本研究以柴达木山羊、柴达木绒山羊和辽宁绒山羊三个群体共147只山羊为材料,利用聚丙烯酰胺凝胶电泳(PAGE)技术检测了5种血液蛋白质(酶)基因座的遗传多态性,并进行了结构基因遗传共适应的研究,结果发现:45个基因座组合中有10个基因座组...本研究以柴达木山羊、柴达木绒山羊和辽宁绒山羊三个群体共147只山羊为材料,利用聚丙烯酰胺凝胶电泳(PAGE)技术检测了5种血液蛋白质(酶)基因座的遗传多态性,并进行了结构基因遗传共适应的研究,结果发现:45个基因座组合中有10个基因座组合处于遗传不平衡状态,并且这些遗传不平衡皆单纯由遗传共适应差异造成;除辽宁绒山羊Tf PA 3组合的遗传不平衡包含非等位基因间的遗传共适应差异外,其他基因座组合的遗传不平衡皆由等位基因间的共适应差异,即单基因座的遗传不平衡造成;LAP EsD组合的共适应差异在群体间有遗传传递现象。展开更多
The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assaye...The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assayed for polymorphism among 187 commonly used maize （Zea mays L.） inbreds which represent the genetic diversity in China. The identified 290 alleles served as raw data for estimating population structure using the coalescent linked loci, based on the ADMIXTURE model. Population number, K, has been inferred to be between five and seven. Specifying five subpopulations （K = 5） led to a distinct decrease and specifying K to be greater than six resulted in only minimal increases in the likelihood value. Therefore, population number, K, has been inferred into six subpopulations, which are PA, BSSS （includes Reid）, PB, Lan （Lancaster Sure Crop）, LRC （Luda Reb Cob, a Chinese landrace, and its derivatives）, and SPT （Si-ping-tou, a Chinese landrace and its derivatives）. The Kullback-Leibler distance of pairwise subpopulation was also inferred as n × p （187 ×6） Q matrices, which gave a detailed percentage of genetic composition of six subpopulations and molecular relatedness of each line. The genome-wide linkage disequilibrium （LD） indicated that the asso- ciation studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations, as most of the LD blocks were broken among diverse germplasm. The defined population structure has given us a clear genetic structure of these lines for breeding practice and established a good basis for association analysis.展开更多
In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values w...In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.展开更多
AIM: To investigate the genomic copy number alterations that may harbor key driver genes in gastric tumorigenesis. METHODS: Using high-resolution array comparative genomic hybridization (CGH), we investigated the geno...AIM: To investigate the genomic copy number alterations that may harbor key driver genes in gastric tumorigenesis. METHODS: Using high-resolution array comparative genomic hybridization (CGH), we investigated the genomic alterations of 20 advanced primary gastric adenocarcinomas (seventeen tubular and three mucinous) of Chinese patients from the Jilin province. Ten matching adjacent normal regions from the same patients were also studied. RESULTS: The most frequent imbalances detected in these cancer samples were gains of 3q26.31-q27.2, 5p, 8q, 11p, 18p, 19q and 20q and losses of 3p, 4p,18q and 21q. The use of high-resolution array CGH increased the resolution and sensitivity of the observed genomic changes and identified focal genetic imbalances, which included 54 gains and 16 losses that were smaller than 1 Mb in size. The most interesting focal imbalances were the intergenic loss/homozygous deletion of the fragile histidine triad gene and the amplicons 11q13, 18q11.2 and 19q12, as well as the novel amplicons 1p36.22 and 11p15.5. CONCLUSION: These regions, especially the focal amplicons, may harbor key driver genes that will serve as biomarkers for either the diagnosis or the prognosis of gastric cancer, and therefore, a large-scale investigation is recommended.展开更多
Retinoic acid level in the retina/choroid is altered in induced myopia models.All-trans-retinol dehydrogenase(RDH8) is an important enzyme of retinoic acid metabolism.This study aimed to investigate the association of...Retinoic acid level in the retina/choroid is altered in induced myopia models.All-trans-retinol dehydrogenase(RDH8) is an important enzyme of retinoic acid metabolism.This study aimed to investigate the association of the RDH8 gene with high myopia.Three single nucleotide polymorphisms(SNPs) [RDH851(rs2233789) ,RDH8E5a(rs1644731) ,and RDH855b(rs3760753) ]were selected,based on the linkage disequilibrium pattern of RDH8 from a previous study,and genotyped for 160 Han Chinese nuclear families with highly myopic(-10 diopters or worse) offspring as well as in an independent group with 166 highly myopic cases(-10 diopters or worse) and 211 controls. Family-based association analysis was performed using the family-based association test(FBAT) package,and genotype relative risk(GRR) was calculated using the GenAssoc program.Population-based association analysis was performed using Chi-square test.These SNPs were in linkage equilibrium with each other.SNPs RDH851(rs2233789) and RDH8E5a(rs1644731) both did not show association with high myopia.SNP RDH855b(rs3760753) demonstrated significant association(P=0.0269) with a GRR of 0.543(95%confidence interval=0.304-0.968,P=0.038) .The association became statistically insignificant,however,after multiple comparison correction.Haplotype analysis did not show a significant association either.Population-based association analysis also showed no significant association(P>0.05) .Our family-and population-based data both suggest that the RDH8 gene is unlikely to be associated with high myopia in Chinese.展开更多
文摘本研究以柴达木山羊、柴达木绒山羊和辽宁绒山羊三个群体共147只山羊为材料,利用聚丙烯酰胺凝胶电泳(PAGE)技术检测了5种血液蛋白质(酶)基因座的遗传多态性,并进行了结构基因遗传共适应的研究,结果发现:45个基因座组合中有10个基因座组合处于遗传不平衡状态,并且这些遗传不平衡皆单纯由遗传共适应差异造成;除辽宁绒山羊Tf PA 3组合的遗传不平衡包含非等位基因间的遗传共适应差异外,其他基因座组合的遗传不平衡皆由等位基因间的共适应差异,即单基因座的遗传不平衡造成;LAP EsD组合的共适应差异在群体间有遗传传递现象。
文摘The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assayed for polymorphism among 187 commonly used maize （Zea mays L.） inbreds which represent the genetic diversity in China. The identified 290 alleles served as raw data for estimating population structure using the coalescent linked loci, based on the ADMIXTURE model. Population number, K, has been inferred to be between five and seven. Specifying five subpopulations （K = 5） led to a distinct decrease and specifying K to be greater than six resulted in only minimal increases in the likelihood value. Therefore, population number, K, has been inferred into six subpopulations, which are PA, BSSS （includes Reid）, PB, Lan （Lancaster Sure Crop）, LRC （Luda Reb Cob, a Chinese landrace, and its derivatives）, and SPT （Si-ping-tou, a Chinese landrace and its derivatives）. The Kullback-Leibler distance of pairwise subpopulation was also inferred as n × p （187 ×6） Q matrices, which gave a detailed percentage of genetic composition of six subpopulations and molecular relatedness of each line. The genome-wide linkage disequilibrium （LD） indicated that the asso- ciation studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations, as most of the LD blocks were broken among diverse germplasm. The defined population structure has given us a clear genetic structure of these lines for breeding practice and established a good basis for association analysis.
基金This work was supported by the Major State Basic Research Development program of Chinathe National High Technology Research and Development Program of China.
文摘In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.
文摘AIM: To investigate the genomic copy number alterations that may harbor key driver genes in gastric tumorigenesis. METHODS: Using high-resolution array comparative genomic hybridization (CGH), we investigated the genomic alterations of 20 advanced primary gastric adenocarcinomas (seventeen tubular and three mucinous) of Chinese patients from the Jilin province. Ten matching adjacent normal regions from the same patients were also studied. RESULTS: The most frequent imbalances detected in these cancer samples were gains of 3q26.31-q27.2, 5p, 8q, 11p, 18p, 19q and 20q and losses of 3p, 4p,18q and 21q. The use of high-resolution array CGH increased the resolution and sensitivity of the observed genomic changes and identified focal genetic imbalances, which included 54 gains and 16 losses that were smaller than 1 Mb in size. The most interesting focal imbalances were the intergenic loss/homozygous deletion of the fragile histidine triad gene and the amplicons 11q13, 18q11.2 and 19q12, as well as the novel amplicons 1p36.22 and 11p15.5. CONCLUSION: These regions, especially the focal amplicons, may harbor key driver genes that will serve as biomarkers for either the diagnosis or the prognosis of gastric cancer, and therefore, a large-scale investigation is recommended.
基金Project supported by the National Natural Science Foundation of China(No.30600693)the Qianjiang Talent Project of Zhejiang Province(No.2010R10068)the Hong Kong Polytechnic University(No.J-BB7P),China
文摘Retinoic acid level in the retina/choroid is altered in induced myopia models.All-trans-retinol dehydrogenase(RDH8) is an important enzyme of retinoic acid metabolism.This study aimed to investigate the association of the RDH8 gene with high myopia.Three single nucleotide polymorphisms(SNPs) [RDH851(rs2233789) ,RDH8E5a(rs1644731) ,and RDH855b(rs3760753) ]were selected,based on the linkage disequilibrium pattern of RDH8 from a previous study,and genotyped for 160 Han Chinese nuclear families with highly myopic(-10 diopters or worse) offspring as well as in an independent group with 166 highly myopic cases(-10 diopters or worse) and 211 controls. Family-based association analysis was performed using the family-based association test(FBAT) package,and genotype relative risk(GRR) was calculated using the GenAssoc program.Population-based association analysis was performed using Chi-square test.These SNPs were in linkage equilibrium with each other.SNPs RDH851(rs2233789) and RDH8E5a(rs1644731) both did not show association with high myopia.SNP RDH855b(rs3760753) demonstrated significant association(P=0.0269) with a GRR of 0.543(95%confidence interval=0.304-0.968,P=0.038) .The association became statistically insignificant,however,after multiple comparison correction.Haplotype analysis did not show a significant association either.Population-based association analysis also showed no significant association(P>0.05) .Our family-and population-based data both suggest that the RDH8 gene is unlikely to be associated with high myopia in Chinese.
