Multiplex polymerase chain reaction （PCR） has been widely used to detect Y-chromosome micredeletions, which is one of the major causes of male infertility. Both the European Academy of Andrology （EAA） and the Euro...Multiplex polymerase chain reaction （PCR） has been widely used to detect Y-chromosome micredeletions, which is one of the major causes of male infertility. Both the European Academy of Andrology （EAA） and the European Molecular Genetics Quality Network （EMQN） have recommended the use of sY84 and sY86 markers for the detection of azoospermia factor a （AZFa） microdeletion during DNA testing for male infertility. In this study, a large-scale analysis of AZF microdeletion in a total of 630 Chinese males, including healthy semen donors （n=200）, infertile males with normal sperm count （n=226） and patients with either nonobstructive azoospermia or severe oligozoospermia （n=204）, was performed. A series of nine sequence-tagged site （STS） markers from the AZF region of the Y chromosome was used to detect microdeletions. All primers were designed based on the recommendations of the National Center for Biotechnology Information. An unusually high incidence （73/630, 11.6%） of sY84-absent but sY86-present genotypes was observed in the AZFa microdeletion screening. Sequencing the sY84-flanking region revealed a total of 73 patients with sY84-absent but sY86-present genotypes have a T-to-G transversion at the fifth base from the 5＇ end of the reverse sY84 primer. These prevalent false positives, which were not only observed in infertile men, but also observed in donors, resulted from a single-nucleotide polymorphism （SNP） named rs72609647 in the targeting sequence of the reverse sY84 primer. Our study suggests that a pre-screening of existence of rs72609647 polymorphism can prevent the frequent false positive results of AZFa microdeletions detection in the infertile Chinese males. Given the SNP rs72609647 was recently found in a deep sequencing of a Chinese individual, the current EAA and EMQN standards may need to be scrutinized among different populations to avoid the potential genetic variations in the primer binding sequences.展开更多
BACKGROUND Polygonum multiflorum is one of the leading causes of herb-induced liver injury in China.HLA-B*35:01 is reported to be a potential biomarker of Polygonum multiflorum-induced liver injury(PM-DILI).However,li...BACKGROUND Polygonum multiflorum is one of the leading causes of herb-induced liver injury in China.HLA-B*35:01 is reported to be a potential biomarker of Polygonum multiflorum-induced liver injury(PM-DILI).However,little is known about the relationship between single-nucleotide polymorphisms(SNPs) and PM-DILI.AIM To identify SNPs that indicate susceptibility to PM-DILI METHODS We conducted a systematic study enrolling 382 participants from four independent hospitals,including 73 PM-DILI patients,118 patients with other drug-induced liver injury(other-DILI) and 191 healthy controls.Whole-exome sequencing was performed for 8 PM-DILI patients and 8 healthy controls who were randomly selected from the above subjects.Nineteen SNPs that showed high frequencies in the 8 PM-DILI patients were selected as candidate SNPs and then screened in 65 PM-DILI patients,118 other-DILI patients and 183 healthy controls using the MassARRAY system.HLA-B high-resolution genotyping was performed for the 73 PM-DILI and 118 other-DILI patients.The Han-MHC database was selected as a population control for HLA-B analysis.P <6.25 x 103 after Bolferroni correction was considered significant.RESULTS The frequencies of rslll686806 in the HLA-A gene,rs1055348 in the HLA-B gene,and rs202047044 in the HLA-DRB1 gene were significantly higher in the PM-DILI group than in the control group [27.2% vs 11.6%,P=1.72×105,odds ratio(OR)=3.96,95% confidence interval(Cl):2.21-7.14;42.5% vs 8.6%,P=1.72×10-19 OR=13.62,95% CI:7.16-25.9;22.9% vs 8.1%,P=4.64×106,OR=4.1,95% CI:2.25-7.47].Only rs1055348 showed a significantly higher frequency in the PM-DILI group than in the other-DILI group(42.5% vs 13.6%,P=1.84×10-10,OR=10.06,95% Cl:5.06-20.0),which suggested that it is a specific risk factor for PM-DILI.rs1055348 may become a tag for HLA-B*35:01 with 100% sensitivity and 97.7% specificity in the PM-DILI group and 100% sensitivity and 98.1% specificity in the other-DILI group.Furthermore,HLA-B*35:01 was confirmed to be associated with PM-DILI with a frequency of 41.1% in the PM-DILI group compared with 11.9%(P=4.30×10-11,OR=11.11,95% CI:5.57-22.19) in the other-DILI group and 2.7%(P=6.22×10-166,OR=62.62,95% Cl:35.91-109.20) in the Han-MHC database.CONCLUSION rslll686806,rs1055348,and rs202047044 are associated with PM-DILI,of which,rs1055348 is specific to PM-DILI.As a tag for HLA-B*35:01,rs1055348 may become an alternative predictive biomarker of PM-DILI.展开更多
Objective To analyze the role of resistin in insulin resistance (IR) through investigating the variation of plasma resistin levels and single-nucleotide polymorphisms (SNPs) in resistin gene 5’ flanking region in str...Objective To analyze the role of resistin in insulin resistance (IR) through investigating the variation of plasma resistin levels and single-nucleotide polymorphisms (SNPs) in resistin gene 5’ flanking region in stroke patients.Methods In 103 atherothrombotic cerebral infarction (ACI) patients, 85 lacunar infarction (LI) patients, 70 intracerebral hemorrhage (ICH) patients, and 86 healthy controls, plasma resistin and insulin levels were measured by ELISA , SNPs in resistin gene 5’ flanking region were detected by PCR and direct DNA sequencing. The subjects’ body height and weight, the body mass index, quantitative insulin sensitivity check index (QUICKI), blood pressure, and the concentration of fasting plasma glucose, triglyceride, total cholesterol, creatinine, low-density lipoprotein, and high-density lipoprotein were also determined. Results QUICKI was significantly lower in the ACI and ICH patients (0.316±0.037 and 0.309±0.032, respectively) than that in the controls (0.342±0.043, P<0.001), while plasma resistin level was significantly higher in the ACI and ICH patients (6.36±3.79 and 7.15±4.27 ng/mL, respectively) than that in the controls (5.28±2.56 ng/mL, P<0.05), but such difference was not observed in the LI patients compared with controls. There was a statistically negative correlation between plasma resistin level with QUICKI (r=-0.228, P<0.001). The distributions of allele and genotype frequencies of resistin gene -420C>G and -537A>C SNPs were not significantly different among the different groups, and those SNPs were not correlated with other clinical and biochemical parameters.Conclusions Plasma resistin is associated with stroke by participating in the development of IR. The SNPs in resistin gene 5’ flanking region has no impact on the plasma resistin level.展开更多
Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and ...Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and improve tenderness;however, there has been no direct correlation demonstrated between beef taste and oleic acid. To investigate genes affecting other fatty acids other than oleic acid, polymorphisms of the fatty acid desaturase 2 (FADS2) gene were genotyped and associations with fatty acid profile in JBK beef were investigated. Amplifications of 5’-flanking regions, 12 exons, and 3’-untranslated regions of the FADS2 gene in three Japanese and five Western cattle breeds via PCR, were amplified, sequenced and SNPs were identified using specific TaqMan genotyping assay. Fatty acid composition of intramuscular adipose tissue of the Trapezius muscle was analyzed in JBK steers. Six of the 15 identified SNPs are novel and have never been registered in any public bovine SNP database. A non-synonymous SNP (rs211580559;C > T;294 Ala > Val) in exon 7 was examined in order to evaluate its association with fatty acid profiles. The data showed that highly significant association existed between rs211580559 and C18:2 (n-6) composition, and accounted for 22.3% of the variation. There were no significant relationships between rs2115-80559 and the other fatty acids. It was concluded that rs211580559 of the FADS2 gene may be a useful selection marker for reducing unfavorable volatiles generated from linoleic acid in JBK beef during the cooking process.展开更多
Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wil...Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.展开更多
Background:Growth retardation is a common complication of chronic kidney disease in children,which can be partially relieved after renal transplantation.This study aimed to develop and validate a predictive model for ...Background:Growth retardation is a common complication of chronic kidney disease in children,which can be partially relieved after renal transplantation.This study aimed to develop and validate a predictive model for growth patterns of children with end-stage renal disease(ESRD)after kidney transplantation using machine learning algorithms based on genomic and clinical variables.Methods:A retrospective cohort of 110 children who received kidney transplants between May 2013 and September 2021 at the First Affiliated Hospital of Zhengzhou University were recruited for whole-exome sequencing(WES),and another 39 children who underwent transplant from October 2021 to March 2022 were enrolled for external validation.Based on previous studies,we comprehensively collected 729 height-related single-nucleotide polymorphisms(SNPs)in exon regions.Seven machine learning algorithms and 10-fold cross-validation analysis were employed for model construction.Results:The 110 children were divided into two groups according to change in height-for-age Z-score.After univariate analysis,age and 19 SNPs were incorporated into the model and validated.The random forest model showed the best prediction efficacy with an accuracy of 0.8125 and an area under curve(AUC)of 0.924,and also performed well in the external validation cohort(accuracy,0.7949;AUC,0.796).Conclusions:A model with good performance for predicting post-transplant growth patterns in children based on SNPs and clinical variables was constructed and validated using machine learning algorithms.The model is expected to guide clinicians in the management of children after renal transplantation,including the use of growth hormone,glucocorticoid withdrawal,and nutritional supplementation,to alleviate growth retardation in children with ESRD.展开更多
Background：Polymorphisms of microRNA （miRNA）,as a novel mechanism,are closely associated with disease states by interfering with miRNA function.Direct correlations have been identified between single-nucleotide pol...Background：Polymorphisms of microRNA （miRNA）,as a novel mechanism,are closely associated with disease states by interfering with miRNA function.Direct correlations have been identified between single-nucleotide polymorphisms （SNPs） in miRNA,but the effect on type 2 diabetes mellitus （T2DM） onset among Chinese population remains unclear.Therefore,the aim of this study was to identify correlations between common SNPs in miR-27a,miR-146a,and miR-124a with T2DM among a Chinese population,as well as to explore diabetic pathological mechanisms and the impact of environmental factors.Methods：SNPscan technology was used to genotype 995 patients newly diagnosed with T2DM and 967 controls.Logistic regression analysis was performed to compare mutation frequencies between cases and controls.Results：We found no significant correlations between all genotypes of these miRNAs and T2DM in our research.However,stratification analysis identified a lower risk of T2DM associated with the rs531564GC genotype among younger subjects （age ＜ 45 years） （adjusted P =0.043; odds ratio [OR] =0.73; 95％ confidence interval [CI] =0.54-0.99）.Furthermore,the rs895819CC genotype in overweight people （24 ＜ body mass index [BMI] ＜ 28） was significantly associated with an increased risk of T2DM （adjusted P =0.042; OR =1.73; 95％ CI =1.02-2.94）,while the rs2910164 genotype in miR-146a was not significantly correlated with T2DM.The genetic risk score was calculated based on the number of risk alleles of the three SNPs and was found to be correlated to total cholesterol （adjusted P =0.021）.Conclusions：The rs531564GC genotype acted as a protective factor to decrease the risk of T2DM in younger subjects （age ＜ 45 years）,while the presence of the rs895819CC genotype increased the risk of illness among overweight subjects （24 ＜ BMI ＜ 28 kg/m2）.The presence of SNPs in miRNA might promote disease by affecting miRNA expression and gene function.Thus,miRNA mimics or inhibitors that directly regulate miRNA expression present novel and promising therapeutic targets.展开更多
Background： Amyotrophic lateral sclerosis （ALS） is a fatal neurodegenerative disease that primarily affects motor neurons and has no effective treatment. Recently, Iida et al. identified a single-nucleotide polymor...Background： Amyotrophic lateral sclerosis （ALS） is a fatal neurodegenerative disease that primarily affects motor neurons and has no effective treatment. Recently, Iida et al. identified a single-nucleotide polymorphism （SNP） rs2275294 in the ZNF512B gene that is significantly associated with susceptibility to ALS in the Japanese population. Here, we performed a case-control study examining the possible association of rs2275294 with risk of sporadic ALS （SALS） in a large Chinese cohort. Methods： To assess this association, we performed a replication study in 953 SALS patients and 1039 age- and gender-matched healthy control subjects, who were recruited from Peking University Third Hospital and the First Affiliated Hospital of Anhui Medical University from January 2004 to December 2013 throughout China. We genotyped the rs2275294 SNP using polymerase chain reaction and direct sequencing. Results： The allele frequency of rs2275294 in ZNF512B was different between Japanese and Chinese. The association in Chinese between ALS patients and controls did not reach statistical significance （P = 0.54; odds ratio = 0.94; 95% confidence interval = 0.76-1.15）. Conclusions： The SNP rs2275294 in ZNF512B is not considered to be associated with ALS susceptibility in the Chinese population. Our study highlights genetic heterogeneity in ALS susceptibility in different population. Given our negative results, further replication study involving larger and more homogeneous samples in different ethnicities should be performed in the future.展开更多
Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contributio...Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contribution to biological diversity and phenotypic variation （Alkan et al., 2011; Bickhart and Liu, 2014）. With the rapid development of the next-generation sequencing technologies and the new assembly methodolo- gies, the multiple de novo assemblies of genomes within a species allow researchers to explore more detailed SV maps （Li et al., 2011）. Compared with the traditional read depth algorithm using the whole-genome resequencing approach and array-based technologies （Baker, 2012; Wang et al., 2012;展开更多
Single-nucleotide polymorphisms(SNPs)are the third generation of genetic markers,having been refined from the first generation of restriction fragment length polymorphisms and the second generation of microsatellite p...Single-nucleotide polymorphisms(SNPs)are the third generation of genetic markers,having been refined from the first generation of restriction fragment length polymorphisms and the second generation of microsatellite polymorphisms.SNPs represent a focal point of current studies of Staphylococcus aureus.On one hand,this review aims to summarize common methodologies for detecting SNPs.These methods have typically included DNA genome sequencing methods and PCR-based detection methods.Alternative methods,such as mass spectrometry,denaturing high-performance liquid chromatography,SNaPshot,and SNP array have also been employed for SNP analysis.On the other hand,we enumerate a series of applications of SNP analysis in investigations of Staphylococcus aureus.SNP analysis can be applied to investigate epidemiological outbreaks and transmission of Staphylococcus aureus infections,the transmission and evolution of antimicrobial resistance genes in Staphylococcus aureus isolates,interactions of Staphylococcus aureus with other bacteria,and the links between Staphylococcus aureus in humans and livestock.展开更多
Our previous studies have demonstrated that ceruloplasmin （CP） dysmetabolism is correlated with Parkinson＇s disease （PD）. However, the causes of decreased serum CP levels in PD patients remain to be clarified. Th...Our previous studies have demonstrated that ceruloplasmin （CP） dysmetabolism is correlated with Parkinson＇s disease （PD）. However, the causes of decreased serum CP levels in PD patients remain to be clarified. This study aimed to explore the potential association between genetic variants of the CP gene and PD. Clinical features, serum CP levels, and the CP gene （both promoter and coding regions） were analyzed in 60 PD patients and 50 controls. A luciferase reporter system was used to investigate the function of promoter single-nucleotide polymorphisms （SNPs）. High-density comparative genomic hybridization microarrays were also used to detect large-scale copy-number variations in CP and an additional 47 genes involved in PD and/or copper/ iron metabolism. The frequencies of eight SNPs （one intronic SNP and seven promoter SNPs of the CP gene） and their haplotypes were significantly different between PD patients, especially those with lowered serum CP levels, and controls. However, the luciferase reporter system revealed no significant effect of the risk haplotype on promoter activity of the CP gene. Neither these SNPs nor their haplotypes were correlated with the Hoehn and Yahr staging of PD. The results of this study suggest that common genetic variants of CP are associated with PD and further investigation is needed to explore their functions in PD.展开更多
Background:Identifying patient-specific flow of signal transduction perturbed by multiple single-nucleotide alterations is critical for improving patient outcomes in cancer cases.However,accurate estimation of mutatio...Background:Identifying patient-specific flow of signal transduction perturbed by multiple single-nucleotide alterations is critical for improving patient outcomes in cancer cases.However,accurate estimation of mutational effects at the pathway level for such patients remains an open problem.While probabilistic pathway topology methods are gaining interest among the scientific community,the overwhelming majority do not account for network perturbation effects from multiple single-nucleotide alterations.Methods:Here we present an improvement of the mutational forks formalism to infer the patient-specific flow of signal transduction based on multiple single-nucleotide alterations,including non-synonymous and synonymous mutations.The lung adenocarcinoma and skin cutaneous melanoma datasets from TCGA Pan-Cancer Atlas have been employed to show the utility of the proposed method.Results:We have comprehensively characterized six mutational forks.The number of mutated nodes ranged from one to four depending on the topological characteristics of a fork.Transitional confidences(TCs)have been computed for every possible combination of single-nucleotide alterations in the fork.The performed analysis demonstrated the capacity of the mutational forks formalism to follow a biologically explainable logic in the identification of high-likelihood signaling routes in lung adenocarcinoma and skin cutaneous melanoma patients.The findings have been largely supported by the evidence from the biomedical literature.Conclusion:We conclude that the formalism has a great chance to enable an assessment of patient-specific flow by leveraging information from multiple single-nucleotide alterations to adjust the transitional likelihoods that are solely based on the canonical view of a disease.展开更多
Background Multi-locus sequence typing （MLST） is widely used to explore the population structure of numerous bacterial pathogens. However, for genotypically-restricted pathogens, the sensitivity of MLST is limited b...Background Multi-locus sequence typing （MLST） is widely used to explore the population structure of numerous bacterial pathogens. However, for genotypically-restricted pathogens, the sensitivity of MLST is limited by a paucity of variation within selected loci. For Bartonella henselae （B. henselae）, although the MLST scheme currently used has been proven useful in defining the overall population structure of the species, its reliability for the accurate delineation of closely-related sequence types, between which allelic variation is usually limited to, at most, one or two nucleotide polymorphisms. Exploitation of high-throughput sequencing data allows a more informed selection of MLST loci and thus, potentially, a means of enhancing the sensitivity of the schemes they comprise. Methods We carried out SOLID resequencing on 12 representative B. henselae isolates and explored these data using single nucleotide polymorphism （SNP） analysis. We determined the number and distribution of SNPs in the genes targeted by the established MLST scheme and modified the position of loci within these genes to capture as much genetic variation as possible. Results Using genome-wide SNP data, we found the distribution of SNPs within each open reading frame （ORF） of MLST loci, which were not represented by the established B. henselae MLST scheme. We then modified the position of loci in the MLST scheme to better reflect the polymorphism in the ORF as a whole. The use of amended loci in this scheme allowed previously indistinguishable ST1 strains to be differentiated. However, the diversity of B. henselae was still rare in China. Conclusions Our study demonstrates the use of SNP analysis to facilitate the selection of MLST loci to augment the currently-described scheme for B. henselae. And the diversity among B. henselae strains in China is markedly less than that observed in B. henselae populations elsewhere in the world.展开更多
Bacterial genome sequencing is a powerful technique for studying the genetic diversity and evolution ofmicrobial populations.However,the detection of genomic variants from sequencing data is challenging due to the pre...Bacterial genome sequencing is a powerful technique for studying the genetic diversity and evolution ofmicrobial populations.However,the detection of genomic variants from sequencing data is challenging due to the presence of contamination,sequencing errors and multiple strains within the same species.Several bioinformatics tools have been developed to address these issues,but their performance and accuracy have not been systematically evaluated.In this study,we compared 10 variant detection pipelines using 18 simulated and 17 real datasets of high-throughput sequences froma bundle of representative bacteria.We assessed the sensitivity of each pipeline under different conditions of coverage,simulation and strain diversity.We also demonstrated the application of these tools to identify consistentmutations in a 30-time repeated sequencing dataset of Staphylococcus hominis.We found that HaplotypeCaller,but not Mutect2,from the GATK tool set showed the best performance in terms of accuracy and robustness.CFSAN and Snippy performed not as well in several simulated and real sequencing datasets.Our results provided a comprehensive benchmark and guidance for choosing the optimal variant detection pipeline for high-throughput bacterial genome sequencing data.展开更多
Objective To identify the association of thyroid stimulating hormone receptor(TSHR)gene intron 1 susceptible loci and 4p14 susceptible locus rs6832151 polymorphisms with Graves’disease(GD)in Han Chinese population in...Objective To identify the association of thyroid stimulating hormone receptor(TSHR)gene intron 1 susceptible loci and 4p14 susceptible locus rs6832151 polymorphisms with Graves’disease(GD)in Han Chinese population in Bengbu,Anhui,China.The gene-gene interaction among TSHR intron 1 susceptible loci and 4p14susceptible locus rs6832151 was also investigated.Methods The genotypes of the single-nucleotide polymor-展开更多
Hypertension(HT)is a major risk factor for cardiovascular diseases.Krüppel-like factors(KLFs)are important transcription factors in eukaryotes.Studies have reported that KLF4 and KLF5 are correlated with several ...Hypertension(HT)is a major risk factor for cardiovascular diseases.Krüppel-like factors(KLFs)are important transcription factors in eukaryotes.Studies have reported that KLF4 and KLF5 are correlated with several cardiovascular diseases,but population-based studies on associations between HT and KLF4 or KLF5 have rarely been reported.Therefore,the current study investigated the associations of genetic variants and m RNA expression levels of KLF4 and KLF5 with HT,as well as the effects of antihypertensive drugs on the expression levels of these genes.The associations of one single-nucleotide polymorphism(SNP)in KLF4 and three SNPs in KLF5with HT were analyzed using a combination of case-control and cohort studies.The study populations were selected from a community-based cohort in four regions of Jiangsu province.The risks of HT were estimated through logistic and Cox regression analyses.In addition,m RNA expression levels of KLF4 and KLF5 were detected in 246 controls and 385 HT cases selected from the aforementioned cohort.Among the HT cases,263were not taking antihypertensive drugs[AHD(-)]and 122 were taking antihypertensive drugs[AHD(+)].In the case-control study,SNP rs9573096(C>T)in KLF5 was significantly associated with an increased risk of HT in the additive model(adjusted odds ratio[OR],1.106;95%confidence interval[CI],1.009 to 1.212).In the cohort study of the normotensive population,rs9573096 in KLF5 was also significantly associated with an increased risk of HT in the additive model(adjusted hazards ratio[HR],1.199;95%CI,1.070 to 1.344).KLF4 and KLF5m RNA expression levels were significantly higher in the AHD(-)group than in the control group(P<0.05),but lower in the AHD(+)group than in the AHD(-)group(P<0.05).The current study demonstrated the associations of KLF4 and KLF5 genetic variants with hypertension,as well as the association of the indicative variations in m RNA expression levels of KLF4 and KLF5 with the risk of hypertension and antihypertensive treatment.展开更多
Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,ar...Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,are still largely unknown,especially at the genome level,despite their importance in understanding the formation and outbreak of massive green tides.In the present study,the restriction site-associated DNA genotyping approach(2b-RAD)was adopted to identify the genome-wide single-nucleotide polymorphisms(SNPs)of 54 individual thalli including samples collected from Subei Shoal in 2019 and Qingdao coast from 2019 to 2021.SNPs genotype results revealed that most of the thalli in 2019 and 2020 were haploid gametophytes,while only half of the thalli were gametophytes in 2021,indicating flexibility in the reproductive strategies for the formation of the green tides among different years and the dominance of asexual and vegetative reproductive mode for the floating period.Besides,population analysis was conducted,and it revealed a very low genetic diversity among samples from Subei Shoal and the Qingdao coast in the same year and a higher divergence among samples in different years.The results showed the efficiency of 2b-RAD in the exploration of SNPs in U.prolifera and provided the first genome-wide scale evidence for the origin of the large-scale green tides on the Qingdao coast.This study improved our understanding of the reproductive strategy and genetic diversity of the green tide causative species and will help further reveal the biological causes of the green tide in China.展开更多
Objective: Vacuolating megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a recently described syndrome with autosomal recessive mode of inheritance. Its possible gene was located on chromosomal 22q ...Objective: Vacuolating megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a recently described syndrome with autosomal recessive mode of inheritance. Its possible gene was located on chromosomal 22q tel with 3-cM. The purpose of this study was to narrow down the genetical distance on chromosomal 22q tel with MLC. Methods: Thirty-nine MLC patients in 33 families were collected,and the linkage analysis and haplotype analysis of twelve informative families were done, using seven microsatellite markers and four SNP markers. Results: The maximum tow-point LOD score for marker 355c18 was 6.65 at recombination fraction 0.02. The haplotype analysis narrowed down the critical region of MLC to 250 kb on chromosomal 22q tel. Conclusion: One of the causing genes of MLC was located on chromosomal 22q tel with 250 kb. Four candidate genes were considered. The heterogeneity of one informative family indicated possible existence of a second locus for MLC.展开更多
Ischemic stroke is a complicated disease, and its pathogenesis has been attributed to the occurrence of genetic polymorphisms.Evidence has suggested that the microRNA let-7a is involved in the pathogenesis of ischemic...Ischemic stroke is a complicated disease, and its pathogenesis has been attributed to the occurrence of genetic polymorphisms.Evidence has suggested that the microRNA let-7a is involved in the pathogenesis of ischemic stroke.Pri-miRNA is the primary transcript, which undergoes several processing steps to generate pre-miRNA and, later, mature miRNAs.In this case-control study, we analyzed the distribution of prilet-7a-2 variants in patients at a high risk for ischemic stroke and the interactions of pri-let-7a-2 variants and environmental factors.Blood samples and clinical information were collected from 1086 patients with ischemic stroke and 836 healthy controls between December 2013 and December 2015 at the First Affiliated Hospital of China Medical University.We found that the rs1143770 CC genotype and the C allele were associated with a decreased risk of ischemic stroke, whereas the rs629367 CC genotype was associated with an increased risk for ischemic stroke.Moreover, these two single-nucleotide polymorphisms were in linkage disequilibrium in this study sample.We analyzed gene-environment interactions and found that rs1143770 exerted a combined effect on the pathogenesis of ischemic stroke, together with alcohol use, smoking, and a history of hypertension.Therefore, the detection of pri-let-7a-2 polymorphisms may increase the awareness of ischemic stroke risk.This study was approved by the Institutional Ethics Committee of the First Affiliated Hospital of China Medical University, China(approval No.2012-38-1) on February 20, 2012, and was registered with the Chinese Clinical Trial Registry(registration number: ChiCTR-COC-17013559) on December 27, 2017.展开更多
Irritable bowel syndrome(IBS) is the most common functional gastrointestinal disorder characterized by presence of abdominal pain or discomfort associated with altered bowel habits. It has three main subtypes- constip...Irritable bowel syndrome(IBS) is the most common functional gastrointestinal disorder characterized by presence of abdominal pain or discomfort associated with altered bowel habits. It has three main subtypes- constipation predominant IBS(C-IBS),diarrhea predominant IBS(D-IBS) and IBS with mixed featuresof both diarrhea as well as constipation(M-IBS). Its pathophysiology and underlying mechanisms remain elusive. It is traditionally believed that IBS is a result of multiple factors including hypersensitivity of the bowel,altered bowel motility,inflammation and stress. Initial studies have shown familial aggregation of IBS suggesting shared genetic or environmental factors. Twin studies of IBS from different parts of world have shown higher concordance rates among monozygotic twins than dizygotic twins,and thus suggesting a genetic component to this disorder. Multiple studies have tried to link single-nucleotide polymorphisms(SNPs) to IBS but there is little evidence that these SNPs are functional. Various molecules have been studied and investigated by the researchers. Serotonin,a known neurotransmitter and a local hormone in the enteric nervous system,has been most extensively explored. At this time,the underlying gene pathways,genes and functional variants linked with IBS remain unknown and the promise of genetically-determined risk prediction and personalize medicine remain unfulfilled. However,molecular biological technologies continue to evolve rapidly and genetic investigations offer much promise in the intervention,treatment and prevention of IBS.展开更多
基金ACKNOWLEDGMENTS This research was supported by the Major State Basic Research Development Program of China （973 Program, Noso 2006GB504005 and 2009CB941700）, the National Natural Science Foundation of China （No. 30872765） and the Basic Research Key Program of Shanghai （10]C1410800）. Shi-Wei Duan is sponsored partly by the K. C. Wong Magna Fund of Ningbo University. Wethank Dr Ching-Ling Chen for kind suggestions regarding English in drafting this paper.
文摘Multiplex polymerase chain reaction （PCR） has been widely used to detect Y-chromosome micredeletions, which is one of the major causes of male infertility. Both the European Academy of Andrology （EAA） and the European Molecular Genetics Quality Network （EMQN） have recommended the use of sY84 and sY86 markers for the detection of azoospermia factor a （AZFa） microdeletion during DNA testing for male infertility. In this study, a large-scale analysis of AZF microdeletion in a total of 630 Chinese males, including healthy semen donors （n=200）, infertile males with normal sperm count （n=226） and patients with either nonobstructive azoospermia or severe oligozoospermia （n=204）, was performed. A series of nine sequence-tagged site （STS） markers from the AZF region of the Y chromosome was used to detect microdeletions. All primers were designed based on the recommendations of the National Center for Biotechnology Information. An unusually high incidence （73/630, 11.6%） of sY84-absent but sY86-present genotypes was observed in the AZFa microdeletion screening. Sequencing the sY84-flanking region revealed a total of 73 patients with sY84-absent but sY86-present genotypes have a T-to-G transversion at the fifth base from the 5＇ end of the reverse sY84 primer. These prevalent false positives, which were not only observed in infertile men, but also observed in donors, resulted from a single-nucleotide polymorphism （SNP） named rs72609647 in the targeting sequence of the reverse sY84 primer. Our study suggests that a pre-screening of existence of rs72609647 polymorphism can prevent the frequent false positive results of AZFa microdeletions detection in the infertile Chinese males. Given the SNP rs72609647 was recently found in a deep sequencing of a Chinese individual, the current EAA and EMQN standards may need to be scrutinized among different populations to avoid the potential genetic variations in the primer binding sequences.
基金the National Natural Science Foundation of China,No.81470849the China Mega-Project for Infectious Diseases,No.2017ZX10203202.
文摘BACKGROUND Polygonum multiflorum is one of the leading causes of herb-induced liver injury in China.HLA-B*35:01 is reported to be a potential biomarker of Polygonum multiflorum-induced liver injury(PM-DILI).However,little is known about the relationship between single-nucleotide polymorphisms(SNPs) and PM-DILI.AIM To identify SNPs that indicate susceptibility to PM-DILI METHODS We conducted a systematic study enrolling 382 participants from four independent hospitals,including 73 PM-DILI patients,118 patients with other drug-induced liver injury(other-DILI) and 191 healthy controls.Whole-exome sequencing was performed for 8 PM-DILI patients and 8 healthy controls who were randomly selected from the above subjects.Nineteen SNPs that showed high frequencies in the 8 PM-DILI patients were selected as candidate SNPs and then screened in 65 PM-DILI patients,118 other-DILI patients and 183 healthy controls using the MassARRAY system.HLA-B high-resolution genotyping was performed for the 73 PM-DILI and 118 other-DILI patients.The Han-MHC database was selected as a population control for HLA-B analysis.P <6.25 x 103 after Bolferroni correction was considered significant.RESULTS The frequencies of rslll686806 in the HLA-A gene,rs1055348 in the HLA-B gene,and rs202047044 in the HLA-DRB1 gene were significantly higher in the PM-DILI group than in the control group [27.2% vs 11.6%,P=1.72×105,odds ratio(OR)=3.96,95% confidence interval(Cl):2.21-7.14;42.5% vs 8.6%,P=1.72×10-19 OR=13.62,95% CI:7.16-25.9;22.9% vs 8.1%,P=4.64×106,OR=4.1,95% CI:2.25-7.47].Only rs1055348 showed a significantly higher frequency in the PM-DILI group than in the other-DILI group(42.5% vs 13.6%,P=1.84×10-10,OR=10.06,95% Cl:5.06-20.0),which suggested that it is a specific risk factor for PM-DILI.rs1055348 may become a tag for HLA-B*35:01 with 100% sensitivity and 97.7% specificity in the PM-DILI group and 100% sensitivity and 98.1% specificity in the other-DILI group.Furthermore,HLA-B*35:01 was confirmed to be associated with PM-DILI with a frequency of 41.1% in the PM-DILI group compared with 11.9%(P=4.30×10-11,OR=11.11,95% CI:5.57-22.19) in the other-DILI group and 2.7%(P=6.22×10-166,OR=62.62,95% Cl:35.91-109.20) in the Han-MHC database.CONCLUSION rslll686806,rs1055348,and rs202047044 are associated with PM-DILI,of which,rs1055348 is specific to PM-DILI.As a tag for HLA-B*35:01,rs1055348 may become an alternative predictive biomarker of PM-DILI.
基金"135 Project"Key Talent Fund of Public Health Department of Jiangsu Province
文摘Objective To analyze the role of resistin in insulin resistance (IR) through investigating the variation of plasma resistin levels and single-nucleotide polymorphisms (SNPs) in resistin gene 5’ flanking region in stroke patients.Methods In 103 atherothrombotic cerebral infarction (ACI) patients, 85 lacunar infarction (LI) patients, 70 intracerebral hemorrhage (ICH) patients, and 86 healthy controls, plasma resistin and insulin levels were measured by ELISA , SNPs in resistin gene 5’ flanking region were detected by PCR and direct DNA sequencing. The subjects’ body height and weight, the body mass index, quantitative insulin sensitivity check index (QUICKI), blood pressure, and the concentration of fasting plasma glucose, triglyceride, total cholesterol, creatinine, low-density lipoprotein, and high-density lipoprotein were also determined. Results QUICKI was significantly lower in the ACI and ICH patients (0.316±0.037 and 0.309±0.032, respectively) than that in the controls (0.342±0.043, P<0.001), while plasma resistin level was significantly higher in the ACI and ICH patients (6.36±3.79 and 7.15±4.27 ng/mL, respectively) than that in the controls (5.28±2.56 ng/mL, P<0.05), but such difference was not observed in the LI patients compared with controls. There was a statistically negative correlation between plasma resistin level with QUICKI (r=-0.228, P<0.001). The distributions of allele and genotype frequencies of resistin gene -420C>G and -537A>C SNPs were not significantly different among the different groups, and those SNPs were not correlated with other clinical and biochemical parameters.Conclusions Plasma resistin is associated with stroke by participating in the development of IR. The SNPs in resistin gene 5’ flanking region has no impact on the plasma resistin level.
文摘Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and improve tenderness;however, there has been no direct correlation demonstrated between beef taste and oleic acid. To investigate genes affecting other fatty acids other than oleic acid, polymorphisms of the fatty acid desaturase 2 (FADS2) gene were genotyped and associations with fatty acid profile in JBK beef were investigated. Amplifications of 5’-flanking regions, 12 exons, and 3’-untranslated regions of the FADS2 gene in three Japanese and five Western cattle breeds via PCR, were amplified, sequenced and SNPs were identified using specific TaqMan genotyping assay. Fatty acid composition of intramuscular adipose tissue of the Trapezius muscle was analyzed in JBK steers. Six of the 15 identified SNPs are novel and have never been registered in any public bovine SNP database. A non-synonymous SNP (rs211580559;C > T;294 Ala > Val) in exon 7 was examined in order to evaluate its association with fatty acid profiles. The data showed that highly significant association existed between rs211580559 and C18:2 (n-6) composition, and accounted for 22.3% of the variation. There were no significant relationships between rs2115-80559 and the other fatty acids. It was concluded that rs211580559 of the FADS2 gene may be a useful selection marker for reducing unfavorable volatiles generated from linoleic acid in JBK beef during the cooking process.
基金funded by the National Natural Science Foundation of China(grant no.32270238 and 31870311).
文摘Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.
基金National Natural Science Foundation of China(No.82270792)
文摘Background:Growth retardation is a common complication of chronic kidney disease in children,which can be partially relieved after renal transplantation.This study aimed to develop and validate a predictive model for growth patterns of children with end-stage renal disease(ESRD)after kidney transplantation using machine learning algorithms based on genomic and clinical variables.Methods:A retrospective cohort of 110 children who received kidney transplants between May 2013 and September 2021 at the First Affiliated Hospital of Zhengzhou University were recruited for whole-exome sequencing(WES),and another 39 children who underwent transplant from October 2021 to March 2022 were enrolled for external validation.Based on previous studies,we comprehensively collected 729 height-related single-nucleotide polymorphisms(SNPs)in exon regions.Seven machine learning algorithms and 10-fold cross-validation analysis were employed for model construction.Results:The 110 children were divided into two groups according to change in height-for-age Z-score.After univariate analysis,age and 19 SNPs were incorporated into the model and validated.The random forest model showed the best prediction efficacy with an accuracy of 0.8125 and an area under curve(AUC)of 0.924,and also performed well in the external validation cohort(accuracy,0.7949;AUC,0.796).Conclusions:A model with good performance for predicting post-transplant growth patterns in children based on SNPs and clinical variables was constructed and validated using machine learning algorithms.The model is expected to guide clinicians in the management of children after renal transplantation,including the use of growth hormone,glucocorticoid withdrawal,and nutritional supplementation,to alleviate growth retardation in children with ESRD.
基金This work was funded by the National Natural Science Foundation of China，The Natural Science Foundation of Heilongjiang Province
文摘Background：Polymorphisms of microRNA （miRNA）,as a novel mechanism,are closely associated with disease states by interfering with miRNA function.Direct correlations have been identified between single-nucleotide polymorphisms （SNPs） in miRNA,but the effect on type 2 diabetes mellitus （T2DM） onset among Chinese population remains unclear.Therefore,the aim of this study was to identify correlations between common SNPs in miR-27a,miR-146a,and miR-124a with T2DM among a Chinese population,as well as to explore diabetic pathological mechanisms and the impact of environmental factors.Methods：SNPscan technology was used to genotype 995 patients newly diagnosed with T2DM and 967 controls.Logistic regression analysis was performed to compare mutation frequencies between cases and controls.Results：We found no significant correlations between all genotypes of these miRNAs and T2DM in our research.However,stratification analysis identified a lower risk of T2DM associated with the rs531564GC genotype among younger subjects （age ＜ 45 years） （adjusted P =0.043; odds ratio [OR] =0.73; 95％ confidence interval [CI] =0.54-0.99）.Furthermore,the rs895819CC genotype in overweight people （24 ＜ body mass index [BMI] ＜ 28） was significantly associated with an increased risk of T2DM （adjusted P =0.042; OR =1.73; 95％ CI =1.02-2.94）,while the rs2910164 genotype in miR-146a was not significantly correlated with T2DM.The genetic risk score was calculated based on the number of risk alleles of the three SNPs and was found to be correlated to total cholesterol （adjusted P =0.021）.Conclusions：The rs531564GC genotype acted as a protective factor to decrease the risk of T2DM in younger subjects （age ＜ 45 years）,while the presence of the rs895819CC genotype increased the risk of illness among overweight subjects （24 ＜ BMI ＜ 28 kg/m2）.The presence of SNPs in miRNA might promote disease by affecting miRNA expression and gene function.Thus,miRNA mimics or inhibitors that directly regulate miRNA expression present novel and promising therapeutic targets.
基金The research was supported by grants from the National Natural Science Foundation of China
文摘Background： Amyotrophic lateral sclerosis （ALS） is a fatal neurodegenerative disease that primarily affects motor neurons and has no effective treatment. Recently, Iida et al. identified a single-nucleotide polymorphism （SNP） rs2275294 in the ZNF512B gene that is significantly associated with susceptibility to ALS in the Japanese population. Here, we performed a case-control study examining the possible association of rs2275294 with risk of sporadic ALS （SALS） in a large Chinese cohort. Methods： To assess this association, we performed a replication study in 953 SALS patients and 1039 age- and gender-matched healthy control subjects, who were recruited from Peking University Third Hospital and the First Affiliated Hospital of Anhui Medical University from January 2004 to December 2013 throughout China. We genotyped the rs2275294 SNP using polymerase chain reaction and direct sequencing. Results： The allele frequency of rs2275294 in ZNF512B was different between Japanese and Chinese. The association in Chinese between ALS patients and controls did not reach statistical significance （P = 0.54; odds ratio = 0.94; 95% confidence interval = 0.76-1.15）. Conclusions： The SNP rs2275294 in ZNF512B is not considered to be associated with ALS susceptibility in the Chinese population. Our study highlights genetic heterogeneity in ALS susceptibility in different population. Given our negative results, further replication study involving larger and more homogeneous samples in different ethnicities should be performed in the future.
基金supported by the National High Technology Research and Development Program of China(863 Program)(No.2013AA102502)the National Natural Science Foundation of China(Nos.31372284 and 31402046)+1 种基金the Fund of Fok Ying-Tung Education Foundation(No.141117)the Fund for Distinguished Young Scientists of Sichuan Province(No. 2013JQ0013)
文摘Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contribution to biological diversity and phenotypic variation （Alkan et al., 2011; Bickhart and Liu, 2014）. With the rapid development of the next-generation sequencing technologies and the new assembly methodolo- gies, the multiple de novo assemblies of genomes within a species allow researchers to explore more detailed SV maps （Li et al., 2011）. Compared with the traditional read depth algorithm using the whole-genome resequencing approach and array-based technologies （Baker, 2012; Wang et al., 2012;
文摘Single-nucleotide polymorphisms(SNPs)are the third generation of genetic markers,having been refined from the first generation of restriction fragment length polymorphisms and the second generation of microsatellite polymorphisms.SNPs represent a focal point of current studies of Staphylococcus aureus.On one hand,this review aims to summarize common methodologies for detecting SNPs.These methods have typically included DNA genome sequencing methods and PCR-based detection methods.Alternative methods,such as mass spectrometry,denaturing high-performance liquid chromatography,SNaPshot,and SNP array have also been employed for SNP analysis.On the other hand,we enumerate a series of applications of SNP analysis in investigations of Staphylococcus aureus.SNP analysis can be applied to investigate epidemiological outbreaks and transmission of Staphylococcus aureus infections,the transmission and evolution of antimicrobial resistance genes in Staphylococcus aureus isolates,interactions of Staphylococcus aureus with other bacteria,and the links between Staphylococcus aureus in humans and livestock.
基金supported by the National Natural Science Foundation of China (81200973)the National Basic Research Development Program of China (2011CBA00400)an Independent Scientific Research Project of Hehai University (20520133484)
文摘Our previous studies have demonstrated that ceruloplasmin （CP） dysmetabolism is correlated with Parkinson＇s disease （PD）. However, the causes of decreased serum CP levels in PD patients remain to be clarified. This study aimed to explore the potential association between genetic variants of the CP gene and PD. Clinical features, serum CP levels, and the CP gene （both promoter and coding regions） were analyzed in 60 PD patients and 50 controls. A luciferase reporter system was used to investigate the function of promoter single-nucleotide polymorphisms （SNPs）. High-density comparative genomic hybridization microarrays were also used to detect large-scale copy-number variations in CP and an additional 47 genes involved in PD and/or copper/ iron metabolism. The frequencies of eight SNPs （one intronic SNP and seven promoter SNPs of the CP gene） and their haplotypes were significantly different between PD patients, especially those with lowered serum CP levels, and controls. However, the luciferase reporter system revealed no significant effect of the risk haplotype on promoter activity of the CP gene. Neither these SNPs nor their haplotypes were correlated with the Hoehn and Yahr staging of PD. The results of this study suggest that common genetic variants of CP are associated with PD and further investigation is needed to explore their functions in PD.
文摘Background:Identifying patient-specific flow of signal transduction perturbed by multiple single-nucleotide alterations is critical for improving patient outcomes in cancer cases.However,accurate estimation of mutational effects at the pathway level for such patients remains an open problem.While probabilistic pathway topology methods are gaining interest among the scientific community,the overwhelming majority do not account for network perturbation effects from multiple single-nucleotide alterations.Methods:Here we present an improvement of the mutational forks formalism to infer the patient-specific flow of signal transduction based on multiple single-nucleotide alterations,including non-synonymous and synonymous mutations.The lung adenocarcinoma and skin cutaneous melanoma datasets from TCGA Pan-Cancer Atlas have been employed to show the utility of the proposed method.Results:We have comprehensively characterized six mutational forks.The number of mutated nodes ranged from one to four depending on the topological characteristics of a fork.Transitional confidences(TCs)have been computed for every possible combination of single-nucleotide alterations in the fork.The performed analysis demonstrated the capacity of the mutational forks formalism to follow a biologically explainable logic in the identification of high-likelihood signaling routes in lung adenocarcinoma and skin cutaneous melanoma patients.The findings have been largely supported by the evidence from the biomedical literature.Conclusion:We conclude that the formalism has a great chance to enable an assessment of patient-specific flow by leveraging information from multiple single-nucleotide alterations to adjust the transitional likelihoods that are solely based on the canonical view of a disease.
文摘Background Multi-locus sequence typing （MLST） is widely used to explore the population structure of numerous bacterial pathogens. However, for genotypically-restricted pathogens, the sensitivity of MLST is limited by a paucity of variation within selected loci. For Bartonella henselae （B. henselae）, although the MLST scheme currently used has been proven useful in defining the overall population structure of the species, its reliability for the accurate delineation of closely-related sequence types, between which allelic variation is usually limited to, at most, one or two nucleotide polymorphisms. Exploitation of high-throughput sequencing data allows a more informed selection of MLST loci and thus, potentially, a means of enhancing the sensitivity of the schemes they comprise. Methods We carried out SOLID resequencing on 12 representative B. henselae isolates and explored these data using single nucleotide polymorphism （SNP） analysis. We determined the number and distribution of SNPs in the genes targeted by the established MLST scheme and modified the position of loci within these genes to capture as much genetic variation as possible. Results Using genome-wide SNP data, we found the distribution of SNPs within each open reading frame （ORF） of MLST loci, which were not represented by the established B. henselae MLST scheme. We then modified the position of loci in the MLST scheme to better reflect the polymorphism in the ORF as a whole. The use of amended loci in this scheme allowed previously indistinguishable ST1 strains to be differentiated. However, the diversity of B. henselae was still rare in China. Conclusions Our study demonstrates the use of SNP analysis to facilitate the selection of MLST loci to augment the currently-described scheme for B. henselae. And the diversity among B. henselae strains in China is markedly less than that observed in B. henselae populations elsewhere in the world.
基金supported by Zhejiang Provincial Natural Science Foundation(LY20H030006)Key Research&Development Program of Zhejiang(2023C03045)+2 种基金Fundamental Research Funds for the Central Universities(2022ZFJH003)Jinan Microecological Biomedicine Shandong Laboratory(JNL-2022036C)Public Welfare Project of Jinhua City,Zhejiang(2021-4-359).
文摘Bacterial genome sequencing is a powerful technique for studying the genetic diversity and evolution ofmicrobial populations.However,the detection of genomic variants from sequencing data is challenging due to the presence of contamination,sequencing errors and multiple strains within the same species.Several bioinformatics tools have been developed to address these issues,but their performance and accuracy have not been systematically evaluated.In this study,we compared 10 variant detection pipelines using 18 simulated and 17 real datasets of high-throughput sequences froma bundle of representative bacteria.We assessed the sensitivity of each pipeline under different conditions of coverage,simulation and strain diversity.We also demonstrated the application of these tools to identify consistentmutations in a 30-time repeated sequencing dataset of Staphylococcus hominis.We found that HaplotypeCaller,but not Mutect2,from the GATK tool set showed the best performance in terms of accuracy and robustness.CFSAN and Snippy performed not as well in several simulated and real sequencing datasets.Our results provided a comprehensive benchmark and guidance for choosing the optimal variant detection pipeline for high-throughput bacterial genome sequencing data.
文摘Objective To identify the association of thyroid stimulating hormone receptor(TSHR)gene intron 1 susceptible loci and 4p14 susceptible locus rs6832151 polymorphisms with Graves’disease(GD)in Han Chinese population in Bengbu,Anhui,China.The gene-gene interaction among TSHR intron 1 susceptible loci and 4p14susceptible locus rs6832151 was also investigated.Methods The genotypes of the single-nucleotide polymor-
基金supported by the National Natural Science Foundation of China(Grant Nos.81872686 and 82173611)the National Key Research and Development Program of China(Grant No.2018YFC2000703)the Priority Academic Program for the Development of Jiangsu Higher Education Institutions(Public Health and Preventive Medicine)。
文摘Hypertension(HT)is a major risk factor for cardiovascular diseases.Krüppel-like factors(KLFs)are important transcription factors in eukaryotes.Studies have reported that KLF4 and KLF5 are correlated with several cardiovascular diseases,but population-based studies on associations between HT and KLF4 or KLF5 have rarely been reported.Therefore,the current study investigated the associations of genetic variants and m RNA expression levels of KLF4 and KLF5 with HT,as well as the effects of antihypertensive drugs on the expression levels of these genes.The associations of one single-nucleotide polymorphism(SNP)in KLF4 and three SNPs in KLF5with HT were analyzed using a combination of case-control and cohort studies.The study populations were selected from a community-based cohort in four regions of Jiangsu province.The risks of HT were estimated through logistic and Cox regression analyses.In addition,m RNA expression levels of KLF4 and KLF5 were detected in 246 controls and 385 HT cases selected from the aforementioned cohort.Among the HT cases,263were not taking antihypertensive drugs[AHD(-)]and 122 were taking antihypertensive drugs[AHD(+)].In the case-control study,SNP rs9573096(C>T)in KLF5 was significantly associated with an increased risk of HT in the additive model(adjusted odds ratio[OR],1.106;95%confidence interval[CI],1.009 to 1.212).In the cohort study of the normotensive population,rs9573096 in KLF5 was also significantly associated with an increased risk of HT in the additive model(adjusted hazards ratio[HR],1.199;95%CI,1.070 to 1.344).KLF4 and KLF5m RNA expression levels were significantly higher in the AHD(-)group than in the control group(P<0.05),but lower in the AHD(+)group than in the AHD(-)group(P<0.05).The current study demonstrated the associations of KLF4 and KLF5 genetic variants with hypertension,as well as the association of the indicative variations in m RNA expression levels of KLF4 and KLF5 with the risk of hypertension and antihypertensive treatment.
基金Supported by the Laoshan Laboratory (No.LSKJ202204005)the Mount Tai Scholar Climbing Plan to Song SUNthe Open Fund of CAS Key Laboratory of Marine Ecology and Environmental Sciences,Institute of Oceanology,Chinese Academy of Sciences (No.KLMEES201801)
文摘Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,are still largely unknown,especially at the genome level,despite their importance in understanding the formation and outbreak of massive green tides.In the present study,the restriction site-associated DNA genotyping approach(2b-RAD)was adopted to identify the genome-wide single-nucleotide polymorphisms(SNPs)of 54 individual thalli including samples collected from Subei Shoal in 2019 and Qingdao coast from 2019 to 2021.SNPs genotype results revealed that most of the thalli in 2019 and 2020 were haploid gametophytes,while only half of the thalli were gametophytes in 2021,indicating flexibility in the reproductive strategies for the formation of the green tides among different years and the dominance of asexual and vegetative reproductive mode for the floating period.Besides,population analysis was conducted,and it revealed a very low genetic diversity among samples from Subei Shoal and the Qingdao coast in the same year and a higher divergence among samples in different years.The results showed the efficiency of 2b-RAD in the exploration of SNPs in U.prolifera and provided the first genome-wide scale evidence for the origin of the large-scale green tides on the Qingdao coast.This study improved our understanding of the reproductive strategy and genetic diversity of the green tide causative species and will help further reveal the biological causes of the green tide in China.
文摘Objective: Vacuolating megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a recently described syndrome with autosomal recessive mode of inheritance. Its possible gene was located on chromosomal 22q tel with 3-cM. The purpose of this study was to narrow down the genetical distance on chromosomal 22q tel with MLC. Methods: Thirty-nine MLC patients in 33 families were collected,and the linkage analysis and haplotype analysis of twelve informative families were done, using seven microsatellite markers and four SNP markers. Results: The maximum tow-point LOD score for marker 355c18 was 6.65 at recombination fraction 0.02. The haplotype analysis narrowed down the critical region of MLC to 250 kb on chromosomal 22q tel. Conclusion: One of the causing genes of MLC was located on chromosomal 22q tel with 250 kb. Four candidate genes were considered. The heterogeneity of one informative family indicated possible existence of a second locus for MLC.
基金supported by the National Natural Science Foundation of China, No.81901189the Natural Science Foundation of Liaoning Province of China, No.2019-BS-147(both to YZW)。
文摘Ischemic stroke is a complicated disease, and its pathogenesis has been attributed to the occurrence of genetic polymorphisms.Evidence has suggested that the microRNA let-7a is involved in the pathogenesis of ischemic stroke.Pri-miRNA is the primary transcript, which undergoes several processing steps to generate pre-miRNA and, later, mature miRNAs.In this case-control study, we analyzed the distribution of prilet-7a-2 variants in patients at a high risk for ischemic stroke and the interactions of pri-let-7a-2 variants and environmental factors.Blood samples and clinical information were collected from 1086 patients with ischemic stroke and 836 healthy controls between December 2013 and December 2015 at the First Affiliated Hospital of China Medical University.We found that the rs1143770 CC genotype and the C allele were associated with a decreased risk of ischemic stroke, whereas the rs629367 CC genotype was associated with an increased risk for ischemic stroke.Moreover, these two single-nucleotide polymorphisms were in linkage disequilibrium in this study sample.We analyzed gene-environment interactions and found that rs1143770 exerted a combined effect on the pathogenesis of ischemic stroke, together with alcohol use, smoking, and a history of hypertension.Therefore, the detection of pri-let-7a-2 polymorphisms may increase the awareness of ischemic stroke risk.This study was approved by the Institutional Ethics Committee of the First Affiliated Hospital of China Medical University, China(approval No.2012-38-1) on February 20, 2012, and was registered with the Chinese Clinical Trial Registry(registration number: ChiCTR-COC-17013559) on December 27, 2017.
文摘Irritable bowel syndrome(IBS) is the most common functional gastrointestinal disorder characterized by presence of abdominal pain or discomfort associated with altered bowel habits. It has three main subtypes- constipation predominant IBS(C-IBS),diarrhea predominant IBS(D-IBS) and IBS with mixed featuresof both diarrhea as well as constipation(M-IBS). Its pathophysiology and underlying mechanisms remain elusive. It is traditionally believed that IBS is a result of multiple factors including hypersensitivity of the bowel,altered bowel motility,inflammation and stress. Initial studies have shown familial aggregation of IBS suggesting shared genetic or environmental factors. Twin studies of IBS from different parts of world have shown higher concordance rates among monozygotic twins than dizygotic twins,and thus suggesting a genetic component to this disorder. Multiple studies have tried to link single-nucleotide polymorphisms(SNPs) to IBS but there is little evidence that these SNPs are functional. Various molecules have been studied and investigated by the researchers. Serotonin,a known neurotransmitter and a local hormone in the enteric nervous system,has been most extensively explored. At this time,the underlying gene pathways,genes and functional variants linked with IBS remain unknown and the promise of genetically-determined risk prediction and personalize medicine remain unfulfilled. However,molecular biological technologies continue to evolve rapidly and genetic investigations offer much promise in the intervention,treatment and prevention of IBS.
