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Novel polymorphic EST-based microsatellite marker isolation and characterization from

Manosh Kumar BISWAS,Peng CHEN,Mohamed Hamdy AMAR,Xiuxin DENG

《农业科学与工程前沿(英文)》 2015年 第2卷 第1期   页码 60-65 doi: 10.15302/J-FASE-2015048

摘要: Novel simple sequence repeat (SSR) markers were developed to evaluate their utility for genetic diversity and breeding studies of and related species. A total of 108 primer pairs were characterized by PCR amplification experiments. Among these, 61 were polymorphic and transferable to other citrus species. The number of alleles per locus ranged from 2 to 6, with an average of 2.37 alleles per locus. The expected heterozygosity and observed heterozygosity ranged from 0 to 0.83 and 0 to 1.00, respectively. These novel polymorphic SSR markers will be useful for citrus cultivar identification and evaluation as well as breeding studies.

关键词: microsatellite     polymorphism     Poncirus trifoliata    

Detecting genetic hypermutability of gastrointestinal tumor by using a forensic STR kit

Anqi Chen, Suhua Zhang, Jixi Li, Chaoneng Ji, Jinzhong Chen, Chengtao Li

《医学前沿(英文)》 2020年 第14卷 第1期   页码 101-111 doi: 10.1007/s11684-019-0698-4

摘要: Growing evidence suggests that somatic hypermutational status and programmed cell death-1 overexpression are potential predictive biomarkers indicating treatment benefits from immunotherapy using immune checkpoint inhibitors. However, biomarker-matched trials are still limited, and many of the genomic alterations remain difficult to target. To isolate the potential somatic hypermutational tumor from microsatellite instability low/microsatellite stability (MSI-L/MSS) cases, we employed two commercial kits to determine MSI and forensic short tandem repeat (STR) alternations in 250 gastrointestinal (GI) tumors. Three types of forensic STR alternations, namely, allelic loss, Aadd, and Anew, were identified. 62.4% (156/250) of the patients with GI exhibited STR alternation, including 100% (15/15) and 60% (141/235) of the microsatellite high instability and MSI-L/MSS cases, respectively. 30% (75/250) of the patients exhibited STR instability with more than 26.32% (26.32%–84.21%) STR alternation. The cutoff with 26.32% of the STR alternations covered all 15 MSI cases and suggested that it might be a potential threshold. Given the similar mechanism of the mutations of MSI and forensic STR, the widely used forensic identifier STR kit might provide potential usage for identifying hypermutational status in GI cancers.

关键词: mismatch repair protein deficiency (MMR-D)     microsatellite instability (MSI)     short tandem repeats (STR)     gastrointestinal tumor     hypermutability    

The predictive value of chromosome 8p deletion for metastasis of hepatocellular carcinoma: a summary of works in 10 years

QIN Lunxiu, TANG Zhaoyou, GUAN Xinyuan, YE Qinghai, JIA Huliang, REN Ning

《医学前沿(英文)》 2008年 第2卷 第3期   页码 211-215 doi: 10.1007/s11684-008-0041-y

摘要: Hepatocellular carcinoma (HCC) represents an extremely poor prognostic cancer, which is mainly due to the high frequency of metastasis/recurrence after surgical operation. Exploring the molecular mechanisms involved in HCC metastasis could be helpful in the prediction and early diagnosis of HCC recurrence and could also provide new therapeutic targets for HCC metastasis. In the recent decade, we analyzed the genomic aberrations of the clinical specimens, as well as the metastatic models and cell lines of human HCC to identify the genetic markers related to HCC metastasis and to verify their clinical values in the prediction and control of metastasis of HCC. Using the comparative genomic hybridization (CGH) technique, we compared the differences of chromosomal aberrations between primary HCC tumors and their matched metastatic lesions, and found that chromosome 8p deletions might contribute to HCC metastasis. This novel finding was further confirmed by comparison between nude mice models of HCC with different metastatic potentials. By the more sensitive genome-wide microsatellite analysis, 8p deletion was defined to 8p23.3 and 8p11.2, which are two likely regions harboring metastasis-related genes of HCC. Using ‘8p-specific’ microarrays, two novel metastatic suppressors ( and ) were identified, and were proven to suppress invasion and metastasis of HCC. Clinical studies indicate that 8p deletion detected in HCC or circulating plasma DNA of patients is a useful predictor for metastatic recurrence and prognosis, even for patients with early stage HCC. These novel findings are regarded as important advances in the study of the molecular mechanisms of HCC metastasis, which provide not only a holistic view on the molecular cytogenetic bases of HCC metastasis, but also candidate regions for further study to identify metastatic suppressor genes.

关键词: sensitive genome-wide     prediction     genome-wide microsatellite     frequency     Hepatocellular carcinoma    

Expression status of GATA3 and mismatch repair proteins in upper tract urothelial carcinoma

Yue Wang, Jinxia Zhang, Yunfan Wang, Shufang Wang, Yu Zhang, Qi Miao, Fei Gao, Huiying He

《医学前沿(英文)》 2019年 第13卷 第6期   页码 730-740 doi: 10.1007/s11684-019-0687-7

摘要: GATA binding protein 3 (GATA3) and mismatch repair (MMR) deficiency contribute to the development of urothelial carcinoma. However, the combined expression of GATA3 and microsatellite instability (MSI) in upper tract urothelial carcinoma (UTUC) and its prognostic value have not been investigated. Here, we immunohistochemically stained GATA3 and MMR proteins in 108 UTUC samples. GATA3 was positive in 74 cases, and its expression was significantly lower than in adjacent benign urothelium ( <0.001). Loss of GATA3 expression was statistically associated with adverse clinicopathologic parameters, such as advanced stage, lymphovascular invasion, neural invasion, lymph node metastasis, and extensive necrosis. Cancer-specific survival (CSS, =0.028) and disease-free survival (DFS, =0.024) were significantly shorter in patients with GATA3 negative tumors than in patients with GATA3 positive tumors. The absence of MMR proteins was observed in 8.3% of the cases, and focal staining was identified in 13.0%. When using “lax criteria” which resulted in counting cases as negative where MMR staining was in fact focally positive (<5%), we found that GATA3 was inversely associated with MSI ( =0.005). Moreover, GATA3 /microsatellite stability (MS) tumors were correlated with advanced pT stage ( <0.001) and poor outcome ( =0.019 for CSS, =0.016 for DFS) compared with GATA3 /MSI ones. The GATA3 /MSI cases had unfavorable clinical outcomes compared with GATA3 /MSI cases ( =0.008 for CSS, =0.023 for DFS). This finding raises a question as to whether GATA3 interacts with MSI through the TGF- signaling pathway and regulates UTUC progression.

关键词: upper tract urothelial carcinoma     GATA binding protein 3     mismatch repair     microsatellite instability     prognosis    

Genetic variability of Appaloosa horses: a study of a closed breeding population from Argentina

Claudia Malena CORBI-BOTTO,Sebastian Andres SADABA,Elina Ines FRANCISCO,Paula Belen KALEMKERIAN,Juan Pedro LIRON,Egle Etel VILLEGAS-CASTAGNASSO,Guillermo GIOVAMBATTISTA,Pilar PERAL-GARCIA,Silvina DIAZ

《农业科学与工程前沿(英文)》 2014年 第1卷 第3期   页码 175-178 doi: 10.15302/J-FASE-2014019

摘要: The genetic diversity and structure of 72 Appaloosa horses belonging to a closed breeding population from an ecological reserve in Buenos Aires, Argentina, was investigated using eight microsatellite markers from the International Society for Animal Genetics panel. Our data showed that this Appaloosa horse population had an elevated degree of genetic diversity (He= 0.746) and did not present a significant increase of homozygous individuals ( ~0). However, the short tandem repeats, AHT5, ASB2, HTG10 and VHL20, were not in Hardy–Weinberg equilibrium ( -value<0.05). Genetic relationships between this population and other well known horse breeds showed that Appaloosa horses from Argentina could have had their origin in the horses of the Nez Perce’s people in Idaho while other Appaloosa horses may have had influences from Andalusian and Lusitano breeds. This closed breeding population conserves an important degree of Appaloosa genetic diversity and notwithstanding its particular breeding characteristics, represents a valuable genetic resource for conservation.

关键词: horse     genetic diversity     microsatellite     Appaloosa     population structure     conservation    

标题 作者 时间 类型 操作

Novel polymorphic EST-based microsatellite marker isolation and characterization from

Manosh Kumar BISWAS,Peng CHEN,Mohamed Hamdy AMAR,Xiuxin DENG

期刊论文

Detecting genetic hypermutability of gastrointestinal tumor by using a forensic STR kit

Anqi Chen, Suhua Zhang, Jixi Li, Chaoneng Ji, Jinzhong Chen, Chengtao Li

期刊论文

The predictive value of chromosome 8p deletion for metastasis of hepatocellular carcinoma: a summary of works in 10 years

QIN Lunxiu, TANG Zhaoyou, GUAN Xinyuan, YE Qinghai, JIA Huliang, REN Ning

期刊论文

Expression status of GATA3 and mismatch repair proteins in upper tract urothelial carcinoma

Yue Wang, Jinxia Zhang, Yunfan Wang, Shufang Wang, Yu Zhang, Qi Miao, Fei Gao, Huiying He

期刊论文

Genetic variability of Appaloosa horses: a study of a closed breeding population from Argentina

Claudia Malena CORBI-BOTTO,Sebastian Andres SADABA,Elina Ines FRANCISCO,Paula Belen KALEMKERIAN,Juan Pedro LIRON,Egle Etel VILLEGAS-CASTAGNASSO,Guillermo GIOVAMBATTISTA,Pilar PERAL-GARCIA,Silvina DIAZ

期刊论文