OBJECTIVES: Due to the genetic feature of high diversity than other DNA markers, short tandem repeat (STR) plays key roles in forensic, anthropology, and population genetics. Newly introduced multiple STR kit is more valuable because of the greatly improved discriminatory power with the increase in the number of STR loci. The genetic polymorphic data are essential for the application and research in specific population. This study aims to investigate the genetic polymorphism of Han population residing in Yuncheng district, Shanxi Province, to evaluate the application of 23 STR loci in forensic personal identification and paternity test, and to explore the genetic relationship of Han population between Yuncheng and other populations. METHODS: A total of 23 STR loci were amplified from 525 healthy unrelated individuals from the Han nationality in Yuncheng, Shanxi Province using the AGCU EX25 amplification kit. The products were detected and separated by ABI 3500 Genetic Analyzer. Alleles were genotyped by GeneMapper ID (Version 3.2) software, and corresponding frequencies and forensic parameters were calculated. We calculated the genetic distance and plotted the neighboring-joining tree with other 13 population. RESULTS: The allele frequency of the 23 STRs ranged from 0.0010 to 0.5090. No deviation from Hardy-Weinberg equilibrium ( CONCLUSIONS These 23 STRs are highly genetic polymorphic and informative in the Han population of Yuncheng, Shanxi Province, which can provide basic data for forensic personal identification, paternity testing, and population genetic research.
Asian Continental Ancestry Group/genetics* ; China ; Ethnic Groups/genetics* ; Gene Frequency ; Genetic Loci ; Genetics, Population ; Humans ; Microsatellite Repeats/genetics* ; Polymorphism, Genetic

As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits, a number of packages for checking NGS data quality have sprung up in public domains. In addition to the quality of sequencing data, sample quality issues, such as gender mismatch, abnormal inbreeding coefficient, cryptic relatedness, and population outliers, can also have fundamental impact on downstream analysis. However, there is a lack of tools specialized in identifying problematic samples from NGS data, often due to the limitation of sample size and variant counts. We developed SeqSQC, a Bioconductor package, to automate and accelerate sample cleaning in NGS data of any scale. SeqSQC is designed for efficient data storage and access, and equipped with interactive plots for intuitive data visualization to expedite the identification of problematic samples. SeqSQC is available at http://bioconductor.org/packages/SeqSQC.
Breast Neoplasms ; genetics ; Cohort Studies ; Continental Population Groups ; genetics ; Female ; Genome, Human ; High-Throughput Nucleotide Sequencing ; methods ; standards ; Humans ; Software ; Whole Exome Sequencing

Objective To derive the formulae for likelihood ratio （LR） calculation of half sibling relationships when both mothers participate. Methods Based on the fact that both biological mothers participate in the identification of half sibling relationship between the two individuals, test hypothesis for the identification of half sibling relationship was established. Conditional probability ratios of genetic evidence under null hypothesis and alternative hypothesis conditions were simplified, and then applied to a real case of half sibling relationship identification. At the same time, the LR of half sibling relationships under the assumption that only a single biological mother or none of the biological mothers participate were respectively calculated. Results In the cases of identification of half sibling relationship from same fathers, with no biological father involved, after the same genetic indicator test analysis, when both biological mothers participate in the identification, the accumulated LR value was higher than that of accumulated LR with only a single biological mother or no parents participating. Conclusion When the autosome STR test is used for the identification and analysis of half sibling relationship between two individuals, the calculation of LR is more simple, intuitive and operable with both mothers participating. The biological mothers should participate in the test as much as possible, otherwise the number of STR loci would need to be increased for a more specific conclusion.
Alleles ; Female ; Forensic Genetics ; Genotype ; Humans ; Likelihood Functions ; Models, Genetic ; Mothers ; Population Groups ; Siblings

BACKGROUND: The rs1520220 polymorphism in the insulin-like growth factor 1 (IGF1) gene has been reported to affect cancer susceptibly in several studies. However, the results of the relevant studies are inconsistent. We conduct a current meta-analysis to investigate the association between rs1520220 and cancer susceptibly. METHODS: Three databases (PubMed, Embase, and Web of Science) were searched for studies regarding the relationship between rs1520220 and cancer susceptibly. Odds ratios (ORs) and the related 95% confidence intervals (CIs) were employed to assess the strength of the associations. A stratified analysis was performed according to cancer type, ethnicity, and quality score, and when results were obtained from no fewer than two studies, these results were pooled. RESULTS: There was no positive association between rs1520220 and overall cancer risk. However, the analysis stratified by ethnicity revealed that rs1520220 significantly increased cancer susceptibility in Asian populations (allele model OR = 1.10, 95%Cl = 1.00-1.21, p = 0.040; homozygote model OR = 1.22, 95%Cl = 1.01-1.47, p = 0.040; dominant model OR = 1.19, 95%Cl = 1.01-1.39, p = 0.033). No significantly association was detected in Caucasian populations. The analysis stratified by cancer type suggested that rs1520220 was not associated with susceptibility to breast cancer. CONCLUSIONS The results of our meta-analysis demonstrate that the role of IGF1 rs1520220 in cancer susceptibility varies by ethnicity and cancer type and that rs1520220 increases cancer susceptibility in Asian populations.
Asian Continental Ancestry Group ; Continental Population Groups ; Gene Frequency ; Genetic Predisposition to Disease ; Humans ; Insulin-Like Growth Factor I ; genetics ; Neoplasms ; ethnology ; genetics ; Odds Ratio ; Polymorphism, Single Nucleotide

OBJECTIVES: To select a Y-STR marker system with strong haplotype identification ability, appropriate mutation rate and high compatibility and to assess its forensic application. METHODS: The 24 Y-STR loci were tested by self-built fluorescent multiplex system, and the forensic assessment was conducted by 139 pairs of father-son samples collected in Jinan, Shandong province. RESULTS: Totally 176 alleles were identified among the 24 Y-STR loci in the sample of 139 unrelated individuals labeled with father, and the gene diversity （GD） distributed between 0.083 7 （DYS645）-0.966 9 （DYS385a/b）. According to the 24 Y-STR loci, 139 different haplotypes were detected from 139 unrelated male individuals labeled with father in Han population of Shandong province and with no shared haplotype observed. The overall haplotype diversity （HD） was 1 and the discrimination capacity （DC） was 1. A total of 5 one-step mutations events were observed among the 24 Y-STR loci in 139 pairs of father-son. The average mutation rate was 0.001 5 [95% CI （0.000 5, 0.003 5）]. CONCLUSIONS The system of 24 Y-STR loci shows a strong individual recognition ability and low mutation rate in the population in Jinan, Shandong province, and it has good application value in forensic science.
Alleles ; China ; Chromosomes, Human, Y ; Forensic Genetics ; Forensic Sciences ; Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Male ; Mutation Rate ; Population Groups

OBJECTIVES: To investigate the genetic polymorphisms of 27 Y-STR in Dongxiang population of Gansu province, and to explore the population genetic relationship and the value of forensic application. METHODS: The genotyping of 27 Y-STR loci in 526 unrelated male individuals in Dongxiang population of Gansu province were detected by STRtyper-27Y kit. The allele frequencies and haplotype diversity were also calculated. Combining with other genetics data of 14 loci in same populations, which have been published at home and abroad, the genetic distance and clustering relationship in Dongxiang population of Gansu province were calculated. RESULTS: Totally 55 haplotypes were found in the DYS385a/b biallelic loci, 39 haplotypes in DYF387S1 loci, and 4-16 alleles in the rest 23 single copy STR loci. The GD value was from 0.453 9 （DYS391） to 0.957 5 （DYS385a/b）. Totally 471 haplotypes were observed in 27 Y-STR loci in 526 individuals, and the value of haplotypes diversity was 0.999 5. The genetic distance between Dongxiang and Tibetan populations of Gansu province was the closest （0.068 2）, while it was the longest between Dongxiang population in Gansu province and Han population in Henan province （0.084 7）. The result of dimensional analysis established upon the genetic distance was basically matched with that of the cluster analysis. CONCLUSIONS The 27 Y-STR loci show a high genetic polymorphism in Dongxiang population of Gansu province, which has significance for the Y-STR database establishment, population genetics study and forensic practice.
Alleles ; Asian People/genetics* ; China ; Chromosomes, Human, Y ; Gene Frequency ; Genetics, Population ; Haplotypes ; Humans ; Male ; Microsatellite Repeats ; Polymorphism, Genetic/genetics* ; Population Groups

Asthma exacerbation (AE) usually denotes worsening of asthma symptoms that requires intense management to prevent further deterioration. AE has been reported to correlate with clinical and demographic factors, such as race, gender, and treatment compliance as well as environmental factors, such as viral infection, smoking, and air pollution. In addition, recent observations suggest that there are likely to be genetic factors specific to AE. Understanding genetic factors specific to AE is essential to develop therapy tailored for exacerbation-prone asthma. Here, we summarize the results of studies involving genetic risk factors for AE. To simplify and enhance understanding, we reviewed the studies according to the following categories: hypothesis-driven approaches, hypothesis-free approaches, gene-environment interactions, and pharmacogenetics.
Air Pollution ; Asthma* ; Compliance ; Continental Population Groups ; Demography ; Gene-Environment Interaction ; Genetics ; Genome-Wide Association Study ; Humans ; Pharmacogenetics ; Risk Factors ; Smoke ; Smoking

OBJECTIVETo validate the efficiency of 27-plex single nucleotide polymorphism (SNP) multiplex system for ancestry inference.

METHODSThe 27-plex SNP system was validated for its sensitivity and species specificity. A total of 533 samples were collected from African, Southern Chinese Han, China's ethic minorities (Yi, Hui, Miao, Tibet, and Uygur), European, Central Asian, Western Asian, Southern Asian, Southeast Asian and South American populations for clustering analysis of the genotypes by citing 3 representative continental ancestral groups [East Asia (CHB), Europe (CEU), and Africa (YRI)] from HapMap database.

RESULTSThe system sensitivity is 0.125 ng. Twenty and six genotypes were detected in chimpanzee and monkeys, respectively. Except in rs10496971, no more products were found in other animals. The system was capable of differentiating intercontinental populations but not of distinguishing between East Asian and Southeast Asian population or between Southern Chinese Han population and Chinese Ethnic populations (Hui, Miao, Yi and Tibet). This system achieved a 100% accuracy for intercontinental population source inference for 46 blind test samples.

CONCLUSION27-plex SNPs multiplex system has a high sensitivity and species specificity and can correctly differentiate the ancestry origins of individuals from African, European and East Asian for criminal case investigation. But this system is not capable of distinguishing subpopulation groups and more specific ancestry-informative markers are needed to improve its recognition of Southeast Asian and Chinese ethnic populations.

Animals ; Asian Continental Ancestry Group ; genetics ; China ; Ethnic Groups ; Gene Frequency ; Genetics, Population ; Genotype ; Humans ; Polymorphism, Single Nucleotide ; Primates ; genetics

OBJECTIVETo evaluate the value of PowerPlex21 System (Promega) and study the genetic polymorphism of its 20 short-tandem repeat (STR) loci in southern Chinese Han population.

METHODSWe conducted genotyping experiments using PowerPlex21 System on 20 autosomal STR loci (D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433 and FGA) in 2367 unrelated Chinese Han individuals living in South China. The allele frequencies and parameters commonly used in forensic science were statistically analyzed in these individuals and compared with the reported data of other populations.

RESULTSThe PowerPlex21 System had a power of discrimination (PD) ranging from 0.7839 to 0.9852 and a power of exclusion (PE) ranging from 0.2974 to 0.8099 for the 20 loci. No significant deviation from Hardy-Weinberg expectations was found for all the loci except for D5S818. This southern Chinese Han population had significant differences in the allele frequencies from 8 ethnic groups reported in China, and showed significant differences at 8 to 20 STR foci from 5 foreign populations. The allele frequency at the locus D1S1656 in this southern Chinese Han population differed significantly from those in the 5 foreign populations and from 3 reported Han populations in Beijing, Zhejiang Province and Fujian Province of China. The neighbor-joining phylogenetictree showed clustering of all the Asian populations in one branch, while the northern Italian and Argentina populations clustered in a separate branch. This southern Chinese Han population had the nearest affinity with the Yi ethnic population in Yunnan Province of China.

CONCLUSIONThe 20 STR loci are highly polymorphic in this southern Chinese Han population, suggesting the value of this set of STR loci in forensic personal identification, paternity testing and anthropological study.

Asian Continental Ancestry Group ; genetics ; China ; Cluster Analysis ; Ethnic Groups ; Forensic Sciences ; Gene Frequency ; Genetics, Population ; Genotype ; Humans ; Microsatellite Repeats ; Polymorphism, Genetic

Although marathon has been considered as a simple or natural event, the multiple factors affect its performance such as physique and physical fitness including physical, technical, and mental factors. Academic disciplinary topics for talent identification in marathon performance are supported by physical characteristics, exercise physiology, biochemistry, nutrition, psychology, biomechanics, development and growth, evaluation and measurement. The scientific factors of marathon consist of physical and physiological characteristics of runners, overcoming trial of environmental effects, nutritional and psychological approach, ergogenic aid, effective training program, shoes and clothes. Especially, cardiopulmonary-related physical fitness is evaluated by maximal oxygen uptake, anaerobic threshold, oxygen transport rate, and lactate tolerance. These scientific approaches for the improvement of running performance have been applied to the pick-up of excellent runner, exercise training, and actual running race for the overcome of limiting factors as environmental condition, exercise-induced fatigue, and injury, etc. In conclusion, we must consider the scientific factors for actual running race with physiological or psychological paradigm, technical application, nutritional approach, genetic analysis and information and communication and technology (ICT) convergence science for the scientific consideration of improvement in marathon running performance.
Anaerobic Threshold ; Aptitude ; Biochemistry ; Clothing ; Continental Population Groups ; Education ; Fatigue ; Genetics ; Growth and Development ; Humans ; Lactic Acid ; Oxygen ; Physical Fitness ; Physiology ; Psychology ; Running ; Shoes ; Sports*