Browsing by Author "Jamsheer, A."

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    Genome sequencing in families with congenital limb malformations
    (Springer-Verlag., 2021) Elsner, J.; Mensah, M.A.; Holtgrewe, M.; Hertzberg, J.; Bigoni, S.; Busche, A.; Coutelier, M.; de Silva, D.C.; Elçioglu, N.; Filges, I.; Gerkes, E.; Girisha, K.M.; Graul-Neumann, L.; Jamsheer, A.; Krawitz, P.; Kurth, I.; Markus, S.; Megarbane, A.; Reis, A.; Reuter, M.S.; Svoboda, D.; Teller, C.; Tuysuz, B.; Türkmen, S.; Wilson, M.; Woitschach, R.; Vater, I.; Caliebe, A.; Hülsemann, W.; Horn, D.; Mundlos, S.; Spielmann, M.
    ABSTRACT: The extensive clinical and genetic heterogeneity of congenital limb malformation calls for comprehensive genome-wide analysis of genetic variation. Genome sequencing (GS) has the potential to identify all genetic variants. Here we aim to determine the diagnostic potential of GS as a comprehensive one-test-for-all strategy in a cohort of undiagnosed patients with congenital limb malformations. We collected 69 cases (64 trios, 1 duo, 5 singletons) with congenital limb malformations with no molecular diagnosis after standard clinical genetic testing and performed genome sequencing. We also developed a framework to identify potential noncoding pathogenic variants. We identified likely pathogenic/disease-associated variants in 12 cases (17.4%) including four in known disease genes, and one repeat expansion in HOXD13. In three unrelated cases with ectrodactyly, we identified likely pathogenic variants in UBA2, establishing it as a novel disease gene. In addition, we found two complex structural variants (3%). We also identified likely causative variants in three novel high confidence candidate genes. We were not able to identify any noncoding variants. GS is a powerful strategy to identify all types of genomic variants associated with congenital limb malformation, including repeat expansions and complex structural variants missed by standard diagnostic approaches. In this cohort, no causative noncoding SNVs could be identified.
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    Noncoding copy-number variations are associated with congenital limb malformation
    (Nature Publishing Group, 2018) Flöttmann, R.; Kragesteen, B.K.; Geuer, S.; Socha, M.; Allou, L.; Sowińska-Seidler, A.; Bosquillon de Jarcy, L.; Wagner, J.; Jamsheer, A.; Oehl-Jaschkowitz, B.; Wittler, L.; de Silva, D.; Kurth, I.; Maya, I.; Santos-Simarro, F.; Hülsemann, W.; Klopocki, E.; Mountford, R.; Fryer, A.; Borck, G.; Horn, D.; Lapunzina, P.; Wilson, M.; Mascrez, B.; Duboule, D.; Mundlos, S.; Spielmann, M.
    PurposeCopy-number variants (CNVs) are generally interpreted by linking the effects of gene dosage with phenotypes. The clinical interpretation of noncoding CNVs remains challenging. We investigated the percentage of disease-associated CNVs in patients with congenital limb malformations that affect noncoding cis-regulatory sequences versus genes sensitive to gene dosage effects.MethodsWe applied high-resolution copy-number analysis to 340 unrelated individuals with isolated limb malformation. To investigate novel candidate CNVs, we re-engineered human CNVs in mice using clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing.ResultsOf the individuals studied, 10% harbored CNVs segregating with the phenotype in the affected families. We identified 31 CNVs previously associated with congenital limb malformations and four novel candidate CNVs. Most of the disease-associated CNVs (57%) affected the noncoding cis-regulatory genome, while only 43% included a known disease gene and were likely to result from gene dosage effects. In transgenic mice harboring four novel candidate CNVs, we observed altered gene expression in all cases, indicating that the CNVs had a regulatory effect either by changing the enhancer dosage or altering the topological associating domain architecture of the genome.Conclusion:Our findings suggest that CNVs affecting noncoding regulatory elements are a major cause of congenital limb malformations.