Browsing by Author "Ossowski, Stephan"

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  • A de novo nonsense mutation in MAGEL2 in a patient initially diagnosed as Opitz-C: similarities between Schaaf-Yang and Opitz-C syndromes
    Urreizti, Roser; Cueto González, Anna María; Franco Valls, Héctor; Mort Farre, Sílvia; Roca Ayats, Neus; Ponomarenko, Julia; Cozzuto, Luca; Company, Carlos; Bosio, Mattia; Ossowski, Stephan; Montfort, Magda; Hecht, Jochen; Tizzano, Eduardo F.; Cormand, Bru; Vilageliu, Lluïsa; Opitz, John M.; Neri, Giovanni; Grinberg, Daniel; Balcells, Susana (Nature Publishing Group, 2017)
    Opitz trigonocephaly C syndrome (OTCS) is a rare genetic disorder characterized by craniofacial anomalies, variable intellectual and psychomotor disability, and variable cardiac defects with a high mortality rate. Different ...
  • A family carrying a homozygous LACC1 truncated mutation expands the clinical phenotype of this disease beyond systemic-onset juvenile idiopathic arthritis
    Aróstegui, Juan Ignacio; Rabionet, Raquel; Remesal, Agustín; Mensa Vilaró, Anna; Murias, Sara; Alcobendas, Rosa; González-Roca, Eva; Dreschsel, Oliver; Ruíz Ortiz, Estíbaliz; Puig, Anna; Comas, David, 1969-; Ossowski, Stephan; Yagüe, Jordi L.; Estivill, Xavier, 1955-; Merino, Rosa (BioMed Central, 2015)
    We identified a consanguineous Moroccan family with three affected siblings diagnosed with rheumatoid factor-negative polyarticular juvenile idiopathic arthritis. They all suffered from an early-onset (2-4 years-old) chronic ...
  • A global metagenomic map of urban microbiomes and antimicrobial resistance
    Danko, David; Hecht, Jochen; Mutai, Beth; Ossowski, Stephan; International MetaSUB Consortium (Elsevier, 2021)
    We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an ...
  • A Single Amino Acid Deletion (ΔF1502) in the S6 Segment of CaV2.1 Domain III Associated with Congenital Ataxia Increases Channel Activity and Promotes Ca2+ Influx
    Bahamonde Santos, María Isabel, 1972-; Serra Pascual, Selma A., 1981-; Drechsel, Oliver; Rahman, Rubayte; Marcé-Grau, Anna; Prieto, Marta; Ossowski, Stephan; Macaya, Alfons; Fernández-Fernández, José Manuel, 1967- (Public Library of Science (PLoS), 2015)
    Mutations in the CACNA1A gene, encoding the pore-forming CaV2.1 (P/Q-type) channel α1A subunit, result in heterogeneous human neurological disorders, including familial and sporadic hemiplegic migraine along with episodic ...
  • Allele balance bias identifies systematic genotyping errors and false disease associations
    Muyas, Francesc; Bosio, Mattia; Puig, Anna; Sušak, Hana, 1985-; Domènech Salgado, Laura, 1989-; Escaramís, Geòrgia; Zapata Ortiz, Luis, 1985-; Demidov, German, 1990-; Estivill, Xavier, 1955-; Rabionet, Raquel; Ossowski, Stephan (Wiley, 2019)
    In recent years, next-generation sequencing (NGS) has become a cornerstone of clinical genetics and diagnostics. Many clinical applications require high precision, especially if rare events such as somatic mutations in ...
  • Analysis of a long-term outbreak of XDR Pseudomonas aeruginosa: a molecular epidemiological study
    Willmann, Matthias; Bezdan, Daniela; Zapata Ortiz, Luis, 1985-; Sušak, Hana, 1985-; Vogel, Wichard; Schröppel, Klaus; Liese, Jan; Weidenmaier, Christopher; Autenrieth, Ingo B.; Ossowski, Stephan; Peter, Silke (Oxford University Press, 2015)
    OBJECTIVES: Here we report on a long-term outbreak from 2009 to 2012 with an XDR Pseudomonas aeruginosa on two wards at a university hospital in southern Germany. METHODS: Whole-genome sequencing was performed on the ...
  • Biallelic loss-of-function LACC1/FAMIN mutations presenting as rheumatoid factor-negative polyarticular juvenile idiopathic arthritis
    Rabionet, Raquel; Remesal, Agustín; Mensa Vilaró, Anna; Murías, Sara; Alcobendas, Rosa; González-Roca, Eva; Ruíz Ortiz, Estíbaliz; Antón, Jordi; Iglesias, Estibaliz; Modesto, Consuelo; Comas, David, 1969-; Puig, Anna; Drechsel, Oliver; Ossowski, Stephan; Yagüe, Jordi L.; Merino, Rosa; Estivill, Xavier, 1955-; Aróstegui, Juan Ignacio (Nature Research, 2019)
    Juvenile idiopathic arthritis (JIA) is a complex rheumatic disease with both autoimmune and autoinflammatory components. Recently, familial cases of systemic-onset JIA have been attributed to mutations in LACC1/FAMIN. We ...
  • Chromatin-wide profiling of DYRK1A reveals a role as a gene-specific RNA polymerase II CTD kinase
    Vona, Chiara Di; Bezdan, Daniela; Islam, Abul, 1978-; Salichs Fradera, Eulàlia; López Bigas, Núria; Ossowski, Stephan; Luna, Susana de la (Elsevier, 2015)
    DYRK1A is a dosage-sensitive protein kinase that fulfills key roles during development and in tissue homeostasis, and its dysregulation results in human pathologies. DYRK1A is present in both the nucleus and cytoplasm of ...
  • Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms
    Zapata Ortiz, Luis, 1985-; Ding, Jia; Willing, Eva-Maria; Hartwig, Benjamin; Bezdan, Daniela; Jiao, Wen-Biao; Patel, Vipul; Velikkakam, James Geo; Koornneef, Maarten; Ossowski, Stephan; Schneeberger, Korbinian (National Academy of Sciences, 2016)
    Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually ...
  • Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
    Cortés-Ciriano, Isidro; Lee, Jake June-Koo; Xi, Ruibin; Jain, Dhawal; Jung, Youngsook L.; Yang, Lixing; Gordenin, Dmitry; Klimczak, Leszek J.; Zhang, Cheng-Zhong; Pellman, David S.; PCAWG Structural Variation Working Group; Park, Peter J.; PCAWG Consortium; Ossowski, Stephan; Pearson, John V. (Nature Research, 2020)
    Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may ...
  • Computational analysis of epigenomic variability and its effect on regulatory activity
    Jhanwar, Shalu, 1986- (Universitat Pompeu Fabra, 2017-01-11)
    Epigenetics provides a plausible link between the environment and changes in gene expression that might contribute to disease phenotypes. The main goal of the thesis is to study epigenomic variability and their effect on ...
  • Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing
    Trujillano Lidón, Daniel, 1987-; Bullich, Gemma; Ossowski, Stephan; Ballarín, José; Torra, Roser; Estivill, Xavier, 1955-; Ars, Elisabet (Wiley, 2014)
    Molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) relies on mutation screening of PKD1 and PKD2, which is complicated by extensive allelic heterogeneity and the presence of six highly homologous ...
  • Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
    Akdemir, Kadir C.; Le, Victoria T.; Chandran, Sahaana; Li, Yilong; Verhaak, Roel G.; Beroukhim, Rameen; Campbell, Peter J.; Chin, Linda; PCAWG Structural Variation Working Group; Dixon, Jesse R.; Futreal, P. Andrew; PCAWG Consortium; Ossowski, Stephan (Nature Research, 2020)
    Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, and boundaries separating ...
  • eDiVA-Classification and prioritization of pathogenic variants for clinical diagnostics
    Bosio, Mattia; Drechsel, Oliver; Rahman, Rubayte; Muyas, Francesc; Rabionet, Raquel; Bezdan, Daniela; Domènech Salgado, Laura, 1989-; Hor, Hyun; Schott, Jean-Jacques; Munell, Francina; Colobran, Roger; Macaya, Alfons; Estivill, Xavier, 1955-; Ossowski, Stephan (Wiley, 2019)
    Mendelian diseases have shown to be an and efficient model for connecting genotypes to phenotypes and for elucidating the function of genes. Whole-exome sequencing (WES) accelerated the study of rare Mendelian diseases in ...
  • Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation
    Sušak, Hana, 1985-; Serra Saurina, Laura; Demidov, German, 1990-; Rabionet, Raquel; Domènech Salgado, Laura, 1989-; Bosio, Mattia; Muyas Remolar, Francesc, 1992-; Estivill, Xavier, 1955-; Escaramís, Geòrgia; Ossowski, Stephan (Public Library of Science (PLoS), 2021)
    Rare variants are thought to play an important role in the etiology of complex diseases and may explain a significant fraction of the missing heritability in genetic disease studies. Next-generation sequencing facilitates ...
  • Environmental enrichment induces epigenomic and genome organization changes relevant for cognition
    Espeso Gil, Sergio, 1985-; Holik, Aliaksei Z.; Bonnin, Sarah; Jhanwar, Shalu, 1986-; Chandrasekaran, Sandhya; Pique Regi, Roger; Albaigès-Ràfols, Júlia; Maher, Michael; Permanyer, Jon; Irimia, Manuel; Friedländer, Marc R.; Pons Espinal, Meritxell, 1986-; Akbarian, Schahram; Dierssen, Mara; Maass, Philipp G.; Hor, Charlotte N.; Ossowski, Stephan (Frontiers, 2021)
    In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the ...
  • Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa
    Peter, Silke; Oberhettinger, Philipp; Schuele, Leonard; Dinkelacker, Ariane; Vogel, Wichard; Dörfel, Daniela; Bezdan, Daniela; Ossowski, Stephan; Marschal, Matthias; Liese, Jan; Willmann, Matthias (BioMed Central, 2017)
    BACKGROUND: Pseudomonas putida is a Gram-negative, non-fermenting bacterium frequently encountered in various environmental niches. P. putida rarely causes disease in humans, though serious infections and outbreaks have ...
  • Genomic footprints of activated telomere maintenance mechanisms in cancer
    Sieverling, Lina; Hong, Chen; Koser, Sandra D.; Ginsbach, Philip; Kleinheinz, Kortine; Hutter, Barbara; Braun, Delia M.; Cortés-Ciriano, Isidro; Xi, Ruibin; Kabbe, Rolf; Park, Peter J.; Eils, Roland; Schlesner, Matthias; PCAWG Structural Variation Working Group; Brors, Benedikt; Rippe, Karsten; Jones, David T. W.; Feuerbach, Lars; PCAWG Consortium; Ossowski, Stephan; Estivill, Xavier, 1955- (Nature Research, 2020)
    Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ...
  • High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
    Zhang, Yikun; Chen, Fengju; Fonseca, Nuno; He, Yao; Fujita, Masashi; Nakagawa, Hidewaki; Zhang, Zemin; Brazma, Alvis; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group; Creighton, Chad J.; PCAWG Consortium; Ossowski, Stephan (Nature Research, 2020)
    The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing ...
  • Highly accurate variant detection for identification of tumor mutations and mosaic variants
    Muyas Remolar, Francesc, 1992- (Universitat Pompeu Fabra, 2019-12-20)
    The rapid development of high-throughput sequencing technologies pushed forward the fields of medical genomics and precision medicine, creating many new applications for diagnostics and clinical studies that require high ...