Scallop is a popular sea food and an important aquaculture shellfish.Identification of genes and genetic variants relating to scallop growth could benefit high-yielding scallop breeding.Myostatin(MSTN) is a conservati...Scallop is a popular sea food and an important aquaculture shellfish.Identification of genes and genetic variants relating to scallop growth could benefit high-yielding scallop breeding.Myostatin(MSTN) is a conservative regulator of muscle growth,and has become one of the most important target genes for genetic improvement of the production of farmed animals.In this study,four single nucleotide polymorphisms(SNPs) were identified in the 5' flanking region of MSTN gene(Cf MSTN) in Zhikong scallop(Chlamys farreri).The association of these SNPs with scallop growth traits,including shell length,shell height,body weight and striated muscle weight was analyzed.The SNP g-1162G>T was found to associate with shell length,shell height,and striated muscle weight.The TT type scallops showed significantly higher trait values than those of GT type,and the GG type individuals exhibited median values.On the contrary,significantly more Cf MSTN transcripts were detected in the striated muscle of GT type scallops than in those of TT and GG type ones.Our results suggested that Cf MSTN might regulate the scallop muscle growth negatively,and SNP g-1162G>T can be used as a candidate marker for the selective breeding of high-yielding scallop.展开更多
Alzheimer's disease(AD) is a serious neurodegenerative disorder and its cause remains largely elusive.In past years,genome-wide association(GWA) studies have provided an effective means for AD research.However,the...Alzheimer's disease(AD) is a serious neurodegenerative disorder and its cause remains largely elusive.In past years,genome-wide association(GWA) studies have provided an effective means for AD research.However,the univariate method that is commonly used in GWA studies cannot effectively detect the biological mechanisms associated with this disease.In this study,we propose a new strategy for the GWA analysis of AD that combines random forests with enrichment analysis.First,backward feature selection using random forests was performed on a GWA dataset of AD patients carrying the apolipoprotein gene(APOEε4) and 1058 susceptible single nucleotide polymorphisms(SNPs) were detected,including several known AD-associated SNPs.Next,the susceptible SNPs were investigated by enrichment analysis and significantly-associated gene functional annotations,such as 'alternative splicing','glycoprotein',and 'neuron development',were successfully discovered,indicating that these biological mechanisms play important roles in the development of AD in APOEε4 carriers.These findings may provide insights into the pathogenesis of AD and helpful guidance for further studies.Furthermore,this strategy can easily be modified and applied to GWA studies of other complex diseases.展开更多
Functional studies have suggested the important role of early growth response I （EGR1） and Laminin a2- chain （LAMA,？.） in human eye development. Genetic studies have reported a significant association of the sing...Functional studies have suggested the important role of early growth response I （EGR1） and Laminin a2- chain （LAMA,？.） in human eye development. Genetic studies have reported a significant association of the single nu- cleotide polymorphism （SNP） in the LAMA2 gene with myopia. This study aimed to evaluate the association of the tagging SNPs （tSNPs） in the EGR1 and LAMA2 genes with high myopia in two independent Han Chinese populations. Four tSNPs （rs11743810 in the EGR1 gene; rs2571575, rs9321170, and rs1889891 in the LAMA2 gene） were se- lected, according to the HapMap database （http：//hapmap.ncbi.nlm.nih.gov）, and were genotyped using the ligase detection reaction （LDR） approach for 167 Hart Chinese nuclear families with extremely highly myopic offspring （〈-10.0 diopters） and an independent group with 485 extremely highly myopic cases （〈-10.0 diopters） and 499 con- trois. Direct sequencing was used to confirm the LDR results in twenty randomly selected subjects. Family-based association analysis was performed using the family-based association test （FBAT） software package （Version 1.5.5）. Population-based association analysis was performed using the Chi-square test. The association analysis power was estimated using online software （http：lldesign.cs.ucla.edu）. The FBAT demonstrated that all four tSNPs tested did not show association with high myopia （P〉0.05）. Haplotype analysis of tSNPs in the LAMA2 genes also did not show a significant association （P〉0.05）. Meanwhile, population-based association analysis also showed no significant asso- ciation results with high myopia （P〉0.05）. On the basis of our family- and population-based analyses for the Han Chinese population, we did not find positive association signals of the four SNPs in the LAMA2 and EGR1 genes with high myopia.展开更多
OBJECTIVE:To explore the association among lifestyle,clinical examination,polymorphisms in CDH1 gene and Traditional Chinese Medicine(TCM)syndrome differentiation of gastric cancer(GC). METHODS:A hospital-based popula...OBJECTIVE:To explore the association among lifestyle,clinical examination,polymorphisms in CDH1 gene and Traditional Chinese Medicine(TCM)syndrome differentiation of gastric cancer(GC). METHODS:A hospital-based population of 387 GC patients was investigated in Jiangsu province.Relevant information regarding lifestyle and clinical examination were collected by a standard questionnaire.Four known single nucleotide polymorphisms(SNPs)in CDH1 were investigated by polymerase chain reaction-ligation detection reaction methods.Statistical analysis was conducted by SPSS 16.0 software.RESULTS:The results showed that meal duration and the status of glutamic pyruvic transaminase were significantly associated with TCM syndrome differentiation of GC(both P<0.05).None of the four SNPs in the E-cadherin(CDH1)gene achieved significant differences in their distributions among the nine syndrome types of GC(both P>0.05).However,significant differences were observed in rs13689 genotype distributions between several pairs of syndrome types of GC,suggesting that rs13689 is correlated with the syndrome differentiation of GC.CONCLUSION:Integrated analysis of lifestyle,clinical examination and CDH1 gene polymorphisms can contribute to a better understanding of the GC syndrome types and may improve the efficacy of interventions by stratifying disease according to TCM criteria.展开更多
基金supported by the National High-Tech R&D Program (863 Program,2012AA10A402)Doctoral Fund of Ministry of Education of China (20120132130 002)the National Key Technology R&D Program of China (2011BAD13B06)
文摘Scallop is a popular sea food and an important aquaculture shellfish.Identification of genes and genetic variants relating to scallop growth could benefit high-yielding scallop breeding.Myostatin(MSTN) is a conservative regulator of muscle growth,and has become one of the most important target genes for genetic improvement of the production of farmed animals.In this study,four single nucleotide polymorphisms(SNPs) were identified in the 5' flanking region of MSTN gene(Cf MSTN) in Zhikong scallop(Chlamys farreri).The association of these SNPs with scallop growth traits,including shell length,shell height,body weight and striated muscle weight was analyzed.The SNP g-1162G>T was found to associate with shell length,shell height,and striated muscle weight.The TT type scallops showed significantly higher trait values than those of GT type,and the GG type individuals exhibited median values.On the contrary,significantly more Cf MSTN transcripts were detected in the striated muscle of GT type scallops than in those of TT and GG type ones.Our results suggested that Cf MSTN might regulate the scallop muscle growth negatively,and SNP g-1162G>T can be used as a candidate marker for the selective breeding of high-yielding scallop.
基金supported by the National Natural Science Foundation of China (Nos. 2100230024 and 2100230023)
文摘Alzheimer's disease(AD) is a serious neurodegenerative disorder and its cause remains largely elusive.In past years,genome-wide association(GWA) studies have provided an effective means for AD research.However,the univariate method that is commonly used in GWA studies cannot effectively detect the biological mechanisms associated with this disease.In this study,we propose a new strategy for the GWA analysis of AD that combines random forests with enrichment analysis.First,backward feature selection using random forests was performed on a GWA dataset of AD patients carrying the apolipoprotein gene(APOEε4) and 1058 susceptible single nucleotide polymorphisms(SNPs) were detected,including several known AD-associated SNPs.Next,the susceptible SNPs were investigated by enrichment analysis and significantly-associated gene functional annotations,such as 'alternative splicing','glycoprotein',and 'neuron development',were successfully discovered,indicating that these biological mechanisms play important roles in the development of AD in APOEε4 carriers.These findings may provide insights into the pathogenesis of AD and helpful guidance for further studies.Furthermore,this strategy can easily be modified and applied to GWA studies of other complex diseases.
基金Project supported by the Natural Science Foundation of Zhejiang Province(No.LY14H120003)the Qianjiang Talent Project of Zhejiang Province(No.2013R10040),China
文摘Functional studies have suggested the important role of early growth response I （EGR1） and Laminin a2- chain （LAMA,？.） in human eye development. Genetic studies have reported a significant association of the single nu- cleotide polymorphism （SNP） in the LAMA2 gene with myopia. This study aimed to evaluate the association of the tagging SNPs （tSNPs） in the EGR1 and LAMA2 genes with high myopia in two independent Han Chinese populations. Four tSNPs （rs11743810 in the EGR1 gene; rs2571575, rs9321170, and rs1889891 in the LAMA2 gene） were se- lected, according to the HapMap database （http：//hapmap.ncbi.nlm.nih.gov）, and were genotyped using the ligase detection reaction （LDR） approach for 167 Hart Chinese nuclear families with extremely highly myopic offspring （〈-10.0 diopters） and an independent group with 485 extremely highly myopic cases （〈-10.0 diopters） and 499 con- trois. Direct sequencing was used to confirm the LDR results in twenty randomly selected subjects. Family-based association analysis was performed using the family-based association test （FBAT） software package （Version 1.5.5）. Population-based association analysis was performed using the Chi-square test. The association analysis power was estimated using online software （http：lldesign.cs.ucla.edu）. The FBAT demonstrated that all four tSNPs tested did not show association with high myopia （P〉0.05）. Haplotype analysis of tSNPs in the LAMA2 genes also did not show a significant association （P〉0.05）. Meanwhile, population-based association analysis also showed no significant asso- ciation results with high myopia （P〉0.05）. On the basis of our family- and population-based analyses for the Han Chinese population, we did not find positive association signals of the four SNPs in the LAMA2 and EGR1 genes with high myopia.
基金Supported by National Natural Science Foundation of China(30973715 and 81001502)Jiangsu Natural Science Foundation(BK2008461)+2 种基金Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)Research Fund for the Doctoral Program of Higher Education of China(20103237110011)Young Teachers in Nanjing University of Chinese Medicine
文摘OBJECTIVE:To explore the association among lifestyle,clinical examination,polymorphisms in CDH1 gene and Traditional Chinese Medicine(TCM)syndrome differentiation of gastric cancer(GC). METHODS:A hospital-based population of 387 GC patients was investigated in Jiangsu province.Relevant information regarding lifestyle and clinical examination were collected by a standard questionnaire.Four known single nucleotide polymorphisms(SNPs)in CDH1 were investigated by polymerase chain reaction-ligation detection reaction methods.Statistical analysis was conducted by SPSS 16.0 software.RESULTS:The results showed that meal duration and the status of glutamic pyruvic transaminase were significantly associated with TCM syndrome differentiation of GC(both P<0.05).None of the four SNPs in the E-cadherin(CDH1)gene achieved significant differences in their distributions among the nine syndrome types of GC(both P>0.05).However,significant differences were observed in rs13689 genotype distributions between several pairs of syndrome types of GC,suggesting that rs13689 is correlated with the syndrome differentiation of GC.CONCLUSION:Integrated analysis of lifestyle,clinical examination and CDH1 gene polymorphisms can contribute to a better understanding of the GC syndrome types and may improve the efficacy of interventions by stratifying disease according to TCM criteria.
