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  1. AU="Abdallah, Hamza Hadj"
  2. AU="Wang, Yanlan"
  3. AU="Regueiro, Benito"
  4. AU="Bar-Nur, Ori"
  5. AU="Hollander, Jonathan A"
  6. AU="Polidoro, Silvia"
  7. AU="Dausset, J"
  8. AU=Eijkholt Marleen
  9. AU=Sousa Braian L A AU=Sousa Braian L A
  10. AU="Fresel, Marielle"
  11. AU="Ilana Babaev"
  12. AU="Tang, Hang"
  13. AU="McBride, Erin"

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  1. Artikel ; Online: CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients.

    Requena, Francisco / Abdallah, Hamza Hadj / García, Alejandro / Nitschké, Patrick / Romana, Sergi / Malan, Valérie / Rausell, Antonio

    Nucleic acids research

    2021  Band 49, Heft W1, Seite(n) W93–W103

    Abstract: Copy Number Variants (CNVs) are an important cause of rare diseases. Array-based Comparative Genomic Hybridization tests yield a ∼12% diagnostic rate, with ∼8% of patients presenting CNVs of unknown significance. CNVs interpretation is particularly ... ...

    Abstract Copy Number Variants (CNVs) are an important cause of rare diseases. Array-based Comparative Genomic Hybridization tests yield a ∼12% diagnostic rate, with ∼8% of patients presenting CNVs of unknown significance. CNVs interpretation is particularly challenging on genomic regions outside of those overlapping with previously reported structural variants or disease-associated genes. Recent studies showed that a more comprehensive evaluation of CNV features, leveraging both coding and non-coding impacts, can significantly improve diagnostic rates. However, currently available CNV interpretation tools are mostly gene-centric or provide only non-interactive annotations difficult to assess in the clinical practice. Here, we present CNVxplorer, a web server suited for the functional assessment of CNVs in a clinical diagnostic setting. CNVxplorer mines a comprehensive set of clinical, genomic, and epigenomic features associated with CNVs. It provides sequence constraint metrics, impact on regulatory elements and topologically associating domains, as well as expression patterns. Analyses offered cover (a) agreement with patient phenotypes; (b) visualizations of associations among genes, regulatory elements and transcription factors; (c) enrichment on functional and pathway annotations and (d) co-occurrence of terms across PubMed publications related to the query CNVs. A flexible evaluation workflow allows dynamic re-interrogation in clinical sessions. CNVxplorer is publicly available at http://cnvxplorer.com.
    Mesh-Begriff(e) Animals ; DNA Copy Number Variations ; Gene Expression ; Genome, Human ; Humans ; Internet ; Mice, Knockout ; Phenotype ; Protein Interaction Mapping ; Rare Diseases/diagnosis ; Rare Diseases/genetics ; Regulatory Sequences, Nucleic Acid ; Software ; Mice
    Sprache Englisch
    Erscheinungsdatum 2021-05-21
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab347
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Additional evidence for the role of chromosomal imbalances and SOX8, ZNRF3 and HHAT gene variants in early human testis development.

    Rjiba, Khouloud / Mougou-Zerelli, Soumaya / Hamida, Imen Hadj / Saad, Ghada / Khadija, Bochra / Jelloul, Afef / Slimani, Wafa / Hasni, Yosra / Dimassi, Sarra / Khelifa, Hela Ben / Sallem, Amira / Kammoun, Molka / Abdallah, Hamza Hadj / Gribaa, Moez / Bignon-Topalovic, Joelle / Chelly, Sami / Khairi, Hédi / Bibi, Mohamed / Kacem, Maha /
    Saad, Ali / Bashamboo, Anu / McElreavey, Kenneth

    Reproductive biology and endocrinology : RB&E

    2023  Band 21, Heft 1, Seite(n) 2

    Abstract: Background: Forty-six ,XY Differences/Disorders of Sex Development (DSD) are characterized by a broad phenotypic spectrum ranging from typical female to male with undervirilized external genitalia, or more rarely testicular regression with a typical ... ...

    Abstract Background: Forty-six ,XY Differences/Disorders of Sex Development (DSD) are characterized by a broad phenotypic spectrum ranging from typical female to male with undervirilized external genitalia, or more rarely testicular regression with a typical male phenotype. Despite progress in the genetic diagnosis of DSD, most 46,XY DSD cases remain idiopathic.
    Methods: To determine the genetic causes of 46,XY DSD, we studied 165 patients of Tunisian ancestry, who presented a wide range of DSD phenotypes. Karyotyping, candidate gene sequencing, and whole-exome sequencing (WES) were performed.
    Results: Cytogenetic abnormalities, including a high frequency of sex chromosomal anomalies (85.4%), explained the phenotype in 30.9% (51/165) of the cohort. Sanger sequencing of candidate genes identified a novel pathogenic variant in the SRY gene in a patient with 46,XY gonadal dysgenesis. An exome screen of a sub-group of 44 patients with 46,XY DSD revealed pathogenic or likely pathogenic variants in 38.6% (17/44) of patients.
    Conclusion: Rare or novel pathogenic variants were identified in the AR, SRD5A2, ZNRF3, SOX8, SOX9 and HHAT genes. Overall our data indicate a genetic diagnosis rate of 41.2% (68/165) in the group of 46,XY DSD.
    Mesh-Begriff(e) Female ; Humans ; Male ; 3-Oxo-5-alpha-Steroid 4-Dehydrogenase/genetics ; Acyltransferases/genetics ; Gonadal Dysgenesis, 46,XY/genetics ; Membrane Proteins/genetics ; Mutation ; Phenotype ; Sex Differentiation ; Sexual Development/genetics ; SOXE Transcription Factors/genetics ; Testis/growth & development ; Ubiquitin-Protein Ligases/genetics
    Chemische Substanzen 3-Oxo-5-alpha-Steroid 4-Dehydrogenase (EC 1.3.99.5) ; Acyltransferases (EC 2.3.-) ; HHAT protein, human (EC 2.3.1.-) ; Membrane Proteins ; SOX8 protein, human ; SOXE Transcription Factors ; SRD5A2 protein, human (EC 1.3.99.5) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; ZNRF3 protein, human (EC 2.3.2.27)
    Sprache Englisch
    Erscheinungsdatum 2023-01-11
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2119215-7
    ISSN 1477-7827 ; 1477-7827
    ISSN (online) 1477-7827
    ISSN 1477-7827
    DOI 10.1186/s12958-022-01045-7
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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