)、印第安人群 (GIH)、欧洲人群 (CEU) 比较, 差异均有统计学意义 ( P<0.05); 与北京汉族人群 (HCB) 比较差异无统计学意义 ( P>0.05)。rs2275913 位点基因型及等位基因频率与 YRI、GIH、CEU 人群比较差异均有统计学 意义 ( P<0.05), 与 HCB 人群比较差异无统计学意义 ( P>0.05); 而与 JPT 人群相比, 基因型频率差异无统计学意义 ( P>0.05), 但等位基因频率差异有统计学意义 ( P<0.05)。 结论 IL-17A 基因rs3819024、rs2275913 基因位点多态性在不同 种族和地区间存在差异。

Characterization of LILRB3 and LILRA6 allelic variants in the Japanese population.

Leukocyte immunoglobulin (Ig)-like receptors (LILRs) are encoded by members of a human multigene family, comprising 11 protein-coding genes and two pseudogenes. Among the LILRs, LILRB3 and LILRA6 show the highest homology with each other, along with high allelic and copy number variations. Therefore, it has been difficult to discriminate between them, both genetically and functionally, precluding disease association studies of LILRB3 and LILRA6. In this study, we carefully performed variant screening of LILRB3 and LILRA6 by cDNA cloning from Japanese individuals and identified four allelic lineages showing significantly high non-synonymous-to-synonymous ratios in pairwise comparisons. Furthermore, the extracellular domains of the LILRB3*JP6 and LILRA6*JP1 alleles were identical at the DNA level, suggesting that gene conversion-like events diversified LILRB3 and LILRA6. To determine the four allelic lineages from genomic DNA, we established a lineage typing method that accurately estimated the four allelic lineages in addition to specific common alleles from genomic DNA. Analysis of LILRA6 copy number variation revealed one, two, and three copies of LILRA6 in the Japanese-in-Tokyo (JPT) population. Flow cytometric analysis showed that an anti-LILRB3 antibody did not recognize the second most common lineage in the Japanese population, indicating significant amino acid differences across the allelic lineages. Taken together, our findings indicate that our lineage typing is useful for classifying the lineage-specific functions of LILRB3 and LILRA6, serving as the basis for disease association studies.

Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population.

A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese.

Genetic polymorphisms of pharmacogenomic VIP variants in the Dai population from Yunnan province.

BackgroundPharmacogenomics plays a crucial role in individualized therapy, but the variant information of pharmacogenomics in the Dai population is limited. We therefore aimed to screen very important pharmacogenetic (VIP) in the Dai population and compared differences between Dai and other 25 populations.MethodsIn this study, we genotyped 73 VIP variants from the PharmGKB and compared genotype distribution of variants in Dai with other 25 populations by χ2 test. To assess the genetic relationship among 26 populations, we performed the structure analysis. In addition, pair‐wise F‐statistics (Fst) was calculated to measure the population differentiation.ResultsWe found 12, 10, 13, 17, 11, 39, 46, 46, 45, 43, 49, 46, 46, 46, 49, 45, 41, 42, 48, 53, 45, 50, 50, 51, 47, and 50 significantly different variants in Dai compared with other 25 populations. Genetic structure analysis showed Dai had close relationships with CDX (Chinese Dai in Xishuangbanna), CHB (Han Chinese in Beijing), JPT (Japanese in Tokyo), and KHV (Kinh in Ho Chi Minh City, Vietnam). Moreover, Dai is the most similar to KHV according to Fst analysis.ConclusionsOur study complement the pharmacogenomics information of Dai population from Yunnan province and provide a theoretical basis for personalized medicine.

Multiomics Evaluation of Gastrointestinal and Other Clinical Characteristics of COVID-19

Since December 2019, coronavirus disease 2019 (COVID-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has produced a worldwide panic. Beyond the principal human-to-human transmission method by droplet and contact, there is still limited knowledge about possible alternate transmission methods to guide clinical care. Recent clinical studies have observed digestive symptoms in patients with COVID-19,1 possibly because of the enrichment and infection of SARS-CoV-2 in the gastrointestinal tract, mediated by virus receptor of angiotensin converting enzyme 2 (ACE2),2 which suggests the potential for a fecal-oral route of SARS-CoV-2 transmission.3,4 However, there is still a large gap in the biological knowledge of COVID-19. In this study, via a bulk-to-cell strategy focusing on ACE2, we performed an integrated omics analysis at the genome, transcriptome, and proteome levels in bulk tissues and single cells across species to decipher the potential routes for SARS-CoV-2 infection in depth.

WITHDRAWN: Genetic polymorphisms of pharmacogenomic VIP variants in the Wa population from southwest China

Abstract Inter-population differences in drug responses are primarily associated with pharmacogenes. Widespread researches have been focused on major populations, but less is known about minorities, such as Wa in southwestern China. The study aimed to investigate the genotype frequencies of randomly selected very important pharmacogenetic (VIP) variants and population genetics in the Wa ethnic. We genotyped 71 VIP variants selected from the PharmGKB database and compared our data with 11 HapMap populations. We found that the frequency distribution of Wa is most similar with CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan), and genotype frequencies of VKORC1, PGST2 and VDR in Wa differed significantly between Wa and the other populations, excluding CHB and JPT (p

Microhaplotype: Ability of personal identification and being ancestry informative marker

Microhaplotype is a new type of genetic marker. Due to the multi-allelic characteristic, microhaplotype could have much better personal identification ability compared to the bi-allelic SNPs. Microhaplotype could also have alleles associated with specific populations. With this research, phased data from 1000 genomes project were used to evaluate the ability as personal identification and ancestry informative marker. Totally 50 previously selected microhaplotype loci and 568 unrelated individuals from six regions around the globe were enrolled. Including Africans, Europeans, East Asians, Americans. Specifically from African Caribbeans in Barbados (ACB), Americans of African Ancestry in SW USA (ASW), Northern and Western European Ancestry (CEU), Han Chinese in Beijing, China (CHB), Southern Han Chinese (CHS) and Japanese in Tokyo, Japan (JPT). The range of SNPs number per locus among the 50 loci has a range from 3 to 10. The allele number range of the 50 microhaplotype is 4–47. The median heterozygosity for these 50 loci is 0.67 for the 6 populations studied and ranges from 0.07–0.92. To assess the power as AIM, we applied standard population analysis approach of STRUCTURE analysis. Visual inspection of cluster plots suggests a close match between the co-ancestry patterns seen in ACB and ASW as well as in CHB, CHS and JPT.

Genetic polymorphisms of multidrug and toxin extrusion proteins (MATE1 and MATE2) in South Indian population.

Introduction: Drug transporters are key determinants of pharmacokinetic and pharmacodynamic profiles of certain drugs. SLC47A1 (MATE1) and SLC47A2 (MATE2) are major efflux transporters involved in the hepatic and renal excretion of many cationic drugs including metformin. Our study was proposed to determine the normative frequencies of the single nucleotide polymorphisms (SNPs) rs2289669 and rs12943590 in the SLC47A1 and SLC47A2 genes, respectively, in South Indian population and also to compare those with those of the HapMap populations. Methods: One hundred two unrelated healthy volunteers from South India were enrolled in the study. Genomic DNA was extracted by ‘phenol-chloroform extraction method’ from the peripheral blood leucocytes and genotyping was accomplished by real-time polymerase chain reaction using TaqMan SNP genotyping assay method. Results: In contrast to other populations, the minor allele in SLC47A1 gene was found to be "G" with a frequency of 46.6% in South Indian population. The populations of Hans Chinese in Beijing (HCB) [P = 0.017] and Japanese in Tokyo (JPT) [P < 0.001] had significantly different genotype and allele frequencies (SNP rs2289669) compared to those of South Indian population. Similarly, in the SNP rs12943590 of SLC47A2 gene, the genotype and allele frequencies of South Indian population differed significantly from those of Yoruba in Ibadan, Nigeria (YRI) [P < 0.001] and Utah residents with Northern and Western European ancestry (CEU) [P = 0.005] populations. Conclusion: Thus, the allele and genotype distributions of SLC47A1 and SLC47A2 gene polymorphisms were established in South Indian population and were found to be different from the frequencies of other ethnicities.

Comparison of Genetic Variants in Cancer-Related Genes between Chinese Hui and Han Populations

BackgroundThe Chinese Hui population, as the second largest minority ethnic group in China, may have a different genetic background from Han people because of its unique demographic history. In this study, we aimed to identify genetic differences between Han and Hui Chinese from the Ningxia region of China by comparing eighteen single nucleotide polymorphisms in cancer-related genes.MethodsDNA samples were collected from 99 Hui and 145 Han people from the Ningxia Hui Autonomous Region in China, and SNPs were detected using an improved multiplex ligase detection reaction method. Genotyping data from six 1000 Genomes Project population samples (99 Utah residents with northern and western European ancestry (CEU), 107 Toscani in Italy (TSI), 108 Yoruba in Ibadan (YRI), 61 of African ancestry in the southwestern US (ASW), 103 Han Chinese in Beijing (CHB), and 104 Japanese in Tokyo (JPT)) were also included in this study. Differences in the distribution of alleles among the populations were assessed using χ2 tests, and FST was used to measure the degree of population differentiation.ResultsWe found that the genetic diversity of many SNPs in cancer-related genes in the Hui Chinese in Ningxia was different from that in the Han Chinese in Ningxia. For example, the allele frequencies of four SNPs (rs13361707, rs2274223, rs465498, and rs753955) showed different genetic distributions (p<0.05) between Chinese Ningxia Han and Chinese Ningxia Hui. Five SNPs (rs730506, rs13361707, rs2274223, rs465498 and rs753955) had different FST values (FST >0.000) between the Hui and Han populations.ConclusionsThese results suggest that some SNPs associated with cancer-related genes vary among different Chinese ethnic groups. We suggest that population differences should be carefully considered in evaluating cancer risk and prognosis as well as the efficacy of cancer therapy.

The population genetics of pharmacogenomics VIP variants in the Sherpa population

Polymorphic distributions of pharmacogenes among some ethnicities are under-represented in current pharmacogenetic research. Particularly, there is a paucity of pharmacogenetic information in the Sherpa population in Tibet. We used the Sequenom MassARRAY single nucleotide polymorphism (SNP) genotyping technology to detect 86 very important pharmacogene (VIP) variants in Sherpas and compared the genotypic frequencies of these variants with HapMap populations. Overall, 59 of the 60 previously reported variants in the HapMap populations were found in our study. We found minimal differences between populations of Sherpas and Chinese Han in Beijing (CHB), Chinese in Metropolitan Denver, Colorado (CHD), Japanese in Tokyo, Japan (JPT), and Mexicans in Los Angeles, California (MEX) after a strict Bonferroni correction. Only 8, 4, 5, 4 VIP genotypes, respectively, were different in these groups. Additionally, pairwise FST values and clustering analyses showed that the VIP variants in the Sherpa population exhibited a close genetic affinity with the CHB and JPT populations, but they were most similar to the CHD population. Our results contribute to a better understanding of the molecular basis underlying ethnic differences in drug response, which may potentially benefit the development of personalized medicine for the Sherpa population.

Identification and Characterization of CD300H, a New Member of the Human CD300 Immunoreceptor Family

Recruitment of circulating monocytes and neutrophils to infection sites is essential for host defense against infections. Here, we identified a previously unannotated gene that encodes an immunoglobulin-like receptor, designated CD300H, which is located in the CD300 gene cluster. CD300H has a short cytoplasmic tail and associates with the signaling adaptor proteins, DAP12 and DAP10. CD300H is expressed on CD16(+) monocytes and myeloid dendritic cells. Ligation of CD300H on CD16(+) monocytes and myeloid dendritic cells with anti-CD300H monoclonal antibody induced the production of neutrophil chemoattractants. Interestingly, CD300H expression varied among healthy subjects, who could be classified into two groups according to "positive" and "negative" expression. Genomic sequence analysis revealed a single-nucleotide substitution (rs905709 (G → A)) at a splice donor site on intron 1 on either one or both alleles. The International HapMap Project database has demonstrated that homozygosity for the A allele of single nucleotide polymorphism (SNP) rs905709 ("negative" expression) is highly frequent in Han Chinese in Beijing, Japanese in Tokyo, and Europeans (A/A genotype frequencies 0.349, 0.167, and 0.138, respectively) but extremely rare in Sub-Saharan African populations. Together, these results suggest that CD300H may play an important role in innate immunity, at least in populations that carry the G/G or G/A genotype of CD300H.

A method to associate all possible combinations of genetic and environmental factors using GxE landscape plot.

Genome-wide association studies (GWAS) and linkage analysis has identified many single nucleotide polymorphisms (SNPs) related to disease. There are many unknown SNPs whose minor allele frequencies (MAFs) as low as 0.005 having intermediate effects with odds ratio between 1.5~3.0. Low frequency variants having intermediate effects on disease pathogenesis are believed to have complex interactions with environmental factors called gene-environment interactions (GxE). Hence, we describe a model using 3D Manhattan plot called GxE landscape plot to visualize the association of p-values for gene-environment interactions (GxE). We used the Gene-Environment iNteraction Simulator 2 (GENS2) program to simulate interactions between two genetic loci and one environmental factor in this exercise. The dataset used for training contains disease status, gender, 20 environmental exposures and 100 genotypes for 170 subjects, and p-values were calculated by Cochran-Mantel-Haenszel chi-squared test on known data. Subsequently, we created a 3D GxE landscape plot of negative logarithm of the association of p-values for all the possible combinations of genetic and environmental factors with their hierarchical clustering. Thus, the GxE landscape plot is a valuable model to predict association of p-values for GxE and similarity among genotypes and environments in the context of disease pathogenesis.AbbreviationsGxE - Gene-environment interactions, GWAS - Genome-wide association study, MAFs - Minor allele frequencies, SNPs - Single nucleotide polymorphisms, EWAS - Environment-wide association study, FDR - False discovery rate, JPT+CHB - HapMap population of Japanese in Tokyo, Japan - Han Chinese in Beijing.

Genetic polymorphisms in very important pharmacogenomic (VIP) variants in the Tibetan population.

Genetic polymorphisms of very important pharmacogenomic (VIP) variants are important for personalized medicine. However, these have not been extensively studied in the Tibetan population. In this study, 82 VIP variants were detected in the Tibetan and Han (HAN) populations from northwestern China. Subsequently, we compared the differences between the Tibetan population and ten populations, including the HAN, Japanese in Tokyo (JPT), Mexican ancestry in Los Angeles (MEX), Toscans in Italy (TSI), African ancestry in Southwest USA (ASW), Luhya in California Webuye, Kenya (LWK), Gujarati Indians in Houston, Texas (GIH), Maasai in Kinyawa, Kenya (MKK), Yoruba in Ibadan, Nigeria (YRI), and Utah residents with Northern and Western European ancestry from the CEPH collection (CEU). Using the χ(2) test, we identified differences in the frequency distribution of 4, 4, 7, 10, 11, 11, 13, 15, 19, and 20 loci in the Tibetan population, compared to the HAN, JPT, MEX, TSI, ASW, LWK, GIH, MKK, YRI, and CEU populations, respectively [P < 0.05/(82*10)]. rs2115819, rs9934438, and rs689466, located in the ALOX5 (arachidonate 5-lipoxygenase), VKORC1 (vitamin K epoxide reductase complex, subunit 1) and PTGS2 (prostaglandin-endoperoxide synthase 2) genes, respectively, in the Tibetan population were different from those in most of the populations. Our results complement the information provided by the database of pharmacogenomics on Tibetan people, and provide an avenue for personalized treatment in the Tibetan population.

Genetic polymorphisms of VIP variants in the Tajik ethnic group of northwest China.

BackgroundIndividual response to medications varies significantly among different populations, and great progress in understanding the molecular basis of drug action has been made in the past 50 years. The field of pharmacogenomics seeks to elucidate inherited differences in drug disposition and effects. While we know that different populations and ethnic groups are genetically heterogeneous, we have not found any pharmacogenomics information regarding minority groups, such as the Tajik ethnic group in northwest China.ResultsWe genotyped 85 Very Important Pharmacogene (VIP) variants selected from PharmGKB in 100 unrelated, healthy Tajiks from the Xinjiang Uygur Autonomous Region and compared our data with HapMap data from four major populations around the world: Han Chinese (CHB), Japanese in Tokyo (JPT), Utah Residents with Northern and Western European Ancestry (CEU), and Yorubia in Ibadan, Nigeria (YRI). We found that Tajiks differed from CHB, JPT and YRI in 30, 32, and 32 of the selected VIP genotypes respectively (p < 0.005), while differences between Tajiks and CEU were found in only 6 of the genotypes (p < 0.005). Haplotype analysis also demonstrated differences between the Tajiks and the other four populations.ConclusionOur results contribute to the pharmacogenomics database of the Tajik ethnic group and provide a theoretical basis for safer drug administration that may be useful for diagnosing and treating disease in this population.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0102-y) contains supplementary material, which is available to authorized users.

Effective population size of korean populations.

Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

Genetic polymorphisms of pharmacogenomic VIP variants in the Kyrgyz population from northwest China

Pharmacogenomic variant information is well known for major human populations; however, this information is less commonly studied in minorities. In the present study, we genotyped 85 very important pharmacogenetic (VIP) variants (selected from the PharmGKB database) in the Kyrgyz population and compared our data with other four major human populations including Han Chinese in Beijing, China (CHB), the Japanese in Tokyo, Japan (JPT), a northern and western Europe population (CEU), and the Yoruba in Ibadan, Nigeria (YRI). There were 13, 12 and 16 of the selected VIP variant genotype frequencies in the Kyrgyz which differed from those of the CHB, JPT and CEU, respectively (p<0.005). In the YRI, there were 32 different variants, compared to the Kyrgyz (p<0.005). Genotype frequencies of ADH1B, AHR, CYP3A5, PTGS2, VDR, and VKORC1 in the Kyrgyz differed widely from those in the four populations. Haplotype analyses also showed differences among the Kyrgyz and the other four populations. Our results complement the information provided by the database of pharmacogenomics on Kyrgyz. We provide a theoretical basis for safer drug administration and individualized treatment plans for the Kyrgyz. We also provide a template for the study of pharmacogenomics in various ethnic minority groups in China.

Meta-analysis Followed by Replication Identifies Loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as Associated with Systemic Lupus Erythematosus in Asians

Systemic lupus erythematosus (SLE) is a prototype autoimmune disease with a strong genetic involvement and ethnic differences. Susceptibility genes identified so far only explain a small portion of the genetic heritability of SLE, suggesting that many more loci are yet to be uncovered for this disease. In this study, we performed a meta-analysis of genome-wide association studies on SLE in Chinese Han populations and followed up the findings by replication in four additional Asian cohorts with a total of 5,365 cases and 10,054 corresponding controls. We identified genetic variants in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with the disease. These findings point to potential roles of cell-cycle regulation, autophagy, and DNA demethylation in SLE pathogenesis. For the region involving TET3 and that involving CDKN1B, multiple independent SNPs were identified, highlighting a phenomenon that might partially explain the missing heritability of complex diseases.