The term cholangiocarcinoma (CCA) comprises neoplasms of the intrahepatic, perihilar, and distal bile duct. Five-year survival rates of patients with CCA are below 20 %, and no targeted therapy could prove a benefit in comparison to the standard treatment of cisplatinum and gemcitabine. In recent years, next generation sequencing studies revealed a profound genomic heterogeneity of CCA subtypes potentially affecting the design of future therapy trials. This review provides a concise update on current clinical management of CCA including data of recent genomic studies and differences between CCA subtypes.
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http://dx.doi.org/10.1055/s-0043-102581 | DOI Listing |
Genome
January 2025
USDA-ARS, Wheat, Sorghum & Forage Research Unit, Lincoln, Nebraska, United States.
(2n=2x=14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of from the section and wheat and found that is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from more than 4 MYA and either has not yet been discovered, or is extinct.
View Article and Find Full Text PDFGenome
January 2025
Damietta University Faculty of Science, New Damietta, Damietta, Egypt;
Polyamine oxidase (PAOs) are enzymes associated with polyamine catabolism and play important roles in growth and development and stress tolerance of plants. In the present study, genome-wide discovery and analysis of the PAO family in sorghum was done utilizing model PAO of Arabidopsis. Six PAO genes were found using publicly available genomic data.
View Article and Find Full Text PDFJ Hered
January 2025
Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, 5A, Oester Farimagsgade, Copenhagen, 1353, Denmark.
The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, United States.
Pathway analysis plays a critical role in bioinformatics, enabling researchers to identify biological pathways associated with various conditions by analyzing gene expression data. However, the rise of large, multi-center datasets has highlighted limitations in traditional methods like Over-Representation Analysis (ORA) and Functional Class Scoring (FCS), which struggle with low signal-to-noise ratios (SNR) and large sample sizes. To tackle these challenges, we use a deep learning-based classification method, Gene PointNet, and a novel $P$-value computation approach leveraging the confusion matrix to address pathway analysis tasks.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
This study aimed to investigate the genetic association between glioblastoma (GBM) and unsupervised deep learning-derived imaging phenotypes (UDIPs). We employed a combination of genome-wide association study (GWAS) data, single-nucleus RNA sequencing (snRNA-seq), and scPagwas (pathway-based polygenic regression framework) methods to explore the genetic links between UDIPs and GBM. Two-sample Mendelian randomization analyses were conducted to identify causal relationships between UDIPs and GBM.
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