Genome sequencing in families with congenital limb malformations

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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00439-021-02295-y

CePdAl - a Kondo lattice with partial frustration

Magnetic frustration, which is well-defined in insulating systems with localized magnetic moments, yields exotic ground states like spin ices, spin glasses, or spin liquids. In metals magnetic frustration is less well defined because of the incipient delocalization of magnetic moments by the interaction with conduction electrons, viz., the Kondo effect. Hence, the Kondo effect and magnetic frustration are antithetic phenomena. Here we present experimental data of electrical resistivity, magnetization, specific heat and neutron diffraction on CePdAl, which is one of the rare examples of a geometrically frustrated Kondo lattice, demonstrating that the combination of Kondo effect and magnetic frustration leads to an unusual ground state

Role of the tuning parameter at magnetic quantum phase transitions

Heavy-fermion systems, with their competition betweenKondo and RKKY interactions, offer a rich variety of materials thatmay be driven to a magnetic quantum phase transition. Quite often,a quantum critical point can be approached by chemical substitution,notably of isoelectric ligands of Ce, as in CeCu6−xAux andCePd1−xNixAl. While in the former we compare pressure and concentrationtuning of the magnetic structure, the latter has the additionalfeature of geometric frustration due to the distorted kagom´e sublatticeof Ce atoms in the basal plane. We further present the systemCeAu2Ge2 where minor structural differences between crystals grownfrom Sn or Au-Ge flux lead to pronounced differences in the magneticstructure, with several field-induced phases in samples grown fromAu-Ge flux. Finally, non-isoelectronic substitution of Ti by V is studiedin CeTi1−xVxGe3 where CeTiGe3 is a ferromagnet, thus allowingthe study of ferromagnetic quantum criticality, a rare case for heavyfermionsystems

Next-generation sequencing of 32 genes associated with hereditary aortopathies and related disorders of connective tissue in a cohort of 199 patients

Purpose: Heritable factors play an important etiologic role in connective tissue disorders (CTD) with vascular involvement, and a genetic diagnosis is getting increasingly important for gene-tailored, personalized patient management. Methods: We analyzed 32 disease-associated genes by using targeted next-generation sequencing and exome sequencing in a clinically relevant cohort of 199 individuals. We classified and refined sequence variants according to their likelihood for pathogenicity. Results: We identified 1 pathogenic variant (PV; in FBN1 or SMAD3) in 15 patients (7.5%) and >= 1 likely pathogenic variant (LPV; in COL3A1, FBN1, FBN2, LOX, MYH11, SMAD3, TGFBR1, or TGFBR2) in 19 individuals (9.6%), together resulting in 17.1% diagnostic yield. Thirteen PV/LPV were novel. Of PV/LPV-negative patients 47 (23.6%) showed >= 1 variant of uncertain significance (VUS). Twenty-five patients had concomitant variants. In-depth evaluation of reported/calculated variant classes resulted in reclassification of 19.8% of variants. Conclusion: Variant classification and refinement are essential for shaping mutational spectra of disease genes, thereby improving clinical sensitivity. Obligate stringent multigene analysis is a powerful tool for identifying genetic causes of clinically related CTDs. Nonetheless, the relatively high rate of PV/LPV/VUS-negative patients underscores the existence of yet unknown disease loci and/or oligogenic/polygenic inheritance

A second cohort of CHD3 patients expands the molecular mechanisms known to cause Snijders Blok-Campeau syndrome

There has been one previous report of a cohort of patients with variants in Chromodomain Helicase DNA-binding 3 (CHD3), now recognized as Snijders Blok-Campeau syndrome. However, with only three previously-reported patients with variants outside the ATPase/helicase domain, it was unclear if variants outside of this domain caused a clinically similar phenotype. We have analyzed 24 new patients with CHD3 variants, including nine outside the ATPase/helicase domain. All patients were detected with unbiased molecular genetic methods. There is not a significant difference in the clinical or facial features of patients with variants in or outside this domain. These additional patients further expand the clinical and molecular data associated with CHD3 variants. Importantly we conclude that there is not a significant difference in the phenotypic features of patients with various molecular disruptions, including whole gene deletions and duplications, and missense variants outside the ATPase/helicase domain. This data will aid both clinical geneticists and molecular geneticists in the diagnosis of this emerging syndrome