AIM To investigate the association between 16 insertiondeletions(INDEL)polymorphisms,colorectal cancer(CRC)risk and clinical features in an admixed population.METHODS One hundred and forty patients with CRC and 140 ca...AIM To investigate the association between 16 insertiondeletions(INDEL)polymorphisms,colorectal cancer(CRC)risk and clinical features in an admixed population.METHODS One hundred and forty patients with CRC and 140 cancer-free subjects were examined.Genomic DNA was extracted from peripheral blood samples.Polymorphisms and genomic ancestry distribution were assayed by Multiplex-PCR reaction,separated by capillary electrophoresis on the ABI 3130 Genetic Analyzer instrument and analyzed on GeneMapper ID v3.2.Clinicopathological data were obtained by consulting the patients’clinical charts,intra-operative documentation,and pathology scoring.RESULTS Logistic regression analysis showed that polymorphism variations in IL4 gene was associated with increased CRC risk,while TYMS and UCP2 genes were associated with decreased risk.Reference to anatomical localization of tumor Del allele of NFKB1 and CASP8 were associated with more colon related incidents than rectosigmoid.In relation to the INDEL association with tumor node metastasis(TNM)stage risk,the Ins alleles of ACE,HLAG and TP53(6 bp INDEL)were associated with higher TNM stage.Furthermore,regarding INDEL association with relapse risk,the Ins alleles of ACE,HLAG,and UGT1A1 were associated with early relapse risk,as well as the Del allele of TYMS.Regarding INDEL association with death risk before 10 years,the Ins allele of SGSM3 and UGT1A1 were associated with death risk.CONCLUSION The INDEL variations in ACE,UCP2,TYMS,IL4,NFKB1,CASP8,TP53,HLAG,UGT1A1,and SGSM3 were associated with CRC risk and clinical features in an admixed population.These data suggest that this cancer panel might be useful as a complementary tool for better clinical management,and more studies need to be conducted to confirm these findings.展开更多
AIM:To study the association between genetic ancestry,non-alcoholic fatty liver disease(NAFLD) metabolic characteristics in two cohorts of patients,from Brazil and Portugal. METHODS:We included 131 subjects from Brazi...AIM:To study the association between genetic ancestry,non-alcoholic fatty liver disease(NAFLD) metabolic characteristics in two cohorts of patients,from Brazil and Portugal. METHODS:We included 131 subjects from Brazil [(n = 45 with simple steatosis(S. Steatosis) and n = 86 with nonalcoholic steatohepatitis(NASH)] and 90 patients from Portugal(n = 66,S. Steatosis; n = 24,NASH). All patients had biopsy-proven NAFLD. In histologic evaluation NAFLD activity score was used to assess histology and more than 5 points defined NASH in this study. Patients were divided into two groups according to histology diagnosis:simple steatosis or non-alcoholic statohepatitis. Genetic ancestry was assessed using real-time polymerase chain reaction. Seven ancestry informative markers(AT3-I/D,LPL,Sb19.3,APO,FYNull,PV92,and CKMM) with the greatest ethnicgeographical differential frequencies(≥ 48%) were used to define genetic ancestry. Data were analyzed using R PROJECTS software. Ancestry allele frequencies between groups were analyzed by GENEPOP onlineand the estimation of genetic ancestry contribution was evaluated by ADMIX-95 software. The 5% alpha-error was considered as significant(P < 0.05). RESULTS:In the Brazilian sample,NASH was significantly more frequent among the elderly patients with diabetes(NASH 56 ± 1.1 years old vs S. Steatosis 51 ± 1.5 years old,P = 3.7 x 10-9),dyslipidemia(NASH 63% vs S. Steatosis 37%,P = 0.009),higher fasting glucose levels(NASH 124 ± 5.2 vs S. Steatosis 106 ± 5.3,P = 0.001) and Homeostatic Model of Assessment index > 2.5 [NASH 5.3(70.8%) vs S. Steatosis 4.6(29.2%) P = 0.04]. In the Portuguese study population,dyslipidemia was present in all patients with NASH(P = 0.03) and hypertension was present in a larger percentage of subjects in the S. Steatosis group(P = 0.003,respectively). The genetic ancestry contribution among Brazilian and Portuguese individuals with NASH was similar to those with S. Steatosis from each cohort(Brazilian cohort:P = 0.75; Portuguese cohort:P = 0.97). Nonetheless,the genetic ancestry contribution of the Brazilian and Portuguese population were different,and a greater European and Amerindian ancestry contribution was detected in the Portuguese population while a higher African genetic ancestry contribution was observed in Brazilian population of both NASH and S. Steatosis groups.CONCLUSION:There was no difference between the genetic ancestry contribution among Brazilian and Portuguese individuals with NASH and S. Steatosis from each cohort.展开更多
We have studied the single-neutron stripping reaction induced by ^23O on carbon target at beam energy of 72 MeV//A with a motive to analyze its ground state structure. The partial stripping cross sections as well as l...We have studied the single-neutron stripping reaction induced by ^23O on carbon target at beam energy of 72 MeV//A with a motive to analyze its ground state structure. The partial stripping cross sections as well as longitudinal momentum distribution of ^22O core have been calculated within the framework of the eikonal approximation approach. Several core-neutron spin coupling configurations, corresponding to J^π= 1/2 ＋ as ground state spin parity of ^23O, along with their suitable admixtures have been considered. The major outcome of the present work is that the s and d admixed configuration with a large contribution of s state seems to explain the longitudinal momentum distribution data more satisfactorily.展开更多
The germplasm of breeding large yellow croaker （Pseudosciaena crocea Richardson） was revealed using 12 microsatellite markers. The results showed that the genetic diversities were on a mediated level in the bred Dai...The germplasm of breeding large yellow croaker （Pseudosciaena crocea Richardson） was revealed using 12 microsatellite markers. The results showed that the genetic diversities were on a mediated level in the bred Daiqu and Min - Yue stocks and two hybrid groups, as represented by 4.83 of the mean number of alleles and 0.561 of the average observed heterozygosity. The value of pair- wise differentiation coefficient（ FST ） was only 13. 1% between Daiqu and Min -Yue stocks, demonstrating the low level of differentiation and a close relationship. However, STRUCTURE simulations and phylogenetic tree based on the UPGMA method supported that they are geographically different populations of the same species with distinct genetic structures. Examinations of individual admixture showed that Min - Yue stock had been contaminated by alien individuals. Moreover, the genetic structures of the two hybrid groups resembled those of their parents, especially affected more by their female parents. Finally, the values of average observed heterozygosity between parents and their ascendants were compared and tested, as a result of no detectable differences （P 〉 0. 05）.展开更多
Ancestry composition of populations and individuals has been extensively investigated in recent years due to advances in the genotyping and sequencing technologies. As the number of populations and individuals used fo...Ancestry composition of populations and individuals has been extensively investigated in recent years due to advances in the genotyping and sequencing technologies. As the number of populations and individuals used for ancestry inference increases remarkably, say more than 100 populations or 1000 individuals, it is usually challenging to present the ancestry composition in a traditional way using a rectangular graph. To address this issue, we developed a program,AncestryPainter, which can illustrate the ancestry composition of populations and individuals with a rounded and nice-looking graph to save space. Individuals are depicted as length-fixed bars partitioned into colored segments representing different ancestries, and the population of interest can be highlighted as a pie chart in the center of the circle plot. In addition, AncestryPainter can also be applied to display personal ancestry in a way similar to that for displaying population ancestry.AncestryPainter is publicly available at http://www.picb.ac.cn/PGG/resource.php.展开更多
基金Supported by the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico(CNPq),No.483031/2013-5Rede de Pesquisa em Genomica Populacional Humana,No.Biocomputacional/CAPES-051/2013+1 种基金Fundacao de Amparo a Pesquisa do Estado do Pará,No.155/2014and Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Norte,No.005/2011
文摘AIM To investigate the association between 16 insertiondeletions(INDEL)polymorphisms,colorectal cancer(CRC)risk and clinical features in an admixed population.METHODS One hundred and forty patients with CRC and 140 cancer-free subjects were examined.Genomic DNA was extracted from peripheral blood samples.Polymorphisms and genomic ancestry distribution were assayed by Multiplex-PCR reaction,separated by capillary electrophoresis on the ABI 3130 Genetic Analyzer instrument and analyzed on GeneMapper ID v3.2.Clinicopathological data were obtained by consulting the patients’clinical charts,intra-operative documentation,and pathology scoring.RESULTS Logistic regression analysis showed that polymorphism variations in IL4 gene was associated with increased CRC risk,while TYMS and UCP2 genes were associated with decreased risk.Reference to anatomical localization of tumor Del allele of NFKB1 and CASP8 were associated with more colon related incidents than rectosigmoid.In relation to the INDEL association with tumor node metastasis(TNM)stage risk,the Ins alleles of ACE,HLAG and TP53(6 bp INDEL)were associated with higher TNM stage.Furthermore,regarding INDEL association with relapse risk,the Ins alleles of ACE,HLAG,and UGT1A1 were associated with early relapse risk,as well as the Del allele of TYMS.Regarding INDEL association with death risk before 10 years,the Ins allele of SGSM3 and UGT1A1 were associated with death risk.CONCLUSION The INDEL variations in ACE,UCP2,TYMS,IL4,NFKB1,CASP8,TP53,HLAG,UGT1A1,and SGSM3 were associated with CRC risk and clinical features in an admixed population.These data suggest that this cancer panel might be useful as a complementary tool for better clinical management,and more studies need to be conducted to confirm these findings.
文摘AIM:To study the association between genetic ancestry,non-alcoholic fatty liver disease(NAFLD) metabolic characteristics in two cohorts of patients,from Brazil and Portugal. METHODS:We included 131 subjects from Brazil [(n = 45 with simple steatosis(S. Steatosis) and n = 86 with nonalcoholic steatohepatitis(NASH)] and 90 patients from Portugal(n = 66,S. Steatosis; n = 24,NASH). All patients had biopsy-proven NAFLD. In histologic evaluation NAFLD activity score was used to assess histology and more than 5 points defined NASH in this study. Patients were divided into two groups according to histology diagnosis:simple steatosis or non-alcoholic statohepatitis. Genetic ancestry was assessed using real-time polymerase chain reaction. Seven ancestry informative markers(AT3-I/D,LPL,Sb19.3,APO,FYNull,PV92,and CKMM) with the greatest ethnicgeographical differential frequencies(≥ 48%) were used to define genetic ancestry. Data were analyzed using R PROJECTS software. Ancestry allele frequencies between groups were analyzed by GENEPOP onlineand the estimation of genetic ancestry contribution was evaluated by ADMIX-95 software. The 5% alpha-error was considered as significant(P < 0.05). RESULTS:In the Brazilian sample,NASH was significantly more frequent among the elderly patients with diabetes(NASH 56 ± 1.1 years old vs S. Steatosis 51 ± 1.5 years old,P = 3.7 x 10-9),dyslipidemia(NASH 63% vs S. Steatosis 37%,P = 0.009),higher fasting glucose levels(NASH 124 ± 5.2 vs S. Steatosis 106 ± 5.3,P = 0.001) and Homeostatic Model of Assessment index > 2.5 [NASH 5.3(70.8%) vs S. Steatosis 4.6(29.2%) P = 0.04]. In the Portuguese study population,dyslipidemia was present in all patients with NASH(P = 0.03) and hypertension was present in a larger percentage of subjects in the S. Steatosis group(P = 0.003,respectively). The genetic ancestry contribution among Brazilian and Portuguese individuals with NASH was similar to those with S. Steatosis from each cohort(Brazilian cohort:P = 0.75; Portuguese cohort:P = 0.97). Nonetheless,the genetic ancestry contribution of the Brazilian and Portuguese population were different,and a greater European and Amerindian ancestry contribution was detected in the Portuguese population while a higher African genetic ancestry contribution was observed in Brazilian population of both NASH and S. Steatosis groups.CONCLUSION:There was no difference between the genetic ancestry contribution among Brazilian and Portuguese individuals with NASH and S. Steatosis from each cohort.
文摘We have studied the single-neutron stripping reaction induced by ^23O on carbon target at beam energy of 72 MeV//A with a motive to analyze its ground state structure. The partial stripping cross sections as well as longitudinal momentum distribution of ^22O core have been calculated within the framework of the eikonal approximation approach. Several core-neutron spin coupling configurations, corresponding to J^π= 1/2 ＋ as ground state spin parity of ^23O, along with their suitable admixtures have been considered. The major outcome of the present work is that the s and d admixed configuration with a large contribution of s state seems to explain the longitudinal momentum distribution data more satisfactorily.
基金The National High Technology Research and Development Program of China under contract No.2006AA10A405
文摘The germplasm of breeding large yellow croaker （Pseudosciaena crocea Richardson） was revealed using 12 microsatellite markers. The results showed that the genetic diversities were on a mediated level in the bred Daiqu and Min - Yue stocks and two hybrid groups, as represented by 4.83 of the mean number of alleles and 0.561 of the average observed heterozygosity. The value of pair- wise differentiation coefficient（ FST ） was only 13. 1% between Daiqu and Min -Yue stocks, demonstrating the low level of differentiation and a close relationship. However, STRUCTURE simulations and phylogenetic tree based on the UPGMA method supported that they are geographically different populations of the same species with distinct genetic structures. Examinations of individual admixture showed that Min - Yue stock had been contaminated by alien individuals. Moreover, the genetic structures of the two hybrid groups resembled those of their parents, especially affected more by their female parents. Finally, the values of average observed heterozygosity between parents and their ascendants were compared and tested, as a result of no detectable differences （P 〉 0. 05）.
基金supported by the Strategic Priority Research Program (Grant No. XDB13040100)Key Research Program of Frontier Sciences (Grant No. QYZDJ-SSWSYS009) of the Chinese Academy of Sciences+5 种基金the National Natural Science Foundation (Grant Nos. 91731303,31771388, and 31711530221)the National Science Fund for Distinguished Young Scholars (Grant No. 31525014)the Program of Shanghai Academic Research Leader (Grant No. 16XD1404700)the National Key R&D Program (Grant No. 2016YFC0906403)the Shanghai Municipal Science and Technology Major Project (Grant No. 2017SHZDZX01), Chinathe support of the ‘‘Ten-Thousand Talents” Program for Young Top-notch Talents, China
文摘Ancestry composition of populations and individuals has been extensively investigated in recent years due to advances in the genotyping and sequencing technologies. As the number of populations and individuals used for ancestry inference increases remarkably, say more than 100 populations or 1000 individuals, it is usually challenging to present the ancestry composition in a traditional way using a rectangular graph. To address this issue, we developed a program,AncestryPainter, which can illustrate the ancestry composition of populations and individuals with a rounded and nice-looking graph to save space. Individuals are depicted as length-fixed bars partitioned into colored segments representing different ancestries, and the population of interest can be highlighted as a pie chart in the center of the circle plot. In addition, AncestryPainter can also be applied to display personal ancestry in a way similar to that for displaying population ancestry.AncestryPainter is publicly available at http://www.picb.ac.cn/PGG/resource.php.
