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
Chinese hamster with Chinese characteristics is used in experiments,and it is of great value in the field of medical biology research.However,at present,there is no high-efficiency method for evaluating the genetic qu...Chinese hamster with Chinese characteristics is used in experiments,and it is of great value in the field of medical biology research.However,at present,there is no high-efficiency method for evaluating the genetic quality of Chinese hamsters.Here,we developed a novel Chinese hamster genetic quality detection system using single-nucleotide polymorphism(SNP)markers.To find SNP loci,we conducted whole genome sequencing on 24 Chinese hamsters.Then,we employed an SNP locus screening criterion that we set up previously and initially screened 214 SNP loci with wide genome distribution and high polymorphism level.Subsequently,we developed the SNP detection system using a multitarget region capture technique based on second-generation sequencing,and a 55 SNP panel for genetic evaluation of Chinese hamster populations was developed.PopGen.32.analysis results showed that the average effective allele number,Shannon index,observed heterozygosity,expected heterozygosity,average heterozygosity,polymorphism information,and other genetic parameters of Chinese hamster population A were higher than those in population B.Using scientific screening and optimization,we successfully developed a novel Chinese hamster SNP genetic detection system that can efficiently and accurately analyze the genetic quality of the Chinese hamster population.展开更多
BACKGROUND There are conflicting results on the potential correlation between folic acid and gestational diabetes mellitus(GDM),and the correlation between genetic factors related to folic acid metabolism pathways and...BACKGROUND There are conflicting results on the potential correlation between folic acid and gestational diabetes mellitus(GDM),and the correlation between genetic factors related to folic acid metabolism pathways and GDM remains to be revealed.AIM To examine the association between single-nucleotide polymorphisms(SNPs)of enzyme genes in the folate metabolite pathway as well as that between GDM-related genes and risk for GDM.METHODS A nested case-control study was conducted with GDM cases(n=412)and healthy controls(n=412).DNA was extracted blood samples and SNPs were genotyped using Agena Bioscience’s MassARRAY gene mass spectrometry system.The associations between different SNPs of genes and the risk for GDM were estimated using logistic regression models.The generalized multi-factor dimensionality reduction(GMDR)method was used to analyze gene-gene and gene-environment interactions using the GMDR 0.9 software.RESULTS The variation allele frequency of melatonin receptor 1B(MTNR1B)rs10830963 was higher in the GDM group than in controls(P<0.05).MTNR1B rs10830963 mutant G was associated with risk for GDM[adjusted odds ratio(aOR):1.43;95%confidence interval(95%CI):1.13-1.80]in the additive model.MTNR1B rs10830963 GG+GC was significantly associated with the risk for GDM(aOR:1.65;95%CI:1.23-2.22)in the dominant model.The two-locus model of MTNR1B rs10830963 and CHEMERIN rs4721 was the best model(P<0.05)for gene-gene interactions in the GMDR results.The high-risk rs10830963×rs4721 type of interaction was a risk factor for GDM(aOR:2.09;95%CI:1.49-2.93).CONCLUSION This study does not find an association between SNPs of folate metabolic enzymes and risk for GDM.The G mutant allele of MTNR1B rs10830963 is identified as a risk factor for GDM in the additive model,and there may be gene-gene interactions between MTNR1B rs10830963 and CHEMERIN rs4721.It is conducive to studying the causes of GDM and provides a new perspective for the precise prevention of this disease.展开更多
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
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
Matrix metalloproteinases(MMPs) are implicated in cancer development and progression and are associated with prognosis.Single-nucleotide polymorphisms(SNPs) of MMPs,most frequently located in the promoter region of th...Matrix metalloproteinases(MMPs) are implicated in cancer development and progression and are associated with prognosis.Single-nucleotide polymorphisms(SNPs) of MMPs,most frequently located in the promoter region of the genes,have been shown to influence cancer susceptibility and/or progression.SNPs of MMP-1,-2,-3,-7,-8,-9,-12,-13 and-21 and of the tissue inhibitor of metalloproteinases(TIMPs) TIMP-1 and TIMP-2 have been studied in digestive tract tumors.The contribution of these polymorphisms to the cancer risk and prognosis of gastrointestinal tumors are reviewed in this paper.展开更多
Fructans are major nonstructural carbohydrates in wheat （Triticum aestivum L.）. Fructan 1-fructosyltransferase （1-FFT） is the key enzyme in fructan biosynthesis. In the present study, 96 sequence variants were det...Fructans are major nonstructural carbohydrates in wheat （Triticum aestivum L.）. Fructan 1-fructosyltransferase （1-FFT） is the key enzyme in fructan biosynthesis. In the present study, 96 sequence variants were detected in the 1-FFT-A 1 gene among 26 wheat accessions including UR208, and 15 of them result in amino acid substitutions, forming four haplotypes. Two markers M39 and M2164 were developed based on the InDe121-39 and SNP-2164 polymorphisms to distinguish the three haplotypes in the 1-FFT-AI. 1-FFT-A1 was located on chromosome 4A using marker M2164 and was flanked by markers Xcwm27 and 6-SFT-A 1. By association analysis using a natural wheat population consisted of 154 accessions, the results showed that the two markers were significantly associated with water-soluble carbohydrate （WSC） content in the lower internode stem and total stem at the early and middle grain filling stages, 1 000-grain weight （TGW） at different grain filling stages and peduncle length （PLE）. Comparison of the effects of three haplotypes on agronomic traits indicated that TGW, PLE and total number of spikelets per spike （TNSS）were significantly influenced by haplotypes. Haplll showed a significant positive effect on TGW, PLE and TNSS.展开更多
BACKGROUND Crohn’s disease(CD)is characterized by a multifactorial etiology and a significant impact of genetic traits.While NOD2 mutations represent well established risk factors of CD,the role of other genes is inc...BACKGROUND Crohn’s disease(CD)is characterized by a multifactorial etiology and a significant impact of genetic traits.While NOD2 mutations represent well established risk factors of CD,the role of other genes is incompletely understood.AIM To challenge the hypothesis that single nucleotide polymorphisms(SNPs)in the genes CLEC5 A and CLEC7 A,two members of the C-type lectin domain family of pattern recognition receptors,may be associated with CD.METHODS SNPs in CLEC5 A,CLEC7 A and the known CD risk gene NOD2 were studied using real time PCR-based SNP assays.Therefore,DNA samples from 175 patients and 157 healthy donors were employed.Genotyping data were correlated with clinical characteristics of the patients and the results of gene expression data analyses.RESULTS In accordance with previous studies,rs2066844 and rs2066847 in NOD2 were found to be significantly associated with CD(allelic P values=0.0368 and 0.0474,respectively).Intriguingly,for genotype AA of rs1285933 in CLEC5 A,a potential association with CD(recessive P=0.0523;odds ratio=1.90)was observed.There were no associations between CD and SNPs rs2078178 and rs16910631 in CLEC7 A.Variants of rs1285933 had no impact on CLEC5 A gene expression.In contrast,genotype-dependent differences of CXCL5 expression in peripheral blood mononuclear cells were observed.There is no statistical interactionbetween the tested SNPs of NOD2 and CLEC5 A,suggesting of a novel pathway contributing to the disease.CONCLUSION Our data encourage enlarged follow-up studies to further address an association of SNP rs1285933 in CLEC5 A with CD.The C-type lectin domain family member also deserves attention regarding a potential role in the pathophysiology of CD.展开更多
BACKGROUND Disease-related single nucleotide polymorphisms(SNPs)based genetic risk score(GRS)has been proven to provide independent inherited risk other than family history in multiple cancer types.AIM To evaluate the...BACKGROUND Disease-related single nucleotide polymorphisms(SNPs)based genetic risk score(GRS)has been proven to provide independent inherited risk other than family history in multiple cancer types.AIM To evaluate the potential of GRS in the prediction of pancreatic cancer risk.METHODS In this case-control study(254 cases and 1200 controls),we aimed to evaluate the association between GRS and pancreatic ductal adenocarcinoma(PDAC)risk in the Chinese population.The GRS was calculated based on the genotype information of 18 PDAC-related SNPs for each study subject(personal genotyping information of the SNPs)and was weighted by external odd ratios(ORs).RESULTS GRS was significantly different in cases and controls(1.96±3.84 in PDACs vs 1.09±0.94 in controls,P<0.0001).Logistic regression revealed GRS to be associated with PDAC risk[OR=1.23,95%confidence interval(CI):1.13-1.34,P<0.0001].GRS remained significantly associated with PDAC(OR=1.36,95%CI:1.06-1.74,P=0.015)after adjusting for age and sex.Further analysis revealed an association of increased risk for PDAC with higher GRS.Compared with low GRS(<1.0),subjects with high GRS(2.0)were 99%more likely to have PDAC(OR:1.99,95%CI:1.30-3.04,P=0.002).Participants with intermediate GRS(1.0-1.9)were 39%more likely to have PDAC(OR:1.39,95%CI:1.03-1.84,P=0.031).A positive trend was observed(P trend=0.0006).CONCLUSION GRS based on PDAC-associated SNPs could provide independent information on PDAC risk and may be used to predict a high risk PDAC population.展开更多
Migraine is a complex trait in which multiple genetic loci, as well as environmental factors, likely contribute to its clinical manifestation. Many genetic associations reported in previous studies either have not bee...Migraine is a complex trait in which multiple genetic loci, as well as environmental factors, likely contribute to its clinical manifestation. Many genetic associations reported in previous studies either have not been replicated to date or showed only marginal statistical significance, possibly due to the genetic heterogeneity of the common forms of migraine. One major phenotypic and possibly genetically identifiable migraine subgroup consists of women whose attacks are influenced by fluctuation in gonadal hormones. We hypothesized that for these women, the association between migraine attacks and the menstrual cycle might be attributable to an increased prevalence of genetic polymorphisms in the hypothalamic-pituitary-gonadal axis. We selected 21 such polymerphisms previously reported to be associated with the common forms of migraine and genotyped 1740 individuals (1132 migraineurs) to determine whether any of these selected polymorphisms occurred more frequently in females with hormonally modulated migraine. We were able to confirm the association of migraine with 3 genetic polymorphisms seen in previous studies (rs4680 [COMT], rs2283265 [DRD2], and rs7131056 [DRD2]). Interestingly, we found 2 additional genetic polymorphisms (rs2070762 [TH] and rs6356 [TH]) to be associated with migraine when defining the phenotype as hormonally modulated migraine.展开更多
Background: Identification of risk genes and loci associated with the recurrence and metastasis of breast cancer (BC) is ofutmost importance. Genome-wide association studies (GWASs) represent valuable tools for identi...Background: Identification of risk genes and loci associated with the recurrence and metastasis of breast cancer (BC) is ofutmost importance. Genome-wide association studies (GWASs) represent valuable tools for identifying the disease risk associated with a given single-nucleotide polymorphism (SNP);they offer significant insights into the disease progression mechanism by analyzing SNP information of the entire genome. Though GWAS has already identified several genetic susceptibilitySNPs for BC, their significance in the recurrence and metastasis of this cancer remains unclear. Here, we used a GWASapproach to identify SNPs specifically associated with the risk of BC recurrence and metastasis.Methods: This study adopted a two-stage GWAS approach. In the first stage, 97 pairs of BC patients with or without recurrenceand metastasis, treated at the Shandong Cancer Hospital and Institute from November 2013 to April 2014, were identified usingpropensity score matching. DNA extracted from the patient peripheral blood was then subjected to Illumina ASA chip analysisfor genome-wide SNP detection. In the second stage, the findings were verified in a validation set of 854 BC patients recruited atthe same hospital from May 2014 to June 2015. SNP genotyping was performed using time-of-flight mass spectrometry. The SNPloci and their corresponding genes and pathways were analyzed using the DAVID (https://david.ncifcrf.gov/) online enrichment analysis tool.Results: Based on the GWAS results, 191 SNP-related genes significantly associated with BC recurrence and metastasis wereidentified as expression quantitivative trait loci (p < 0.001). Functional and pathway enrichment analyses subsequently revealedthe potential involvement of glutamatergic synaptic transmission, calcium signaling, and insulin secretion pathways in BCrecurrence and metastasis. Based on genotype correlation and database expression levels, rs10108514, rs12920540, rs4273077,and rs4730155 were found to be significantly associated with the risk of BC recurrence and metastasis.Conclusion: Our study suggests that the SNPs rs10108514, rs12920540, rs4273077, and rs4730155 are correlated with the risk ofBC recurrence and metastasis, potentially by being implicated in glutamatergic synaptic transmission, calcium signaling, andinsulin secretion pathways.展开更多
NPM1 is a protein-coding gene that encodes the nucleophosmin 1(NPM1)protein.The NPM1 protein exhibits dynamic shuttling between the nucleus and cytoplasm and is involved in various cellular processes,such as centrosom...NPM1 is a protein-coding gene that encodes the nucleophosmin 1(NPM1)protein.The NPM1 protein exhibits dynamic shuttling between the nucleus and cytoplasm and is involved in various cellular processes,such as centrosome duplication,protein chaperoning,and DNA repair.Mutations of the NPM1 gene are associated with human acute myeloid leukemia(AML).AML is a complex hematopoietic cell disorder characterized by excessive proliferation of hematopoietic cells of the myeloid lineage in the bone marrow.This study aimed to predict highly damaging missense single-nucleotide polymorphism(SNPs)in the human NPM1 gene that may be associated with AML.In this investigation,we employed a range of in silico tools to analyze the functional and structural consequences of missense SNPs in the human NPM1 gene.The missense SNPs of the NPM1 gene were retrieved from the Ensembl database.We evaluated the functional and structural impacts of missense SNPs using bioinformatics tools,specifically SIFT,PROVEAN,PolyPhen-2,I-Mutant 3.0,MUpro,and MutPred2.The secondary structure was predicted with PSIPRED.The 3-dimensional structure of the NPM1 protein was obtained from AlphaFold,visualization along with mutant models was generated using PyMOL,and all information about physiological properties was taken from the HOPE project.The protein–protein interactions of the NPM1 protein were investigated using STRING.In silico analysis revealed 8 missense mutations(K54N,I59T,L79S,P152A,K193R,K193N,A283G,and I284F)in the human NPM1 gene.These mutations lead to structural alterations in the protein,which disrupt its normal function and may contribute to the development of AML in humans.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
BACKGROUND Transforming growth factor-β(TGF-β)superfamily plays an important role in tumor progression and metastasis.Activin A receptor type 1C(ACVR1C)is a TGF-βtype I receptor that is involved in tumorigenesis th...BACKGROUND Transforming growth factor-β(TGF-β)superfamily plays an important role in tumor progression and metastasis.Activin A receptor type 1C(ACVR1C)is a TGF-βtype I receptor that is involved in tumorigenesis through binding to dif-ferent ligands.AIM To evaluate the correlation between single nucleotide polymorphisms(SNPs)of ACVR1C and susceptibility to esophageal squamous cell carcinoma(ESCC)in Chinese Han population.METHODS In this hospital-based cohort study,1043 ESCC patients and 1143 healthy controls were enrolled.Five SNPs(rs4664229,rs4556933,rs77886248,rs77263459,rs6734630)of ACVR1C were assessed by the ligation detection reaction method.Hardy-Weinberg equilibrium test,genetic model analysis,stratified analysis,linkage disequi-librium test,and haplotype analysis were conducted.RESULTS Participants carrying ACVR1C rs4556933 GA mutant had significantly decreased risk of ESCC,and those with rs77886248 TA mutant were related with higher risk,especially in older male smokers.In the haplotype analysis,ACVR1C Trs4664229Ars4556933Trs77886248Crs77263459Ars6734630 increased risk of ESCC,while Trs4664229Grs4556933Trs77886248Crs77263459Ars6734630 was associated with lower susceptibility to ESCC.CONCLUSION ACVR1C rs4556933 and rs77886248 SNPs were associated with the susceptibility to ESCC,which could provide a potential target for early diagnosis and treatment of ESCC in Chinese Han population.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
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 Key Research and Development Program for Young scientists,Grant/Award Number:2021YFF0703200National Natural Foundation Joint Fund for Regional Innovation and Development,Grant/Award Number:U21A20194+1 种基金National Natural Science Foundation of China,Grant/Award Number:32170540National Key Research and Development Program,Grant/Award Number:2022YFF0711005。
文摘Chinese hamster with Chinese characteristics is used in experiments,and it is of great value in the field of medical biology research.However,at present,there is no high-efficiency method for evaluating the genetic quality of Chinese hamsters.Here,we developed a novel Chinese hamster genetic quality detection system using single-nucleotide polymorphism(SNP)markers.To find SNP loci,we conducted whole genome sequencing on 24 Chinese hamsters.Then,we employed an SNP locus screening criterion that we set up previously and initially screened 214 SNP loci with wide genome distribution and high polymorphism level.Subsequently,we developed the SNP detection system using a multitarget region capture technique based on second-generation sequencing,and a 55 SNP panel for genetic evaluation of Chinese hamster populations was developed.PopGen.32.analysis results showed that the average effective allele number,Shannon index,observed heterozygosity,expected heterozygosity,average heterozygosity,polymorphism information,and other genetic parameters of Chinese hamster population A were higher than those in population B.Using scientific screening and optimization,we successfully developed a novel Chinese hamster SNP genetic detection system that can efficiently and accurately analyze the genetic quality of the Chinese hamster population.
基金Supported by the National Key Research and Development Program of China,No.2021YFC2700700 and No.2021YFC2700704Capital’s Funds for Health Improvement and Research(CFH)in People’s Republic of China,No.2020-1-5112.
文摘BACKGROUND There are conflicting results on the potential correlation between folic acid and gestational diabetes mellitus(GDM),and the correlation between genetic factors related to folic acid metabolism pathways and GDM remains to be revealed.AIM To examine the association between single-nucleotide polymorphisms(SNPs)of enzyme genes in the folate metabolite pathway as well as that between GDM-related genes and risk for GDM.METHODS A nested case-control study was conducted with GDM cases(n=412)and healthy controls(n=412).DNA was extracted blood samples and SNPs were genotyped using Agena Bioscience’s MassARRAY gene mass spectrometry system.The associations between different SNPs of genes and the risk for GDM were estimated using logistic regression models.The generalized multi-factor dimensionality reduction(GMDR)method was used to analyze gene-gene and gene-environment interactions using the GMDR 0.9 software.RESULTS The variation allele frequency of melatonin receptor 1B(MTNR1B)rs10830963 was higher in the GDM group than in controls(P<0.05).MTNR1B rs10830963 mutant G was associated with risk for GDM[adjusted odds ratio(aOR):1.43;95%confidence interval(95%CI):1.13-1.80]in the additive model.MTNR1B rs10830963 GG+GC was significantly associated with the risk for GDM(aOR:1.65;95%CI:1.23-2.22)in the dominant model.The two-locus model of MTNR1B rs10830963 and CHEMERIN rs4721 was the best model(P<0.05)for gene-gene interactions in the GMDR results.The high-risk rs10830963×rs4721 type of interaction was a risk factor for GDM(aOR:2.09;95%CI:1.49-2.93).CONCLUSION This study does not find an association between SNPs of folate metabolic enzymes and risk for GDM.The G mutant allele of MTNR1B rs10830963 is identified as a risk factor for GDM in the additive model,and there may be gene-gene interactions between MTNR1B rs10830963 and CHEMERIN rs4721.It is conducive to studying the causes of GDM and provides a new perspective for the precise prevention of this disease.
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 Fudan 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Matrix metalloproteinases(MMPs) are implicated in cancer development and progression and are associated with prognosis.Single-nucleotide polymorphisms(SNPs) of MMPs,most frequently located in the promoter region of the genes,have been shown to influence cancer susceptibility and/or progression.SNPs of MMP-1,-2,-3,-7,-8,-9,-12,-13 and-21 and of the tissue inhibitor of metalloproteinases(TIMPs) TIMP-1 and TIMP-2 have been studied in digestive tract tumors.The contribution of these polymorphisms to the cancer risk and prognosis of gastrointestinal tumors are reviewed in this paper.
基金supported by the National Natural Science Foundation of China(31461143024)the National Major Project for Developing New Genetically Modified(GM) Crops of China(2016ZX08010005)the Agricultural Science and Technology Innovation Program,China(ASTIP)
文摘Fructans are major nonstructural carbohydrates in wheat （Triticum aestivum L.）. Fructan 1-fructosyltransferase （1-FFT） is the key enzyme in fructan biosynthesis. In the present study, 96 sequence variants were detected in the 1-FFT-A 1 gene among 26 wheat accessions including UR208, and 15 of them result in amino acid substitutions, forming four haplotypes. Two markers M39 and M2164 were developed based on the InDe121-39 and SNP-2164 polymorphisms to distinguish the three haplotypes in the 1-FFT-AI. 1-FFT-A1 was located on chromosome 4A using marker M2164 and was flanked by markers Xcwm27 and 6-SFT-A 1. By association analysis using a natural wheat population consisted of 154 accessions, the results showed that the two markers were significantly associated with water-soluble carbohydrate （WSC） content in the lower internode stem and total stem at the early and middle grain filling stages, 1 000-grain weight （TGW） at different grain filling stages and peduncle length （PLE）. Comparison of the effects of three haplotypes on agronomic traits indicated that TGW, PLE and total number of spikelets per spike （TNSS）were significantly influenced by haplotypes. Haplll showed a significant positive effect on TGW, PLE and TNSS.
文摘BACKGROUND Crohn’s disease(CD)is characterized by a multifactorial etiology and a significant impact of genetic traits.While NOD2 mutations represent well established risk factors of CD,the role of other genes is incompletely understood.AIM To challenge the hypothesis that single nucleotide polymorphisms(SNPs)in the genes CLEC5 A and CLEC7 A,two members of the C-type lectin domain family of pattern recognition receptors,may be associated with CD.METHODS SNPs in CLEC5 A,CLEC7 A and the known CD risk gene NOD2 were studied using real time PCR-based SNP assays.Therefore,DNA samples from 175 patients and 157 healthy donors were employed.Genotyping data were correlated with clinical characteristics of the patients and the results of gene expression data analyses.RESULTS In accordance with previous studies,rs2066844 and rs2066847 in NOD2 were found to be significantly associated with CD(allelic P values=0.0368 and 0.0474,respectively).Intriguingly,for genotype AA of rs1285933 in CLEC5 A,a potential association with CD(recessive P=0.0523;odds ratio=1.90)was observed.There were no associations between CD and SNPs rs2078178 and rs16910631 in CLEC7 A.Variants of rs1285933 had no impact on CLEC5 A gene expression.In contrast,genotype-dependent differences of CXCL5 expression in peripheral blood mononuclear cells were observed.There is no statistical interactionbetween the tested SNPs of NOD2 and CLEC5 A,suggesting of a novel pathway contributing to the disease.CONCLUSION Our data encourage enlarged follow-up studies to further address an association of SNP rs1285933 in CLEC5 A with CD.The C-type lectin domain family member also deserves attention regarding a potential role in the pathophysiology of CD.
文摘BACKGROUND Disease-related single nucleotide polymorphisms(SNPs)based genetic risk score(GRS)has been proven to provide independent inherited risk other than family history in multiple cancer types.AIM To evaluate the potential of GRS in the prediction of pancreatic cancer risk.METHODS In this case-control study(254 cases and 1200 controls),we aimed to evaluate the association between GRS and pancreatic ductal adenocarcinoma(PDAC)risk in the Chinese population.The GRS was calculated based on the genotype information of 18 PDAC-related SNPs for each study subject(personal genotyping information of the SNPs)and was weighted by external odd ratios(ORs).RESULTS GRS was significantly different in cases and controls(1.96±3.84 in PDACs vs 1.09±0.94 in controls,P<0.0001).Logistic regression revealed GRS to be associated with PDAC risk[OR=1.23,95%confidence interval(CI):1.13-1.34,P<0.0001].GRS remained significantly associated with PDAC(OR=1.36,95%CI:1.06-1.74,P=0.015)after adjusting for age and sex.Further analysis revealed an association of increased risk for PDAC with higher GRS.Compared with low GRS(<1.0),subjects with high GRS(2.0)were 99%more likely to have PDAC(OR:1.99,95%CI:1.30-3.04,P=0.002).Participants with intermediate GRS(1.0-1.9)were 39%more likely to have PDAC(OR:1.39,95%CI:1.03-1.84,P=0.031).A positive trend was observed(P trend=0.0006).CONCLUSION GRS based on PDAC-associated SNPs could provide independent information on PDAC risk and may be used to predict a high risk PDAC population.
文摘Migraine is a complex trait in which multiple genetic loci, as well as environmental factors, likely contribute to its clinical manifestation. Many genetic associations reported in previous studies either have not been replicated to date or showed only marginal statistical significance, possibly due to the genetic heterogeneity of the common forms of migraine. One major phenotypic and possibly genetically identifiable migraine subgroup consists of women whose attacks are influenced by fluctuation in gonadal hormones. We hypothesized that for these women, the association between migraine attacks and the menstrual cycle might be attributable to an increased prevalence of genetic polymorphisms in the hypothalamic-pituitary-gonadal axis. We selected 21 such polymerphisms previously reported to be associated with the common forms of migraine and genotyped 1740 individuals (1132 migraineurs) to determine whether any of these selected polymorphisms occurred more frequently in females with hormonally modulated migraine. We were able to confirm the association of migraine with 3 genetic polymorphisms seen in previous studies (rs4680 [COMT], rs2283265 [DRD2], and rs7131056 [DRD2]). Interestingly, we found 2 additional genetic polymorphisms (rs2070762 [TH] and rs6356 [TH]) to be associated with migraine when defining the phenotype as hormonally modulated migraine.
基金Beijing Science and Technology Innovation Fund(Grant No:KC2021-ZZ-0010-1)Shandong Provincial Natural Science Foundation Cancer Prevention Joint Fund(Grant No:ZR2022LZL004)Shanghai Cancer Prevention and Treatment Foundation(Grant No:CYBER-2022-003).
文摘Background: Identification of risk genes and loci associated with the recurrence and metastasis of breast cancer (BC) is ofutmost importance. Genome-wide association studies (GWASs) represent valuable tools for identifying the disease risk associated with a given single-nucleotide polymorphism (SNP);they offer significant insights into the disease progression mechanism by analyzing SNP information of the entire genome. Though GWAS has already identified several genetic susceptibilitySNPs for BC, their significance in the recurrence and metastasis of this cancer remains unclear. Here, we used a GWASapproach to identify SNPs specifically associated with the risk of BC recurrence and metastasis.Methods: This study adopted a two-stage GWAS approach. In the first stage, 97 pairs of BC patients with or without recurrenceand metastasis, treated at the Shandong Cancer Hospital and Institute from November 2013 to April 2014, were identified usingpropensity score matching. DNA extracted from the patient peripheral blood was then subjected to Illumina ASA chip analysisfor genome-wide SNP detection. In the second stage, the findings were verified in a validation set of 854 BC patients recruited atthe same hospital from May 2014 to June 2015. SNP genotyping was performed using time-of-flight mass spectrometry. The SNPloci and their corresponding genes and pathways were analyzed using the DAVID (https://david.ncifcrf.gov/) online enrichment analysis tool.Results: Based on the GWAS results, 191 SNP-related genes significantly associated with BC recurrence and metastasis wereidentified as expression quantitivative trait loci (p < 0.001). Functional and pathway enrichment analyses subsequently revealedthe potential involvement of glutamatergic synaptic transmission, calcium signaling, and insulin secretion pathways in BCrecurrence and metastasis. Based on genotype correlation and database expression levels, rs10108514, rs12920540, rs4273077,and rs4730155 were found to be significantly associated with the risk of BC recurrence and metastasis.Conclusion: Our study suggests that the SNPs rs10108514, rs12920540, rs4273077, and rs4730155 are correlated with the risk ofBC recurrence and metastasis, potentially by being implicated in glutamatergic synaptic transmission, calcium signaling, andinsulin secretion pathways.
文摘NPM1 is a protein-coding gene that encodes the nucleophosmin 1(NPM1)protein.The NPM1 protein exhibits dynamic shuttling between the nucleus and cytoplasm and is involved in various cellular processes,such as centrosome duplication,protein chaperoning,and DNA repair.Mutations of the NPM1 gene are associated with human acute myeloid leukemia(AML).AML is a complex hematopoietic cell disorder characterized by excessive proliferation of hematopoietic cells of the myeloid lineage in the bone marrow.This study aimed to predict highly damaging missense single-nucleotide polymorphism(SNPs)in the human NPM1 gene that may be associated with AML.In this investigation,we employed a range of in silico tools to analyze the functional and structural consequences of missense SNPs in the human NPM1 gene.The missense SNPs of the NPM1 gene were retrieved from the Ensembl database.We evaluated the functional and structural impacts of missense SNPs using bioinformatics tools,specifically SIFT,PROVEAN,PolyPhen-2,I-Mutant 3.0,MUpro,and MutPred2.The secondary structure was predicted with PSIPRED.The 3-dimensional structure of the NPM1 protein was obtained from AlphaFold,visualization along with mutant models was generated using PyMOL,and all information about physiological properties was taken from the HOPE project.The protein–protein interactions of the NPM1 protein were investigated using STRING.In silico analysis revealed 8 missense mutations(K54N,I59T,L79S,P152A,K193R,K193N,A283G,and I284F)in the human NPM1 gene.These mutations lead to structural alterations in the protein,which disrupt its normal function and may contribute to the development of AML in humans.
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 Natural Science Foundation of China,No.82350127 and No.82241013the Shanghai Natural Science Foundation,No.20ZR1411600+2 种基金the Shanghai Shenkang Hospital Development Center,No.SHDC2020CR4039the Bethune Ethicon Excellent Surgery Foundation,No.CESS2021TC04Xuhui District Medical Research Project of Shanghai,No.SHXH201805.
文摘BACKGROUND Transforming growth factor-β(TGF-β)superfamily plays an important role in tumor progression and metastasis.Activin A receptor type 1C(ACVR1C)is a TGF-βtype I receptor that is involved in tumorigenesis through binding to dif-ferent ligands.AIM To evaluate the correlation between single nucleotide polymorphisms(SNPs)of ACVR1C and susceptibility to esophageal squamous cell carcinoma(ESCC)in Chinese Han population.METHODS In this hospital-based cohort study,1043 ESCC patients and 1143 healthy controls were enrolled.Five SNPs(rs4664229,rs4556933,rs77886248,rs77263459,rs6734630)of ACVR1C were assessed by the ligation detection reaction method.Hardy-Weinberg equilibrium test,genetic model analysis,stratified analysis,linkage disequi-librium test,and haplotype analysis were conducted.RESULTS Participants carrying ACVR1C rs4556933 GA mutant had significantly decreased risk of ESCC,and those with rs77886248 TA mutant were related with higher risk,especially in older male smokers.In the haplotype analysis,ACVR1C Trs4664229Ars4556933Trs77886248Crs77263459Ars6734630 increased risk of ESCC,while Trs4664229Grs4556933Trs77886248Crs77263459Ars6734630 was associated with lower susceptibility to ESCC.CONCLUSION ACVR1C rs4556933 and rs77886248 SNPs were associated with the susceptibility to ESCC,which could provide a potential target for early diagnosis and treatment of ESCC in Chinese Han population.
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.
