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Congenital diaphragmatic hernia (CDH) can occur in isolation or in conjunction with other birth defects (CDH+). A molecular etiology can only be identified in a subset of CDH cases. This is due, in part, to an incomplete understanding of the genes that contribute to diaphragm development. Here, we used clinical and molecular data from 36 individuals with CDH+ who are cataloged in the DECIPHER database to identify genes that may play a role in diaphragm development and to discover new phenotypic expansions. Among this group, we identified individuals who carried putatively deleterious sequence or copy number variants affecting CREBBP, SMARCA4, UBA2, and USP9X. The role of these genes in diaphragm development was supported by their expression in the developing mouse diaphragm, their similarity to known CDH genes using data from a previously published and validated machine learning algorithm, and/or the presence of CDH in other individuals with their associated genetic disorders. Our results demonstrate how data from DECIPHER, and other public databases, can be used to identify new phenotypic expansions and suggest that CREBBP, SMARCA4, UBA2, and USP9X play a role in diaphragm development.

BackgroundPrimary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions.ObjectiveWe sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs.MethodsPatients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping.ResultsA likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays.ConclusionThis high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.

Studies of oxygen-isotope-exchanges in two classes of polyoxoions have uncovered some similarities in reaction steps that are also consistent with mineral-dissolution studies. The molecules were polyoxocations of Group 13 and polyoxoanions of Group 5, and the work was motivated by a desire to understand the dissolution of oxide minerals at the molecular scale. Experimentally, oxygen-isotope-exchange rates are found to be intensely sensitive to single-atom substitutions in the structures, even at sites that are otherwise inert. Exchange rates for different structural oxygen sites span several orders of magnitude, yet most oxygens within a molecule exhibit similar pH dependencies to isotopic exchange and these seem to reflect an average proton affinity of the ion. Single-atom substitutions have a dramatic affect on both the pH dependences of oxygen-isotope-exchanges and the overall reactivity of oxygen sites. Molecular dynamic and electronic-structure calculations identify similar steps in the pathways for exchange - (i) solvation forces cause a near-surface metal to detach from an underlying overbonded oxygen. (ii) This newly undercoordinated metal adds an isotopically normal oxygen as either a water, a hydronium ion or an hydroxide ion. (iii) Protons transfer from these adducts to more basic oxygens in the metastable structure. (iv) The metastability is longlived but access to the metastable state depends on the composition and symmetry of the starting structure, which is why single-atom substitutions are so important. (v) Within the metastable structure, oxygens shuffle positions and the metastable state collapses back into a more stable form. Pathways to form these metastable structures depend on the symmetry and composition of the starting geometry, which probably can't be adequately constrained for meaningful simulation at mineral surfaces.

Studies of oxygen-isotope-exchanges in two classes of polyoxoions have uncovered some similarities in reaction steps that are also consistent with mineral-dissolution studies. The molecules were polyoxocations of Group 13 and polyoxoanions of Group 5, and the work was motivated by a desire to understand the dissolution of oxide minerals at the molecular scale. Experimentally, oxygen-isotope-exchange rates are found to be intensely sensitive to single-atom substitutions in the structures, even at sites that are otherwise inert. Exchange rates for different structural oxygen sites span several orders of magnitude, yet most oxygens within a molecule exhibit similar pH dependencies to isotopic exchange and these seem to reflect an average proton affinity of the ion. Single-atom substitutions have a dramatic affect on both the pH dependences of oxygen-isotope-exchanges and the overall reactivity of oxygen sites. Molecular dynamic and electronic-structure calculations identify similar steps in the pathways for exchange - (i) solvation forces cause a near-surface metal to detach from an underlying overbonded oxygen. (ii) This newly undercoordinated metal adds an isotopically normal oxygen as either a water, a hydronium ion or an hydroxide ion. (iii) Protons transfer from these adducts to more basic oxygens in the metastable structure. (iv) The metastability is longlived but access to the metastable state depends on the composition and symmetry of the starting structure, which is why single-atom substitutions are so important. (v) Within the metastable structure, oxygens shuffle positions and the metastable state collapses back into a more stable form. Pathways to form these metastable structures depend on the symmetry and composition of the starting geometry, which probably can't be adequately constrained for meaningful simulation at mineral surfaces.

The intercalation of lithium from solution into the six-membered μ2-oxo rings on the basal planes of gibbsite is well-constrained chemically. The product is a lithiated layered-double hydroxide solid that forms via in situ phase change. The reaction has well established kinetics and is associated with a distinct swelling of the gibbsite as counter ions enter the interlayer to balance the charge of lithiation. Lithium reacts to fill a fixed and well identifiable crystallographic site and has no solvation waters. Our lithium-isotope data shows that 6Li is favored during this intercalation and that the solid-solution fractionation depends on temperature, electrolyte concentration and counter ion identity (whether Cl-, NO3- or ClO4-). We find that the amount of isotopic fractionation between solid and solution (δLisolid-solution) varies with the amount of lithium taken up into the gibbsite structure, which itself depends upon the extent of conversion and also varies with electrolyte concentration and in the counter ion in the order: ClO4-3--. Higher electrolyte concentrations cause more rapid expansion of the gibbsite interlayer and some counter ions, such as Cl-, are more easily taken up than others, probably because they ease diffusion. The relationship between lithium loading and δLisolid-solution indicates two stages: (1) uptake into the crystallographic sites that favors light lithium, in parallel with adsorption of solvated cations, and (2) continued uptake of solvated cations after all available octahedral vacancies are filled; this second stage has no isotopic preference. The two-step reaction progress is supported by solid-state NMR spectra that clearly resolve a second reservoir of lithium in addition to the expected layered double-hydroxide phase.

The intercalation of lithium from solution into the six-membered μ2-oxo rings on the basal planes of gibbsite is well-constrained chemically. The product is a lithiated layered-double hydroxide solid that forms via in situ phase change. The reaction has well established kinetics and is associated with a distinct swelling of the gibbsite as counter ions enter the interlayer to balance the charge of lithiation. Lithium reacts to fill a fixed and well identifiable crystallographic site and has no solvation waters. Our lithium-isotope data shows that 6Li is favored during this intercalation and that the solid-solution fractionation depends on temperature, electrolyte concentration and counter ion identity (whether Cl-, NO3- or ClO4-). We find that the amount of isotopic fractionation between solid and solution (δLisolid-solution) varies with the amount of lithium taken up into the gibbsite structure, which itself depends upon the extent of conversion and also varies with electrolyte concentration and in the counter ion in the order: ClO4-3--. Higher electrolyte concentrations cause more rapid expansion of the gibbsite interlayer and some counter ions, such as Cl-, are more easily taken up than others, probably because they ease diffusion. The relationship between lithium loading and δLisolid-solution indicates two stages: (1) uptake into the crystallographic sites that favors light lithium, in parallel with adsorption of solvated cations, and (2) continued uptake of solvated cations after all available octahedral vacancies are filled; this second stage has no isotopic preference. The two-step reaction progress is supported by solid-state NMR spectra that clearly resolve a second reservoir of lithium in addition to the expected layered double-hydroxide phase.

Electronic-structure calculations show that the ε-isomer of the polyoxoaluminate ion in the Keggin structure [AlO4-(Al(OH)2(H2O))12](7+) is the thermodynamically favoured one. Direct interconversion between the ε- and δ-isomers via cap rotation has a prohibitively high energy barrier in vacuo, suggesting that isomerisation in solution either proceeds via a dissolution-precipitation pathway, or that solvation and/or coordination to counterions reduces the barrier significantly. The implications for the formation of the [Al2O8Al28(OH)56(H2O)26](18+) ion are discussed.

Electronic-structure calculations show that the ε-isomer of the polyoxoaluminate ion in the Keggin structure [AlO4-(Al(OH)2(H2O))12](7+) is the thermodynamically favoured one. Direct interconversion between the ε- and δ-isomers via cap rotation has a prohibitively high energy barrier in vacuo, suggesting that isomerisation in solution either proceeds via a dissolution-precipitation pathway, or that solvation and/or coordination to counterions reduces the barrier significantly. The implications for the formation of the [Al2O8Al28(OH)56(H2O)26](18+) ion are discussed.

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