Han Population In Shanghai Research Articles

Traceability of Geographic Origin Using Human Skin and Oral Microbiota.

To explore the possibility of using human skin and oral microorganisms to estimate the geographic origin of an individual through the sequencing analysis of bacterial 16S rRNA gene. Microbial DNA was extracted from the palm and oral microorganisms of the Han population in Shanghai and Chifeng, Inner Mongolia, and the composition and diversity of the microbiota were analyzed by full-length 16S rRNA gene sequencing. Then, differential species were screened and a geographic location prediction model was constructed. The compositions of palm and oral microorganisms between Shanghai and Chifeng samples were both different. The abundance and uniformity of palm side skin microorganisms were higher in Chifeng samples than in Shanghai samples, while there was no significant difference in oral microorganisms. Permutational multivariate analysis of variance (PERMANOVA) confirmed that the β-diversity between the samples from the two places were statistically significant, and the coefficients of determination (R2) for skin and oral samples were 0.129 and 0.102, respectively. Through principal co-ordinates analysis (PCoA), the samples from the two places could be preliminarily distinguished. The predictive model had the accuracies of 0.90 and 0.83 for the geographic origin using the skin and oral samples, respectively. There are differences in the compositions of palm and oral microbiota between Han populations in Shanghai and Chifeng. The prediction model constructed by the random forest algorithm can trace the unknown individuals from the above two places.

Analysis of Adverse Reactions of Cosmetics in Chinese Han Population in Recent Five Years.

There are still some gaps in the summary and generalization of cosmetic-related adverse reaction reports. The aim of this study is to summarize and analyze the occurrence of cosmetic adverse reactions in Shanghai Han population by using available survey data. Collection, statistics and analysis of patients with cosmetic adverse reactions in Shanghai Huashan Hospital from 2017 to 2021. Among the 1004 patients, most of them (96.71%) were diagnosed as cosmetic contact dermatitis, which often occurred within 3 days of using cosmetics (51.79%). A total of 260 patients were tested with patch test, but the compliance rate was only 18.08%. Among them, 240 patients underwent additional European standard allergen tests, and positive allergens were detected in 210 cases (87.5%). Univariate analysis revealed that dosage form (emulsion and cream), age (≤25 years) and the allergic ingredients triethanolamine, rose oil, propylene glycol, thiomersal and musk ambrette are associated with the occurrence of cosmetic adverse reactions within seven days. A logit prediction model was also successfully constructed: Logit (P) = 1.710-0.796×1+ 1.185×2 -3.650X3-1.335X4. This study complements the data reported on cosmetic adverse reactions in the Chinese Han population and suggests that in future clinical diagnosis and data collection, emphasis should be placed on patch testing, combining the patch test with cosmetic protoplast with the European standard allergen test to improve the detection rate.

Alterations of gut microbiota in gestational diabetes patients during the second trimester of pregnancy in the Shanghai Han population

BackgroundThe causes of gestational diabetes mellitus (GDM) are still unclear. Recent studies have found that the imbalance of the gut microbiome could lead to disorders of human metabolism and immune system, resulting in GDM. This study aims to reveal the different gut compositions between GDM and normoglycemic pregnant women and find the relationship between gut microbiota and GDM.MethodsFecal microbiota profiles from women with GDM (n = 21) and normoglycemic women (n = 32) were assessed by 16S rRNA gene sequencing. Fasting metabolic hormone concentrations were measured using multiplex ELISA.ResultsMetabolic hormone levels, microbiome profiles, and inferred functional characteristics differed between women with GDM and healthy women. Additionally, four phyla and seven genera levels have different correlations with plasma glucose and insulin levels. Corynebacteriales (order), Nocardiaceae (family), Desulfovibrionaceae (family), Rhodococcus (genus), and Bacteroidetes (phylum) may be the taxonomic biomarkers of GDM. Microbial gene functions related to amino sugar and nucleotide sugar metabolism were found to be enriched in patients with GDM.ConclusionOur study indicated that dysbiosis of the gut microbiome exists in patients with GDM in the second trimester of pregnancy, and gut microbiota might be a potential diagnostic biomarker for the diagnosis, prevention, and treatment of GDM.

Association of HIVEP3 Gene and Lnc RNA with Femoral Neck Bone Mineral Content and Hip Geometry by Genome-Wide Association Analysis in Chinese People.

Purpose GWAS has successfully located and analyzed the pathogenic genes of osteoporosis. Genetic studies have found that heritability of BMD is 50%–85% while the other half is caused by hip geometric parameters and tissue horizontal characteristics. This study was designed to study the GWAS of osteoporosis in Shanghai Han population. Methods We collected 1224 unrelated healthy young men (20–40 years old), young women (20–40 years old), and postmenopausal women (over 50 years old) who lived in Shanghai. BMD and hip geometric parameters were measured by dual-energy X-ray absorptiometry. The genomic DNA of peripheral blood was extracted and analyzed by using Illumina Human Asian Screening Array-24 + v1.0 (ASA) gene chip. Statistical analysis was carried out to evaluate the relationship between these SNPs and BMD and hip geometric parameters. Results A total of 1155 subjects were included. We found that one SNP rs35282355 located in the human immunodeficiency virus type 1 enhancer-binding protein 3 gene (HIVEP3) and another 25 SNPs located in LINC RNA were significantly correlated with bone mineral content (BMC) in the femoral neck (P= 2.30 × 10−9, P < 5 × 10−8). We also found that the correlation between SNP rs35282355 and cross-sectional area (CSA) of hip geometry was a significant marginal statistical difference (P = 5.95 × 10−8). Conclusions Through this study, we found that HIVEP3 gene and LINC RNA are potentially correlated with femoral neck BMC. These results provide important information for us to further understand the etiology and genetic pathogenesis of osteoporosis. In the future, we will expand the sample size to verify these loci and carry out molecular research.

Identification of recurrent and novel mutations by whole‑genome sequencing of colorectal tumors from the Han population in Shanghai, eastern China

Previous studies have identified recurrent oncogenic mutations in colorectal cancer (CRC), but there is limited CRC genomic data from the Chinese Han population. Whole-genome sequencing was performed on 10 primary CRC tumors and matched adjacent normal tissues from patients from the Han population in Shanghai, at an average of 27.8× and 27.9× coverage, respectively. In the 10 tumor samples, 32 significant somatic mutated genes were identified, 13 of which were also reported as CRC mutations in The Cancer Genome Atlas Network. All the mutated genes were enriched in functions associated with channel activity, which has rarely been reported in previous studies investigating CRC. Furthermore, 21 chromosomal rearrangements were detected and 4 rearrangements encoded predicted in-frame fusion proteins, including a fusion of phosphorylase kinase regulatory subunit b and NOTCH2 demonstrated in 2 out of 10 tumors. Chromosome 8 was amplified in 1 tumor and chromosome 20 was amplified in 2 out of 10 CRC patients. The present study produced a genomic mutation profile of CRC, which provides a valuable resource for further insight into the mutations that characterize CRC in patients from the Han population in Shanghai, eastern China.

Association between HLA gene polymorphism and cutaneous adverse reactions caused by antiepileptic drugs.

The association between cutaneous adverse drug reactions (cADRs) caused by antiepileptic drugs (AEDs) and human leukocyte antigen-A (HLA-A) and HLA-B genes in Chinese Han population in Shanghai was investigated. Through the case-control study, 30 child patients with AED-induced cADRs (cADRs group), 60 AED-tolerant child patients (AED-tolerant group) and 60 normal children not taking AEDs (normal group) were collected. The HLA-B*15:02 and HLA-A*31:01 genotypes were detected using the polymerase chain reaction-sequence-specific oligonucleotide (PCR-SSO) probe method, and the correlation of HLA-B*15:02 and HLA-A*31:01 genes with the incidence of cADRs was analyzed. The positive rate of HLA-B*15:02 gene was 83.33% in the cADRs group, which was significantly increased compared with that in the AED-tolerant and normal groups (P<0.01). The positive rate of HLA-A*31:01 gene was 63.33% in the cADRs group, which was obviously increased compared with that in the AED-tolerant and normal groups (P<0.01). There were no significant differences in HLA-B*15:02 and HLA-A*31:01 genotypes between the AED-tolerant and normal groups (P>0.05). The results showed that HLA-B*15:02 and HLA-A*31:01 are significantly associated with cADRs in a Chinese Han population in Shanghai, suggesting that HLA-B*15:02 and HLA-A*31:01 genotypes should be detected in the application of AEDs.

Genetic analysis of 29 Y-STR loci in the Chinese Han population from Shanghai

The analysis of Y chromosomal short tandem repeats (Y-STRs) provides important information that can be used to forensic investigation and population studies. In this study, typing of 29 Y-STRs included in the PowerPlex® Y23 system (PPY23) and Yfiler™ Plus system (Yfiler plus) was performed on 843 unrelated male samples from Han population in Shanghai. Besides null, duplicate, and intermediate alleles reported in previous studies, an allele of 10 at DYS643 with a 2-base deletion in the flanking region was initially observed. The gene diversity (GD) values of the 29 Y-STRs range from 0.4186 at DYS438 to 0.9653 at DYS385a/b. The haplotype diversity of two commonly used haplotype sets, PPY23 set and Yfiler plus set is 0.999980 and 0.999997, respectively. Pairwise genetic distances between Han population in Shanghai and other Han populations estimated using Yfiler plus set are slightly larger than that between other Han populations. Visualization of pairwise genetic distances between 17 worldwide populations using multidimensional scaling (MDS) demonstrates the distribution of populations according to their ethno-geographic patterns. Compared with Yfiler set, Yfiler plus set appears to have a relatively high population discrimination capacity for these tested populations. Altogether, these results can provide useful information of Y-STRs for forensic investigation and population studies.

The ALDH2 gene rs671 polymorphism is not associated with essential hypertension

ABSTRACTEssential hypertension (EH) is a worldwide problem. Acetaldehyde dehydrogenase 2 (ALDH2) gene has been suggested to be correlated with EH. However, the results are inconsistent. This study aimed to investigate the associations of ALDH2 rs671 polymorphism with EH in a Chinese Han population in Shanghai. Genotype of ALDH2 rs671 was analyzed in 1923 EH patients and 1115 control subjects. We found no association between ALDH2 rs671 and EH risk or EH-related quantitative blood chemistry values. Furthermore, a meta-analysis was performed and the summary results from 11220 patients and 8339 control subjects were consistent with our findings. These results indicated that rs671 of ALDH2 may not associate with the risk of EH.

Development of the 16 X‐STR loci typing system and genetic analysis in a Shanghai Han population from China

This study developed a new multiplex PCR system that simultaneously amplifies 16 X-STR loci in the same PCR reaction, and the polymorphism and mutation rates of these 16 X-STR loci were explored in a Shanghai Han population from China. These loci included DXS10134, DXS10159, DXS6789, DXS6795, DXS6800, DXS6803, DXS6807, DXS6810, DXS7132, DXS7424, DXS8378, DXS9902, GATA165B12, GATA172D05, GATA31E08, and HPRTB. Samples from 591 unrelated individuals (293 males and 298 females) and 400 two-generation families were successfully analyzed using this multiplex system. Allele frequencies and mutation rates of the 16 loci were investigated, with the comparison of allele frequency distributions among different populations performed. Polymorphism information contents of these loci were all >0.6440 except the locus DXS6800 (0.4706). Nine cases of mutations were detected in the 16 loci from the investigation of 9232 meioses. Pairwise comparisons of allele frequency distributions showed significant differences for most loci among populations from different countries and ethnic groups but not among the Han population living in other areas of China. These results suggest that the 16 X-STR loci system provides highly informative polymorphic data for paternity testing and forensic identification in the Han population in Shanghai, China, as a complementary tool.

Genetic distribution on 20 STR loci from the Han population in Shanghai, China

Genetic distribution on 20 STR loci from the Han population in Shanghai, China

Genetic polymorphisms in 12 autosomal STRs in a Shanghai Han population from China

In this study, a total of 484 unrelated healthy individuals and 359 two-generation families in the Han population in Shanghai, China were successfully analyzed with the Investigator HDplex Kit (Qiagen, Hilden, Germany). Hardy-Weinberg equilibrium tests demonstrated no significant deviation from expected values (p > 0.05) for the 12 autosomal STRs included in this kit. A total of 173 alleles were detected in 12 autosomal STR loci; the largest number of alleles (32) was detected for the SE33 locus. The combined power of discrimination was 0.99999999992. The combined mean exclusion chance in duo cases was 0.99982, whereas the combined mean exclusion chance in trio cases was 0.9999986. The average mutation rate across all loci was 0.0023 (95% confidence intervals: 0.0013-0.0039). These results suggest that the 12 autosomal STR loci can provide highly informative polymorphic data for paternity testing and forensic identification in the Han population in Shanghai, China.

Genetic polymorphisms of 12 X-STR for forensic purposes in Shanghai Han population from China

X-chromosomal short tandem repeats (X-STR) loci are used for forensic practice in recent years in some complex kinship cases. The commercially available kit of Investigator Argus X-12 (Qiagen, Hilden, Germany) makes it possible to examine the markers of DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074, DXS10103-HPRTB-DXS10101 and DXS10146-DXS10134-DXS7423, which belong to four linkage groups of X-chromosome. In this study, a total of 309 unrelated individuals (200 males and 109 females) from Shanghai Han population were successfully analyzed with this kit. Hardy-Weinberg equilibrium tests demonstrated no significant deviation from expected values (P>0.05) for all of the 12 X-STR loci in the Shanghai Han population. Linkage disequilibrium tests were performed for all pairs of loci by the Arlequin v3.1 software and only DXS10103-DXS10101 remained significant after adjustment for multiple testing (P<0.05/66). The combined power of discrimination in males (CDP(M)) was 0.999999996 while in females (CDP(F)) was 0.999999999999995, and the combined mean exclusion chance in duo cases (CMEC(D)) was 0.999998 while in trio cases (CMEC(T)) was 0.999999986. The results suggest that the twelve X-STR loci may provide high polymorphic information for paternity testing and forensic identification in Chinese Han population from Shanghai.

Relationship between tumor necrosis factor-alpha gene and risk of coronary artery disease in Shanghai Han population

Objective To investigate the association of 5 single nucleotide polymorphisms and their haplotypes in the promoter of tumor necrosis factor-α(TNF-α) gene with coronary artery disease(CAD) in Shanghai Han population. MethodsThe genotypes of T-1031C,C-863A,C-857T,G-308A and G-238A polymorphisms were analysed by mass spectrometry in 438 patients with CAD and 330 healthy controls,and concentrations of blood glucose and blood lipid were measured.Results There were significant differences in genotype and allele frequency of C-857T polymorphism between CAD group and control group(P0.05).Patients carrying-857C allele were associated with 1.45-fold higher odds of CAD compared to T allele carriers(95%CI,1.092-1.927).In patients with CAD,serum levels of total cholesterol and low-density lipoprotein cholesterol of C/C genotype and C/T genotype carriers were significantly higher than those of T/T carriers(P0.05).There were significant differences in allele frequency of G-308A polymorphism between two groups(P0.05).Patients carrying-308A allele were associated with 1.43-fold higher odds of CAD compared to noncarriers(95%CI,1.055-1.949).Haplotype analysis indicated that the frequencies of haplotype CCCGA and TCCAG were significantly higher in CAD group than in control group(P0.05 and P0.01),and the risks of suffering from CAD were 2.96 fold and 1.67 fold for homozygous carriers of haplotype CCCGA and TCCAG compared to noncarriers(95%CI,1.176-7.430 and 1.166-2.379).In comparison,the frequency of haplotype TCTGG was significantly lower in CAD group than in controls,which was significantly associated with a decreased risk of CAD(OR,0.57;95%CI,0.415-0.784;P0.01).Conclusion Polymorphisms in the promoter of of TNF-α gene might be associated with the occurrence of CAD in Shanghai Han population.

Association between NMDA receptor subunit 2b gene polymorphism and Alzheimer’s disease in Chinese Han population in Shanghai

N-methyl-D-aspartate (NMDA) receptor has been indicated to be involved in the pathogenesis of Alzheimer's disease (AD). The NMDA receptor subunit 2b (NR2B) has attracted more attention due to its characteristic distribution and selective reduction in AD brain. The present study aimed to explore the association between NMDA gene polymorphism and AD. A total of 63 AD patients and 68 normal controls in Shanghai city were employed in this study. Genotype of C2664T variant (rs1806201) in the exon13 of GRIN2B gene was determined by gene sequencing. Among AD patients, 15 (23.6%) subjects were identified as C/C genotype, and 35 (55.6%) were identified as C/T genotype. The left 13 (20.6%) subjects were identified as T/T genotype. In normal controls, 15 (22.1%) subjects were identified as C/C genotype, 39 (57.4%) as C/T genotype and 14 (20.6%) as T/T genotype. The distribution frequency of neither GRIN2B C2664T genotype (P=0.895) nor allele (P=0.790) was significantly different between AD patients and normal controls, even when the subjects were stratified by gender and age of disease onset in AD patients. The results suggest that there is no relation between GRIN2B C2664T polymorphism and AD in Chinese Han population of Shanghai City.

Application of HLA–DRB1 genotyping by oligonucleotide micro-array technology in forensic medicine

The human leukocyte antigen (HLA) system is known to be the most complex polymorphic system in the human genome. Among all of the HLA loci, HLA–DRB1 has the second largest number of alleles. The purpose of this study is to develop an oligoneucleotide micro-array based HLA–DRB1 typing system for use in forensic identification, anthropology, tissue transplantation, and other genetic research fields. The system was developed by analyzing the HLA–DRB1 (DRB1) genotypes in 1198 unrelated healthy Chinese Han individuals originating from various parts of China and residing in Shanghai, China. Method Polymerase chain reaction (PCR) coupled with the oligonucleotide micro-array technology was used to detect and type HLA–DRB1 alleles of the sample individuals. The reliability, sensitivity, consistency and specificity were evaluated for use in forensic identification. Furthermore, a meta-analysis was carried out by comparing the allele frequencies of the HLA–DRB1 locus with those of other Chinese Han groups, Chinese minorities and other ethnic populations. Results All the DNA samples yielded a 273 bp amplification product, with no other amplification products in this length range. The minimum quantity of DNA detected by this method is 15 ng in a PCR reaction system of 25 μl. The population studied appeared to be not in Hardy–Weinberg equilibrium. Observed heterozygosity (Ho), expected heterozygosity (He), expected probability of exclusion (PE), polymorphic information content (PIC), and discrimination power (DP) of the HLA–DRB1 locus from the Shanghai Han ethnic group were evaluated to be 0.8022, 0.8870, 0.7741, 0.8771, 0.9750, respectively. A total of 25 HLA–DRB1 alleles were identified. HLA–DRB1*09XX, *04XX, *12XX and *15XX were the most frequent DRB1 alleles, which were observed in 58.76% of the sample. One hundred and sixteen genotypes were found. The five most frequent genotypes were: *04XX/*04XX (0.0626), *09XX/*09XX (0.0593), *04XX/*09XX (0.0551), *09XX/*15XX (0.0384) and *08XX/*12XX (0.0351). The meta-analysis showed that there were uniquely distributed features of DRB1 alleles among various ethnic populations and among the studied population groups from various regions with the same ethnic origin. Conclusions An HLA–DRB1 genotyping system has been developed and established based on the oligonucleotide micro-array technology. The HLA–DRB1 typing of the Han population in Shanghai has revealed a relatively high heterogeneity. Information obtained in this study will be useful for medical and forensic applications as well as in anthropology research. Large-scale micro-array detection is highly accurate and reliable for DNA-based HLA–DRB1 genotyping. These results suggest that HLA–DRB1 DNA polymorphisms and the database of the Shanghai Han group have useful applications in processing forensic casework (as personal identification, paternity test), tracing population migration and genetic diagnosis.

The Genetics Characteristics of HLA Alleles and Haplotypes in the Shanghai Han Population

The Genetics Characteristics of HLA Alleles and Haplotypes in the Shanghai Han Population