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Article: Irrigation and Nitrogen Application Promote Population Density through Altered Bud Bank Size and Components in Leymus chinensis

Yu, Dafu / Zheng, Xingyu / Mu, Chunsheng / Wang, Junfeng

Agronomy. 2022 June 15, v. 12, no. 6

2022

Abstract: The bud bank of perennial grasses is a controlling factor in population dynamics and is estrongly affected by soil water and nitrogen status. To explore how the bud bank size and its components affect shoot population density under different soil ... ...

Abstract	The bud bank of perennial grasses is a controlling factor in population dynamics and is estrongly affected by soil water and nitrogen status. To explore how the bud bank size and its components affect shoot population density under different soil moisture and nitrogen contents in spring and autumn. A three-full-factorial field experiment with factors of treatment timing (spring and autumn), nitrogen rate (control and 10 g N m⁻² yr⁻¹) and irrigation rate (control and +40 mm rainfall) was conducted in Leymus chinensis (a C₃ plant) in the northeast of China. The number of two types of buds (axillary shoot bud and rhizome bud), shoot population density, soil properties and rhizome traits (rhizome length and rhizome number) were determined to explore what and how changes in bud bank composition influences shoot population density in spring and autumn. The results showed that: (1) Regardless of the irrigation and nitrogen application timing, the simultaneous irrigation and nitrogen application significantly increased the number of two types of buds and promoted the shoot population density in spring and autumn by 56.75% and 47.74%, respectively. (2) The bud bank was dominated by rhizome buds in spring under control and dominated by axillary shoot buds under the combined irrigation and nitrogen treatment in autumn. Axillary shoot bud was the determining component in the population density increases in both spring and autumn, which were significantly associated with soil available phosphorus, available nitrogen and rhizome length and number. In summary, the number of different buds was strongly impacted by irrigation and nitrogen application at the crucial bud-bank formation stage. Agronomically, the forage yield could be largely increased through the increase in the axillary shoot bud density by using irrigation and nitrogen application in L. chinensis and other rhizomatous perennial grasses.
Keywords	Leymus chinensis ; agronomy ; autumn ; field experimentation ; forage yield ; irrigation rates ; nitrogen ; phosphorus ; population density ; population dynamics ; rain ; rhizomes ; soil water ; spring ; China
Language	English
Dates of publication	2022-0615
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2607043-1
ISSN	2073-4395
ISSN	2073-4395
DOI	10.3390/agronomy12061436
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: TOP2A modulates signaling via the AKT/mTOR pathway to promote ovarian cancer cell proliferation.

Zhang, Kaiwen / Zheng, Xingyu / Sun, Yiqing / Feng, Xinyu / Wu, Xirong / Liu, Wenlu / Gao, Chao / Yan, Ye / Tian, Wenyan / Wang, Yingmei

Cancer biology & therapy

2024 Volume 25, Issue 1, Page(s) 2325126

Abstract: Ovarian cancer (OC) is a form of gynecological malignancy that is associated with worse patient outcomes than any other cancer of the female reproductive tract. Topoisomerase II α (TOP2A) is commonly regarded as an oncogene that is associated with ... ...

Abstract	Ovarian cancer (OC) is a form of gynecological malignancy that is associated with worse patient outcomes than any other cancer of the female reproductive tract. Topoisomerase II α (TOP2A) is commonly regarded as an oncogene that is associated with malignant disease progression in a variety of cancers, its mechanistic functions in OC have yet to be firmly established. We explored the role of TOP2A in OC through online databases, clinical samples, in vitro and in vivo experiments. And initial analyses of public databases revealed high OC-related TOP2A expression in patient samples that was related to poorer prognosis. This was confirmed by clinical samples in which TOP2A expression was elevated in OC relative to healthy tissue. Kaplan-Meier analyses further suggested that higher TOP2A expression levels were correlated with worse prognosis in OC patients. In vitro, TOP2A knockdown resulted in the inhibition of OC cell proliferation, with cells entering G1 phase arrest and undergoing consequent apoptotic death. In rescue assays, TOP2A was confirmed to regulate cell proliferation and cell cycle through AKT/mTOR pathway activity. Mouse model experiments further affirmed the key role that TOP2A plays as a driver of OC cell proliferation. These data provide strong evidence supporting TOP2A as an oncogenic mediator and prognostic biomarker related to OC progression and poor outcomes. At the mechanistic level, TOP2A can control tumor cell growth via AKT/mTOR pathway modulation. These preliminary results provide a foundation for future research seeking to explore the utility of TOP2A inhibitor-based combination treatment regimens in platinum-resistant recurrent OC patients.
MeSH term(s)	Animals ; Female ; Humans ; Mice ; Carcinoma, Ovarian Epithelial ; Cell Proliferation ; DNA Topoisomerases, Type II/genetics ; Ovarian Neoplasms/genetics ; Proto-Oncogene Proteins c-akt ; TOR Serine-Threonine Kinases
Chemical Substances	DNA Topoisomerases, Type II (EC 5.99.1.3) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; TOR Serine-Threonine Kinases (EC 2.7.11.1) ; TOP2A protein, human (EC 5.99.1.3) ; Top2a protein, mouse (EC 5.99.1.3)
Language	English
Publishing date	2024-03-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2146305-0
ISSN	1555-8576 ; 1538-4047
ISSN (online)	1555-8576
ISSN	1538-4047
DOI	10.1080/15384047.2024.2325126
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Article ; Online: Oncological and reproductive outcomes of endometrial atypical hyperplasia and endometrial cancer patients undergoing conservative therapy with hysteroscopic resection: A systematic review and meta-analysis.

Zhao, Shuangshuang / Zhang, Jingying / Yan, Ye / Tian, Lina / Chen, Lingli / Zheng, Xingyu / Sun, Yiqing / Tian, Wenyan / Xue, Fengxia / Wang, Yingmei

Acta obstetricia et gynecologica Scandinavica

2024

Abstract: Introduction: Our objective was to conduct a systematic review and meta-analysis of studies evaluating the oncological and reproductive outcomes of patients with endometrial atypical hyperplasia (AH) and endometrioid endometrial cancer (EEC) undergoing ... ...

Abstract	Introduction: Our objective was to conduct a systematic review and meta-analysis of studies evaluating the oncological and reproductive outcomes of patients with endometrial atypical hyperplasia (AH) and endometrioid endometrial cancer (EEC) undergoing conservative therapy with hysteroscopic resection (HR). Material and methods: This study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement for systematic reviews and meta-analyses. The study strictly followed the methodological framework proposed by the Cochrane Handbook and was retrospectively registered in PROSPERO (CRD42023469986). Searches were conducted in PubMed, Embase, and the Cochrane Library, from inception to October 10, 2023. A checklist based on items of the Newcastle-Ottawa Scale and the Methodological Index for Non-randomized Studies was used for quality assessment. The primary end points for this meta-analysis were complete response (CR), pregnancy, and live birth rates following HR-based therapy in patients with EEC or AH. The secondary end point was the recurrence rate (RR). Results: Twenty-one articles involving 407 patients with clinical stage IA, low or intermediate grade, EEC, and 444 patients with AH managed with HR-based conservative treatment were included for this systematic review. CR to HR-based conservative therapy was achieved in 88.6% of patients with EEC and 97.0% of patients with AH. Of these, 30.6% and 24.2%, respectively, had live births. The overall pooled disease RR was 18.3% and 10.8% in patients with EEC and AH, respectively. Further subset analyses revealed that EEC patients with body mass index (BMI) ≤28 kg/m Conclusions: Hysteroscopic resection followed by progestins appears to be a promising choice for fertility-sparing treatment in young patients with AH and EEC, with effective and safe responses. The live birth rate remains to be improved by providing medical guidance and encouragement.
Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	80019-3
ISSN	1600-0412 ; 0001-6349
ISSN (online)	1600-0412
ISSN	0001-6349
DOI	10.1111/aogs.14815
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Article ; Online: Pan-cancer evaluation of gene expression and somatic alteration data for cancer prognosis prediction.

Zheng, Xingyu / Amos, Christopher I / Frost, H Robert

BMC cancer

2021 Volume 21, Issue 1, Page(s) 1053

Abstract: Background: Over the past decades, approaches for diagnosing and treating cancer have seen significant improvement. However, the variability of patient and tumor characteristics has limited progress on methods for prognosis prediction. The development ... ...

Abstract	Background: Over the past decades, approaches for diagnosing and treating cancer have seen significant improvement. However, the variability of patient and tumor characteristics has limited progress on methods for prognosis prediction. The development of high-throughput omics technologies now provides multiple approaches for characterizing tumors. Although a large number of published studies have focused on integration of multi-omics data and use of pathway-level models for cancer prognosis prediction, there still exists a gap of knowledge regarding the prognostic landscape across multi-omics data for multiple cancer types using both gene-level and pathway-level predictors. Methods: In this study, we systematically evaluated three often available types of omics data (gene expression, copy number variation and somatic point mutation) covering both DNA-level and RNA-level features. We evaluated the landscape of predictive performance of these three omics modalities for 33 cancer types in the TCGA using a Lasso or Group Lasso-penalized Cox model and either gene or pathway level predictors. Results: We constructed the prognostic landscape using three types of omics data for 33 cancer types on both the gene and pathway levels. Based on this landscape, we found that predictive performance is cancer type dependent and we also highlighted the cancer types and omics modalities that support the most accurate prognostic models. In general, models estimated on gene expression data provide the best predictive performance on either gene or pathway level and adding copy number variation or somatic point mutation data to gene expression data does not improve predictive performance, with some exceptional cohorts including low grade glioma and thyroid cancer. In general, pathway-level models have better interpretative performance, higher stability and smaller model size across multiple cancer types and omics data types relative to gene-level models. Conclusions: Based on this landscape and comprehensively comparison, models estimated on gene expression data provide the best predictive performance on either gene or pathway level. Pathway-level models have better interpretative performance, higher stability and smaller model size relative to gene-level models.
MeSH term(s)	Cohort Studies ; DNA Copy Number Variations ; Databases, Genetic ; Gene Expression ; Gene Expression Profiling/methods ; Humans ; Neoplasms/genetics ; Neoplasms/mortality ; Neoplasms/pathology ; Point Mutation ; Predictive Value of Tests ; Prognosis ; Proportional Hazards Models
Language	English
Publishing date	2021-09-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2041352-X
ISSN	1471-2407 ; 1471-2407
ISSN (online)	1471-2407
ISSN	1471-2407
DOI	10.1186/s12885-021-08796-3
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Article ; Online: Comparison of pathway and gene-level models for cancer prognosis prediction.

Zheng, Xingyu / Amos, Christopher I / Frost, H Robert

BMC bioinformatics

2020 Volume 21, Issue 1, Page(s) 76

Abstract: Background: Cancer prognosis prediction is valuable for patients and clinicians because it allows them to appropriately manage care. A promising direction for improving the performance and interpretation of expression-based predictive models involves ... ...

Abstract	Background: Cancer prognosis prediction is valuable for patients and clinicians because it allows them to appropriately manage care. A promising direction for improving the performance and interpretation of expression-based predictive models involves the aggregation of gene-level data into biological pathways. While many studies have used pathway-level predictors for cancer survival analysis, a comprehensive comparison of pathway-level and gene-level prognostic models has not been performed. To address this gap, we characterized the performance of penalized Cox proportional hazard models built using either pathway- or gene-level predictors for the cancers profiled in The Cancer Genome Atlas (TCGA) and pathways from the Molecular Signatures Database (MSigDB). Results: When analyzing TCGA data, we found that pathway-level models are more parsimonious, more robust, more computationally efficient and easier to interpret than gene-level models with similar predictive performance. For example, both pathway-level and gene-level models have an average Cox concordance index of ~ 0.85 for the TCGA glioma cohort, however, the gene-level model has twice as many predictors on average, the predictor composition is less stable across cross-validation folds and estimation takes 40 times as long as compared to the pathway-level model. When the complex correlation structure of the data is broken by permutation, the pathway-level model has greater predictive performance while still retaining superior interpretative power, robustness, parsimony and computational efficiency relative to the gene-level models. For example, the average concordance index of the pathway-level model increases to 0.88 while the gene-level model falls to 0.56 for the TCGA glioma cohort using survival times simulated from uncorrelated gene expression data. Conclusion: The results of this study show that when the correlations among gene expression values are low, pathway-level analyses can yield better predictive performance, greater interpretative power, more robust models and less computational cost relative to a gene-level model. When correlations among genes are high, a pathway-level analysis provides equivalent predictive power compared to a gene-level analysis while retaining the advantages of interpretability, robustness and computational efficiency.
MeSH term(s)	Cohort Studies ; Gene Expression ; Glioma/genetics ; Glioma/mortality ; Humans ; Models, Genetic ; Neoplasms/genetics ; Neoplasms/mortality ; Prognosis ; Proportional Hazards Models
Language	English
Publishing date	2020-02-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-020-3423-z
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Article ; Online: Cancer prognosis prediction using somatic point mutation and copy number variation data: a comparison of gene-level and pathway-based models.

Zheng, Xingyu / Amos, Christopher I / Frost, H Robert

BMC bioinformatics

2020 Volume 21, Issue 1, Page(s) 467

Abstract: Background: Genomic profiling of solid human tumors by projects such as The Cancer Genome Atlas (TCGA) has provided important information regarding the somatic alterations that drive cancer progression and patient survival. Although researchers have ... ...

Abstract	Background: Genomic profiling of solid human tumors by projects such as The Cancer Genome Atlas (TCGA) has provided important information regarding the somatic alterations that drive cancer progression and patient survival. Although researchers have successfully leveraged TCGA data to build prognostic models, most efforts have focused on specific cancer types and a targeted set of gene-level predictors. Less is known about the prognostic ability of pathway-level variables in a pan-cancer setting. To address these limitations, we systematically evaluated and compared the prognostic ability of somatic point mutation (SPM) and copy number variation (CNV) data, gene-level and pathway-level models for a diverse set of TCGA cancer types and predictive modeling approaches. Results: We evaluated gene-level and pathway-level penalized Cox proportional hazards models using SPM and CNV data for 29 different TCGA cohorts. We measured predictive accuracy as the concordance index for predicting survival outcomes. Our comprehensive analysis suggests that the use of pathway-level predictors did not offer superior predictive power relative to gene-level models for all cancer types but had the advantages of robustness and parsimony. We identified a set of cohorts for which somatic alterations could not predict prognosis, and a unique cohort LGG, for which SPM data was more predictive than CNV data and the predictive accuracy is good for all model types. We found that the pathway-level predictors provide superior interpretative value and that there is often a serious collinearity issue for the gene-level models while pathway-level models avoided this issue. Conclusion: Our comprehensive analysis suggests that when using somatic alterations data for cancer prognosis prediction, pathway-level models are more interpretable, stable and parsimonious compared to gene-level models. Pathway-level models also avoid the issue of collinearity, which can be serious for gene-level somatic alterations. The prognostic power of somatic alterations is highly variable across different cancer types and we have identified a set of cohorts for which somatic alterations could not predict prognosis. In general, CNV data predicts prognosis better than SPM data with the exception of the LGG cohort.
MeSH term(s)	DNA Copy Number Variations/genetics ; Humans ; Point Mutation/genetics ; Prognosis
Language	English
Publishing date	2020-10-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-020-03791-0
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Article: Indoor Passive Visual Positioning by CNN-Based Pedestrian Detection.

Wu, Dewen / Chen, Ruizhi / Yu, Yue / Zheng, Xingyu / Xu, Yan / Liu, Zuoya

Micromachines

2022 Volume 13, Issue 9

Abstract: Indoor positioning applications are developing at a rapid pace; active visual positioning is one method that is applicable to mobile platforms. Other methods include Wi-Fi, CSI, and PDR approaches; however, their positioning accuracy usually cannot ... ...

Abstract	Indoor positioning applications are developing at a rapid pace; active visual positioning is one method that is applicable to mobile platforms. Other methods include Wi-Fi, CSI, and PDR approaches; however, their positioning accuracy usually cannot achieve the positioning performance of the active visual method. Active visual users, however, must take a photo to obtain location information, raising confidentiality and privacy issues. To address these concerns, we propose a solution for passive visual positioning based on pedestrian detection and projection transformation. This method consists of three steps: pretreatment, pedestrian detection, and pose estimation. Pretreatment includes camera calibration and camera installation. In pedestrian detection, features are extracted by deep convolutional neural networks using neighboring frame detection results and the map information as the region of interest attention model (RIAM). Pose estimation computes accurate localization results through projection transformation (PT). This system relies on security cameras installed in non-private areas so that pedestrians do not have to take photos. Experiments were conducted in a hall about 100 square meters in size, with 41 test-points for the localization experiment. The results show that the positioning error was 0.48 m (RMSE) and the 90% error was 0.73 m. Therefore, the proposed passive visual method delivers high positioning performance.
Language	English
Publishing date	2022-08-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2620864-7
ISSN	2072-666X
ISSN	2072-666X
DOI	10.3390/mi13091413
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Article ; Online: CCNE1 is a predictive and immunotherapeutic indicator in various cancers including UCEC: a pan-cancer analysis.

Zheng, Xingyu / Chen, Lingli / Liu, Wenlu / Zhao, Shuangshuang / Yan, Ye / Zhao, Jianzhen / Tian, Wenyan / Wang, Yingmei

Hereditas

2023 Volume 160, Issue 1, Page(s) 13

Abstract: Background: CCNE1 plays an important oncogenic role in several tumors, especially high-stage serous ovarian cancer and endometrial cancer. Nevertheless, the fundamental function of CCNE1 has not been explored in multiple cancers. Therefore, ... ...

Abstract	Background: CCNE1 plays an important oncogenic role in several tumors, especially high-stage serous ovarian cancer and endometrial cancer. Nevertheless, the fundamental function of CCNE1 has not been explored in multiple cancers. Therefore, bioinformatics analyses of pan-cancer datasets were carried out to explore how CCNE1 regulates tumorigenesis. Methods: A variety of online tools and cancer databases, including GEPIA2, SangerBox, LinkedOmics and cBioPortal, were applied to investigate the expression of CCNE1 across cancers. The pan-cancer datasets were used to search for links between CCNE1 expression and prognosis, DNA methylation, m6A level, genetic alterations, CCNE1-related genes, and tumor immunity. We verified that CCNE1 has biological functions in UCEC cell lines using CCK-8, EdU, and Transwell assays. Results: In patients with different tumor types, a high mRNA expression level of CCNE1 was related to a poor prognosis. Genes related to CCNE1 were connected to the cell cycle, metabolism, and DNA damage repair, according to GO and KEGG enrichment analyses. Genetic alterations of CCNE1, including duplications and deep mutations, have been observed in various cancers. Immune analysis revealed that CCNE1 had a strong correlation with TMB, MSI, neoantigen, and ICP in a variety of tumor types, and this correlation may have an impact on the sensitivity of various cancers to immunotherapy. CCK-8, EdU and Transwell assays suggested that CCNE1 knockdown can suppress UCEC cell proliferation, migration and invasion. Conclusion: Our study demonstrated that CCNE1 is upregulated in multiple cancers in the TCGA database and may be a promising predictive biomarker for the immunotherapy response in some types of cancers. Moreover, CCNE1 knockdown can suppress the proliferation, migration and invasion of UCEC cells.
MeSH term(s)	Humans ; Cell Division ; Cell Line ; Cell Proliferation ; Cyclin E/genetics ; Neoplasms/genetics ; Neoplasms/therapy ; Oncogene Proteins/genetics
Chemical Substances	CCNE1 protein, human ; Cyclin E ; Oncogene Proteins
Language	English
Publishing date	2023-03-24
Publishing country	England
Document type	Journal Article
ZDB-ID	214294-6
ISSN	1601-5223 ; 0018-0661
ISSN (online)	1601-5223
ISSN	0018-0661
DOI	10.1186/s41065-023-00273-0
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Article ; Online: Compound AC1Q3QWB upregulates CDKN1A and SOX17 by interrupting the HOTAIR-EZH2 interaction and enhances the efficacy of tazemetostat in endometrial cancer.

Chen, Lingli / Zheng, Xingyu / Liu, Wenlu / Sun, Yiqing / Zhao, Shuangshuang / Tian, Lina / Tian, Wenyan / Xue, Fengxia / Kang, Chunsheng / Wang, Yingmei

Cancer letters

2023 Volume 578, Page(s) 216445

Abstract: Endometrial cancer (EC) is a common malignancy of the female reproductive system, with an escalating incidence. Recurrent/metastatic EC presents a poor prognosis. The interaction between the long non-coding RNA (lncRNA) HOTAIR and the polycomb repressive ...

Abstract	Endometrial cancer (EC) is a common malignancy of the female reproductive system, with an escalating incidence. Recurrent/metastatic EC presents a poor prognosis. The interaction between the long non-coding RNA (lncRNA) HOTAIR and the polycomb repressive complex 2 (PRC2) induces abnormal silencing of tumor suppressor genes, exerting a pivotal role in tumorigenesis. We have previously discovered AC1Q3QWB (AQB), a small-molecule compound targeting HOTAIR-EZH2 interaction. In the present study, we unveil that AQB selectively hampers the interaction between HOTAIR and EZH2 within EC cells, thus reversing the epigenetic suppression of tumor suppressor genes. Furthermore, our findings demonstrate AQB's synergistic effect with tazemetostat (TAZ), an EZH2 inhibitor, significantly boosting the expression of CDKN1A and SOX17. This, in turn, induces cell cycle arrest and impedes EC cell proliferation, migration, and invasion. In vivo experiments further validate AQB's potential by enhancing TAZ's anti-tumor efficacy at lower doses. Our results advocate AQB, a recently discovered small-molecule inhibitor, as a promising agent against EC cells. When combined with TAZ, it offers a novel therapeutic strategy for EC treatment.
MeSH term(s)	Humans ; Female ; Enhancer of Zeste Homolog 2 Protein/genetics ; Enhancer of Zeste Homolog 2 Protein/metabolism ; Neoplasm Recurrence, Local/genetics ; Endometrial Neoplasms/drug therapy ; Endometrial Neoplasms/genetics ; Gene Expression Regulation, Neoplastic ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Cell Line, Tumor ; SOXF Transcription Factors/genetics ; SOXF Transcription Factors/metabolism ; Cyclin-Dependent Kinase Inhibitor p21/genetics
Chemical Substances	AC1Q3QWB ; tazemetostat (Q40W93WPE1) ; Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43) ; RNA, Long Noncoding ; EZH2 protein, human (EC 2.1.1.43) ; SOX17 protein, human ; SOXF Transcription Factors ; CDKN1A protein, human ; Cyclin-Dependent Kinase Inhibitor p21
Language	English
Publishing date	2023-10-20
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	195674-7
ISSN	1872-7980 ; 0304-3835
ISSN (online)	1872-7980
ISSN	0304-3835
DOI	10.1016/j.canlet.2023.216445
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Article ; Online: Analytical Validation of a Telomerase Reverse Transcriptase (TERT) Promoter Mutation Assay.

Iyer, Priyanka C / Dadu, Ramona / Barque, Anna / Zanelli, Cleslei / Zheng, Xingyu / Jiang, Huimin / Walsh, P Sean / Hao, Yangyang / Huang, Jing / Klopper, Joshua / Kloos, Richard T / Cabanillas, Maria

The Journal of clinical endocrinology and metabolism

2024

Abstract: Context: TERT promoter mutated thyroid cancers are associated with a decreased rate of disease free and disease specific survival. High quality analytical validation of a diagnostic test promotes confidence in the results which inform clinical decision ... ...

Abstract	Context: TERT promoter mutated thyroid cancers are associated with a decreased rate of disease free and disease specific survival. High quality analytical validation of a diagnostic test promotes confidence in the results which inform clinical decision making. Objective: To demonstrate the analytical validation of the Afirma TERT promoter mutation assay. Methods: TERT promoter C228T and C250T variant detection in genomic DNA (gDNA) was analyzed by assessing variable DNA input and the limit of detection (LOD) of variant allele frequency (VAF). The negative and positive percent agreement (NPA and PPA) of the Afirma TERT test was examined against a reference primer pair as was the analytical specificity from potential interfering substances (RNA and blood gDNA). Further, the intra-run, inter-run and inter-laboratory reproducibility of the assay were tested. Results: The Afirma TERT test is tolerant to variation in DNA input amount (7-13 ng) and can detect expected positive TERT promoter variants down to 5% VAF LOD at 7ng DNA input with > 95% sensitivity. Both NPA and PPA were 100% against the reference primer pair. The test remains accurate in presence of 20% RNA or 80% blood gDNA for an average patient sample that typically has 30% VAF. The test also demonstrated a 100% confirmation rate when compared with an external NGS-based reference assay executed in a non-Veracyte laboratory. Conclusion: The analytical robustness and reproducibility of the Afirma TERT test support its routine clinical use among thyroid nodules with indeterminate cytology that are Afirma GSC suspicious or among Bethesda V/VI nodules.
Language	English
Publishing date	2024-03-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	3029-6
ISSN	1945-7197 ; 0021-972X
ISSN (online)	1945-7197
ISSN	0021-972X
DOI	10.1210/clinem/dgae134
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