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  1. Article ; Online: Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data.

    Crippa, Valentina / Fina, Emanuela / Ramazzotti, Daniele / Piazza, Rocco

    BMC bioinformatics

    2024  Volume 25, Issue 1, Page(s) 72

    Abstract: Background: Copy number alterations (CNAs) are genetic changes commonly found in cancer that involve different regions of the genome and impact cancer progression by affecting gene expression and genomic stability. Computational techniques can analyze ... ...

    Abstract Background: Copy number alterations (CNAs) are genetic changes commonly found in cancer that involve different regions of the genome and impact cancer progression by affecting gene expression and genomic stability. Computational techniques can analyze copy number data obtained from high-throughput sequencing platforms, and various tools visualize and analyze CNAs in cancer genomes, providing insights into genetic mechanisms driving cancer development and progression. However, tools for visualizing copy number data in cancer research have some limitations. In fact, they can be complex to use and require expertise in bioinformatics or computational biology. While copy number data analysis and visualization provide insights into cancer biology, interpreting results can be challenging, and there may be multiple explanations for observed patterns of copy number alterations.
    Results: We created Control-FREEC Viewer, a tool that facilitates effective visualization and exploration of copy number data. With Control-FREEC Viewer, experimental data can be easily loaded by the user. After choosing the reference genome, copy number data are displayed in whole genome or single chromosome view. Gain or loss on a specific gene can be found and visualized on each chromosome. Analysis parameters for subsequent sessions can be stored and images can be exported in raster and vector formats.
    Conclusions: Control-FREEC Viewer enables users to import and visualize data analyzed by the Control-FREEC tool, as well as by other tools sharing a similar tabular output, providing a comprehensive and intuitive graphical user interface for data visualization.
    MeSH term(s) Humans ; Software ; DNA Copy Number Variations ; Genome ; Computational Biology/methods ; Neoplasms/genetics
    Language English
    Publishing date 2024-02-14
    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/s12859-024-05694-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Late relapse of chronic myeloid leukemia after allogeneic bone marrow transplantation points to KANSARL (KANSL1::ARL17A) alteration: a case report with insights on the molecular landscape.

    Fontana, Diletta / Zambrotta, Giovanni Paolo Maria / Scannella, Antonio / Piazza, Rocco / Gambacorti-Passerini, Carlo

    Annals of hematology

    2024  Volume 103, Issue 5, Page(s) 1561–1568

    Abstract: Chronic myeloid leukemia is a myeloproliferative neoplasm characterized by the presence of the Philadelphia chromosome and the consequent BCR::ABL1 oncoprotein. In the era before the introduction of tyrosine kinase inhibitors (TKIs), the only potentially ...

    Abstract Chronic myeloid leukemia is a myeloproliferative neoplasm characterized by the presence of the Philadelphia chromosome and the consequent BCR::ABL1 oncoprotein. In the era before the introduction of tyrosine kinase inhibitors (TKIs), the only potentially curative treatment was allogeneic hematopoietic stem cell transplantation (HSCT). Here, we present the case of a patient affected by CML who experienced a relapse 20 years after allogeneic HSCT. Following relapse, the patient was treated with imatinib and bosutinib, resulting in a deep molecular response and successfully discontinued treatment. Additional analysis including whole-exome sequencing and RNA sequencing provided some insights on the molecular mechanisms of the relapse: the identification of the fusion transcript KANSL1::ARL17A (KANSARL), a cancer predisposition fusion gene, could justify a condition of genomic instability which may be associated with the onset and/or probably the late relapse of his CML.
    MeSH term(s) Humans ; Bone Marrow Transplantation ; Fusion Proteins, bcr-abl/genetics ; Hematopoietic Stem Cell Transplantation/methods ; Imatinib Mesylate/therapeutic use ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy ; Protein Kinase Inhibitors/therapeutic use ; Recurrence ; Oncogene Proteins, Fusion/genetics
    Chemical Substances Fusion Proteins, bcr-abl (EC 2.7.10.2) ; Imatinib Mesylate (8A1O1M485B) ; Protein Kinase Inhibitors ; NSL1 protein, human ; Oncogene Proteins, Fusion
    Language English
    Publishing date 2024-02-07
    Publishing country Germany
    Document type Case Reports ; Journal Article
    ZDB-ID 1064950-5
    ISSN 1432-0584 ; 0939-5555 ; 0945-8077
    ISSN (online) 1432-0584
    ISSN 0939-5555 ; 0945-8077
    DOI 10.1007/s00277-024-05649-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Uh III Zs.181: Show issues Location:
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  3. Article: Myelodysplastic Syndromes/Myeloproliferative Overlap Neoplasms and Differential Diagnosis in the WHO and ICC 2022 Era: A Focused Review.

    Fontana, Diletta / Elli, Elena M / Pagni, Fabio / Piazza, Rocco

    Cancers

    2023  Volume 15, Issue 12

    Abstract: The myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) category comprises a varied group of myeloid neoplastic diseases characterized by clinical and pathologic overlapping features of both myelodysplastic and myeloproliferative neoplasms. ... ...

    Abstract The myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) category comprises a varied group of myeloid neoplastic diseases characterized by clinical and pathologic overlapping features of both myelodysplastic and myeloproliferative neoplasms. For these reasons, these tumors are challenging in terms of diagnosis. The recent World Health Organization (WHO) 2022 classification and the International Consensus Classification (ICC) made changes in the classification of MDS/MPN compared to the previous 2016 WHO classification and improved the diagnostic criteria of these entities. The aim of this review is to describe the main entities reported in the more recent classifications, focusing on chronic myelomonocytic leukemia (CMML), MDS/MPN with neutrophilia (or atypical CML [aCML]), and MDS/MPN with
    Language English
    Publishing date 2023-06-13
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers15123175
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Molecular Pathogenesis of

    Fontana, Diletta / Gambacorti-Passerini, Carlo / Piazza, Rocco

    Frontiers in oncology

    2021  Volume 11, Page(s) 756348

    Abstract: Atypical chronic myeloid leukemia is a rare disease whose pathogenesis has long been debated. It currently belongs to the group of myelodysplastic/myeloproliferative disorders. In this review, an overview on the current knowledge about diagnosis, ... ...

    Abstract Atypical chronic myeloid leukemia is a rare disease whose pathogenesis has long been debated. It currently belongs to the group of myelodysplastic/myeloproliferative disorders. In this review, an overview on the current knowledge about diagnosis, prognosis, and genetics is presented, with a major focus on the recent molecular findings. We describe here the molecular pathogenesis of the disease, focusing on the mechanisms of action of the main mutations as well as on gene expression profiling. We also present the treatment options focusing on emerging targeted therapies.
    Language English
    Publishing date 2021-11-11
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2021.756348
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Impact of

    Fontana, Diletta / Gambacorti-Passerini, Carlo / Piazza, Rocco

    Molecular & cellular oncology

    2021  Volume 8, Issue 2, Page(s) 1877598

    Abstract: Recently we showed that Ethanolamine Kinase 1 ( ...

    Abstract Recently we showed that Ethanolamine Kinase 1 (
    Language English
    Publishing date 2021-02-19
    Publishing country United States
    Document type Journal Article
    ISSN 2372-3556
    ISSN 2372-3556
    DOI 10.1080/23723556.2021.1877598
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Neuroactive Steroid-Gut Microbiota Interaction in T2DM Diabetic Encephalopathy.

    Diviccaro, Silvia / Cioffi, Lucia / Piazza, Rocco / Caruso, Donatella / Melcangi, Roberto Cosimo / Giatti, Silvia

    Biomolecules

    2023  Volume 13, Issue 9

    Abstract: The pathological consequences of type 2 diabetes mellitus (T2DM) also involve the central nervous system; indeed, T2DM patients suffer from learning and memory disabilities with a higher risk of developing dementia. Although several factors have been ... ...

    Abstract The pathological consequences of type 2 diabetes mellitus (T2DM) also involve the central nervous system; indeed, T2DM patients suffer from learning and memory disabilities with a higher risk of developing dementia. Although several factors have been proposed as possible contributors, how neuroactive steroids and the gut microbiome impact brain pathophysiology in T2DM remain unexplored. On this basis, in male Zucker diabetic fatty (ZDF) rats, we studied whether T2DM alters memory abilities using the novel object recognition test, neuroactive steroid levels by liquid chromatography-tandem mass spectrometry, hippocampal parameters using molecular assessments, and gut microbiome composition using 16S next-generation sequencing. Results obtained reveal that T2DM worsens memory abilities and that these are correlated with increased levels of corticosterone in plasma and with a decrease in allopregnanolone in the hippocampus, where neuroinflammation, oxidative stress, and mitochondrial dysfunction were reported. Interestingly, our analysis highlighted a small group of taxa strictly related to both memory impairment and neuroactive steroid levels. Overall, the data underline an interesting role for allopregnanolone and microbiota that may represent candidates for the development of therapeutic strategies.
    MeSH term(s) Humans ; Rats ; Animals ; Male ; Rats, Zucker ; Gastrointestinal Microbiome ; Diabetes Mellitus, Type 2 ; Neurosteroids ; Pregnanolone
    Chemical Substances Neurosteroids ; Pregnanolone (BXO86P3XXW)
    Language English
    Publishing date 2023-08-29
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom13091325
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Characterization of cancer subtypes associated with clinical outcomes by multi-omics integrative clustering.

    Crippa, Valentina / Malighetti, Federica / Villa, Matteo / Graudenzi, Alex / Piazza, Rocco / Mologni, Luca / Ramazzotti, Daniele

    Computers in biology and medicine

    2023  Volume 162, Page(s) 107064

    Abstract: Cancer patients show heterogeneous phenotypes and very different outcomes and responses even to common treatments, such as standard chemotherapy. This state-of-affairs has motivated the need for the comprehensive characterization of cancer phenotypes and ...

    Abstract Cancer patients show heterogeneous phenotypes and very different outcomes and responses even to common treatments, such as standard chemotherapy. This state-of-affairs has motivated the need for the comprehensive characterization of cancer phenotypes and fueled the generation of large omics datasets, comprising multiple omics data reported for the same patients, which might now allow us to start deciphering cancer heterogeneity and implement personalized therapeutic strategies. In this work, we performed the analysis of four cancer types obtained from the latest efforts by The Cancer Genome Atlas, for which seven distinct omics data were available for each patient, in addition to curated clinical outcomes. We performed a uniform pipeline for raw data preprocessing and adopted the Cancer Integration via MultIkernel LeaRning (CIMLR) integrative clustering method to extract cancer subtypes. We then systematically review the discovered clusters for the considered cancer types, highlighting novel associations between the different omics and prognosis.
    MeSH term(s) Humans ; Genomics/methods ; Multiomics ; Neoplasms/genetics ; Genome ; Cluster Analysis
    Language English
    Publishing date 2023-05-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2023.107064
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 653: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  8. Article ; Online: Tyrosine Kinase Inhibitor discontinuation in Chronic Myeloid Leukemia: eligibility criteria and predictors of success.

    Inzoli, Elena / Aroldi, Andrea / Piazza, Rocco / Gambacorti-Passerini, Carlo

    American journal of hematology

    2022  Volume 97, Issue 8, Page(s) 1075–1085

    Abstract: TKI discontinuation proved to be safe and feasible in patients with CML with deep and durable molecular responses, introducing an additional treatment goal for these patients beyond overall survival. However, treatment interruption is a safe procedure ... ...

    Abstract TKI discontinuation proved to be safe and feasible in patients with CML with deep and durable molecular responses, introducing an additional treatment goal for these patients beyond overall survival. However, treatment interruption is a safe procedure only with appropriate patient selection and monitoring. Clinical and biological factors associated with better outcomes do not yet offer a precise stratification of patients according to their risk of relapse. This article aims at reviewing the leading studies present in the field in order to define eligibility criteria for discontinuation and predictors of success.
    MeSH term(s) Humans ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy ; Patient Selection ; Protein Kinase Inhibitors/adverse effects ; Recurrence
    Chemical Substances Protein Kinase Inhibitors
    Language English
    Publishing date 2022-04-12
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 196767-8
    ISSN 1096-8652 ; 0361-8609
    ISSN (online) 1096-8652
    ISSN 0361-8609
    DOI 10.1002/ajh.26556
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1251: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity.

    Graudenzi, Alex / Maspero, Davide / Angaroni, Fabrizio / Piazza, Rocco / Ramazzotti, Daniele

    iScience

    2021  Volume 24, Issue 2, Page(s) 102116

    Abstract: To dissect the mechanisms underlying the inflation of variants in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) genome, we present a large-scale analysis of intra-host genomic diversity, which reveals that most samples exhibit ... ...

    Abstract To dissect the mechanisms underlying the inflation of variants in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) genome, we present a large-scale analysis of intra-host genomic diversity, which reveals that most samples exhibit heterogeneous genomic architectures, due to the interplay between host-related mutational processes and transmission dynamics. The decomposition of minor variants profiles unveils three non-overlapping mutational signatures related to nucleotide substitutions and likely ruled by APOlipoprotein B Editing Complex (APOBEC), Reactive Oxygen Species (ROS), and Adenosine Deaminase Acting on RNA (ADAR), highlighting heterogeneous host responses to SARS-CoV-2 infections. A corrected-for-signatures
    Language English
    Publishing date 2021-01-28
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2021.102116
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data.

    Ramazzotti, Daniele / Maspero, Davide / Angaroni, Fabrizio / Spinelli, Silvia / Antoniotti, Marco / Piazza, Rocco / Graudenzi, Alex

    iScience

    2022  Volume 25, Issue 6, Page(s) 104487

    Abstract: A key task of genomic surveillance of infectious viral diseases lies in the early detection of dangerous variants. Unexpected help to this end is provided by the analysis of deep sequencing data of viral samples, which are typically discarded after ... ...

    Abstract A key task of genomic surveillance of infectious viral diseases lies in the early detection of dangerous variants. Unexpected help to this end is provided by the analysis of deep sequencing data of viral samples, which are typically discarded after creating consensus sequences. Such analysis allows one to detect intra-host low-frequency mutations, which are a footprint of mutational processes underlying the origination of new variants. Their timely identification may improve public-health decision-making with respect to traditional approaches exploiting consensus sequences. We present the analysis of 220,788 high-quality deep sequencing SARS-CoV-2 samples, showing that many spike and nucleocapsid mutations of interest associated to the most circulating variants, including Beta, Delta, and Omicron, might have been intercepted several months in advance. Furthermore, we show that a refined genomic surveillance system leveraging deep sequencing data might allow one to pinpoint emerging mutation patterns, providing an automated data-driven support to virologists and epidemiologists.
    Language English
    Publishing date 2022-05-30
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2022.104487
    Database MEDical Literature Analysis and Retrieval System OnLINE

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