[Simple is not always easy: genetics in general psychiatry]. / Drie patiënten met langdurig onopgehelderde psychiatrische klachten waarbij genetische diagnostiek uitkomst bracht.

Many of the patients who attend the outpatient mental health clinics already have a long history of psychiatric problems. Their symptoms seem easy to classify, but the misdiagnosis of the patients' underlying problems can lead to a long series of costly referrals as inpatients or to an ineffective treatment outcome. In this article we focus on three patients whose history and background circumstances had been analysed in detail and who had also been subjected to a genetic analysis. The analyses pointed to an etiology-based diagnosis which had important implications for their future treatment and its outcome.

Methanol formation from CO2 catalyzed by Fe3S4{111}: formate versus hydrocarboxyl pathways.

Carbon capture and utilisation is one of the most promising techniques to minimize the impact of the increasing amount of carbon dioxide in the atmosphere. Recently, the mineral greigite was shown to be capable of catalysing CO2 conversion, leading to useful small organic molecules. Here, we have carried out a systematic study of the adsorption and selective reduction of CO2 on the Fe3S4{111} surface. We have considered both formate and hydrocarboxyl key intermediates, leading to different reaction pathways via Eley-Rideal and Langmuir-Hinshelwood mechanisms, and we have built a kinetic model considering the wide range of intermediates in the reaction network. Our results show that the mechanism to produce formic acid takes place via formate intermediate mostly on FeA sites, while methanol is formed via hydrocarboxyl intermediates on FeB sites. From the kinetic model, we have derived a reaction constant comparison and determined the limiting step rates. The overall process takes place under very mild conditions, requiring only a small energy input that might come from a chemiosmotic potential.

Surface and shape modification of mackinawite (FeS) nanocrystals by cysteine adsorption: a first-principles DFT-D2 study.

The control of nanoparticle shape offers promise for improving catalytic activity and selectivity through optimization of the structure of the catalytically active site. Here, we have employed density functional theory calculations with a correction for the long-range interactions (DFT-D2) to investigate the effect of adsorption of the amino acid cysteine on the {001}, {011}, {100}, and {111} surfaces of mackinawite, which are commonly found in FeS nanoparticles. We have calculated the surface energies and adsorption energies for all the surfaces considered, and compared the surface energies of the pure and adsorbed systems. Based on the calculated surface energies, we have simulated the thermodynamic crystal morphology of the pure and cysteine-modified FeS nanoparticles using Wulff's construction. The strength of cysteine adsorption is found to be related to the stability of different surfaces, where it adsorbs most strongly onto the least stable FeS{111} surface via bidentate Fe-S and Fe-N chemical bonds and most weakly onto the most stable FeS{001} surface via hydrogen-bonded interactions; the adsorption energy decreases in the order {111} > {100} > {011} > {001}. We demonstrate that the stronger binding of the cysteine to the {011}, {100}, and {111} surfaces rather than to the {001} facet results in shape modulation of the FeS nanoparticles, with the reactive surfaces more expressed in the thermodynamic crystal morphology compared to the unmodified FeS crystals. Information regarding the structural parameters, electronic structures and vibrational frequency assignments of the cysteine-FeS complexes is also presented.

DFT-D2 simulations of water adsorption and dissociation on the low-index surfaces of mackinawite (FeS).

The adsorption and dissociation of water on mackinawite (layered FeS) surfaces were studied using dispersion-corrected density functional theory (DFT-D2) calculations. The catalytically active sites for H2O and its dissociated products on the FeS {001}, {011}, {100}, and {111} surfaces were determined, and the reaction energetics and kinetics of water dissociation were calculated using the climbing image nudged elastic band technique. Water and its dissociation products are shown to adsorb more strongly onto the least stable FeS{111} surface, which presents low-coordinated cations in the surface, and weakest onto the most stable FeS{001} surface. The adsorption energies decrease in the order FeS{111} > FeS{100} > FeS{011} > FeS{001}. Consistent with the superior reactivity of the FeS{111} surface towards water and its dissociation products, our calculated thermochemical energies and activation barriers suggest that the water dissociation reaction will take place preferentially on the FeS nanoparticle surface with the {111} orientation. These findings improve our understanding of how the different FeS surface structures and the relative stabilities dictate their reactivity towards water adsorption and dissociation.

Activation and dissociation of CO2 on the (001), (011), and (111) surfaces of mackinawite (FeS): A dispersion-corrected DFT study.

Iron sulfide minerals, including mackinawite (FeS), are relevant in origin of life theories, due to their potential catalytic activity towards the reduction and conversion of carbon dioxide (CO2) to organic molecules, which may be applicable to the production of liquid fuels and commodity chemicals. However, the fundamental understanding of CO2 adsorption, activation, and dissociation on FeS surfaces remains incomplete. Here, we have used density functional theory calculations, corrected for long-range dispersion interactions (DFT-D2), to explore various adsorption sites and configurations for CO2 on the low-index mackinawite (001), (110), and (111) surfaces. We found that the CO2 molecule physisorbs weakly on the energetically most stable (001) surface but adsorbs relatively strongly on the (011) and (111) FeS surfaces, preferentially at Fe sites. The adsorption of the CO2 on the (011) and (111) surfaces is shown to be characterized by significant charge transfer from surface Fe species to the CO2 molecule, which causes a large structural transformation in the molecule (i.e., forming a negatively charged bent CO2 (-δ) species, with weaker C-O confirmed via vibrational frequency analyses). We have also analyzed the pathways for CO2 reduction to CO and O on the mackinawite (011) and (111) surfaces. CO2 dissociation is calculated to be slightly endothermic relative to the associatively adsorbed states, with relatively large activation energy barriers of 1.25 eV and 0.72 eV on the (011) and (111) surfaces, respectively.

X-linked congenital ptosis and associated intellectual disability, short stature, microcephaly, cleft palate, digital and genital abnormalities define novel Xq25q26 duplication syndrome.

Submicroscopic duplications along the long arm of the X-chromosome with known phenotypic consequences are relatively rare events. The clinical features resulting from such duplications are various, though they often include intellectual disability, microcephaly, short stature, hypotonia, hypogonadism and feeding difficulties. Female carriers are often phenotypically normal or show a similar but milder phenotype, as in most cases the X-chromosome harbouring the duplication is subject to inactivation. Xq28, which includes MECP2 is the major locus for submicroscopic X-chromosome duplications, whereas duplications in Xq25 and Xq26 have been reported in only a few cases. Using genome-wide array platforms we identified overlapping interstitial Xq25q26 duplications ranging from 0.2 to 4.76 Mb in eight unrelated families with in total five affected males and seven affected females. All affected males shared a common phenotype with intrauterine- and postnatal growth retardation and feeding difficulties in childhood. Three had microcephaly and two out of five suffered from epilepsy. In addition, three males had a distinct facial appearance with congenital bilateral ptosis and large protruding ears and two of them showed a cleft palate. The affected females had various clinical symptoms similar to that of the males with congenital bilateral ptosis in three families as most remarkable feature. Comparison of the gene content of the individual duplications with the respective phenotypes suggested three critical regions with candidate genes (AIFM1, RAB33A, GPC3 and IGSF1) for the common phenotypes, including candidate loci for congenital bilateral ptosis, small head circumference, short stature, genital and digital defects.

The surface chemistry of NO(x) on mackinawite (FeS) surfaces: a DFT-D2 study.

We present density functional theory calculations with a correction for the long-range interactions (DFT-D2) of the bulk and surfaces of mackinawite (FeS), and subsequent adsorption and dissociation of NO(x) gases (nitrogen monoxide (NO) and nitrogen dioxide (NO2)). Our results show that these environmentally important molecules interact very weakly with the energetically most stable (001) surface, but adsorb relatively strongly onto the FeS(011), (100) and (111) surfaces, preferentially at Fe sites via charge donation from these surface species. The NOx species exhibit a variety of adsorption geometries, with the most favourable for NO being the monodentate Fe-NO configuration, whereas NO2 is calculated to form a bidentate Fe-NOO-Fe configuration. From our calculated thermochemical energy and activation energy barriers for the direct dissociation of NO and NO2 on the FeS surfaces, we show that NO prefers molecular adsorption, while dissociative adsorption, i.e. NO2 (ads) → [NO(ads) + O(ads)] is preferred over molecular adsorption for NO2 onto the mackinawite surfaces. However, the calculated high activation barriers for the further dissociation of the second N-O bond to produce either [N(ads) and 2O(ads)] or [N(ads) and O2(ads)] suggest that complete dissociation of NO2 is unlikely to occur on the mackinawite surfaces.

Pathogenic or not? Assessing the clinical relevance of copy number variants.

The availability of commercially produced genomic microarrays has resulted in the wide spread implementation of genomic microarrays, often as a first-tier diagnostic test for copy number variant (CNV) screening of patients who are suspected for chromosomal aberrations. Patients with intellectual disability (ID) and/or multiple congenital anomalies (MCA) were traditionally the main focus for this microarray-based CNV screening, but the application of microarrays to other (neurodevelopmental) disorders and tumor diagnostics has also been explored and implemented. The diagnostic workflow for patients with ID is now well established, relying on the identification of rare CNVs and determining their inheritance patterns. However, experience gained through screening large numbers of samples has revealed many subtleties and complexities of CNV interpretation. This has resulted in a better understanding of the contribution of CNVs to genomic disorders not only via de novo occurrence, but also via X-linked and recessive inheritance models as well as through models taking into account mosaicisms, imprinting, and digenic inheritance. In this review, we discuss CNV interpretation within the context of these different genetic disease models and common pitfalls that can occur when searching for supportive evidence that a CNV is clinically relevant.

Adsorption of methylamine on mackinawite (FES) surfaces: a density functional theory study.

We have used density functional theory calculations to investigate the interaction between methylamine (CH3NH2) and the dominant surfaces of mackinawite (FeS), where the surface and adsorption properties of mackinawite have been characterized using the DFT-D2 method of Grimme. Our calculations show that while the CH3NH2 molecule only interacts weakly with the most stable FeS(001), it adsorbs relatively strongly on the FeS(011) and FeS(100) surfaces releasing energies of 1.26 eV and 1.51 eV, respectively. Analysis of the nature of the bonding reveals that the CH3NH2 molecule interacts with the mackinawite surfaces through the lone-pair of electrons located on the N atom. The electron density built up in the bonding region between N and Fe is very much what one would expect of covalent type of bonding. We observe no significant adsorption-induced changes of the FeS surface structures, suggesting that amine capping agents would not distort the FeS nanoparticle surfaces required for active heterogeneous catalytic reactions. The vibrational frequencies and the infrared spectra of adsorbed methylamine have been calculated and assignments for vibrational modes are used to propose a kinetic model for the desorption process, yielding a simulated temperature programmed desorption with a relative desorption temperature of <140 K at the FeS(011) surface and <170 K at FeS(100) surface.

A comparative DFT study of the mechanical and electronic properties of greigite Fe3S4 and magnetite Fe3O4.

Greigite (Fe3S4) and its analogue oxide, magnetite (Fe3O4), are natural minerals with an inverse spinel structure whose atomic-level properties may be difficult to investigate experimentally. Here, [D. Rickard and G. W. Luther, Chem. Rev. 107, 514 (2007)] we have calculated the elastic constants and other macroscopic mechanical properties by applying elastic strains on the unit cells. We also have carried out a systematic study of the electronic properties of Fe3S4 and Fe3O4, where we have used an ab initio method based on spin-polarized density functional theory with the on-site Coulomb repulsion approximation (Ueff is 1.0 and 3.8 eV for Fe3S4 and Fe3O4, respectively). Comparison of the properties of Fe3S4 and Fe3O4 shows that the sulfide is more covalent than the oxide, which explains the low magnetization of saturation of greigite cited in several experimental reports.

A novel microdeletion syndrome at 3q13.31 characterised by developmental delay, postnatal overgrowth, hypoplastic male genitals, and characteristic facial features.

BACKGROUND: Congenital deletions affecting 3q11q23 have rarely been reported and only five cases have been molecularly characterised. Genotype-phenotype correlation has been hampered by the variable sizes and breakpoints of the deletions. In this study, 14 novel patients with deletions in 3q11q23 were investigated and compared with 13 previously reported patients. METHODS: Clinical data were collected from 14 novel patients that had been investigated by high resolution microarray techniques. Molecular investigation and updated clinical information of one cytogenetically previously reported patient were also included. RESULTS: The molecular investigation identified deletions in the region 3q12.3q21.3 with different boundaries and variable sizes. The smallest studied deletion was 580 kb, located in 3q13.31. Genotype-phenotype comparison in 24 patients sharing this shortest region of overlapping deletion revealed several common major characteristics including significant developmental delay, muscular hypotonia, a high arched palate, and recognisable facial features including a short philtrum and protruding lips. Abnormal genitalia were found in the majority of males, several having micropenis. Finally, a postnatal growth pattern above the mean was apparent. The 580 kb deleted region includes five RefSeq genes and two of them are strong candidate genes for the developmental delay: DRD3 and ZBTB20. CONCLUSION: A newly recognised 3q13.31 microdeletion syndrome is delineated which is of diagnostic and prognostic value. Furthermore, two genes are suggested to be responsible for the main phenotype.

Calcite surface structure and reactivity: molecular dynamics simulations and macroscopic surface modelling of the calcite-water interface.

Calcite-water interactions are important not only in carbon sequestration and the global carbon cycle, but also in contaminant behaviour in calcite-bearing host rock and in many industrial applications. Here we quantify the effect of variations in surface structure on calcite surface reactivity. Firstly, we employ classical Molecular Dynamics simulations of calcite surfaces containing an etch pit and a growth terrace, to show that the local environment in water around structurally different surface sites is distinct. In addition to observing the expected formation of more calcium-water interactions and hydrogen-bonds at lower-coordinated sites, we also observed subtle differences in hydrogen bonding around acute versus obtuse edges and corners. We subsequently used this information to refine the protonation constants for the calcite surface sites, according to the Charge Distribution MUltiSite Ion Complexation (CD-MUSIC) approach. The subtle differences in hydrogen bonding translate into markedly different charging behaviour versus pH, in particular for acute versus obtuse corner sites. The results show quantitatively that calcite surface reactivity is directly related to surface topography. The information obtained in this study is not only crucial for the improvement of existing macroscopic surface models of the reactivity of calcite towards contaminants, but also improves our atomic-level understanding of mineral-water interactions.

SNP array analysis in constitutional and cancer genome diagnostics--copy number variants, genotyping and quality control.

Array-based comparative genomic hybridization analysis of genomic DNA was first applied in postnatal diagnosis for patients with intellectual disability (ID) and/or congenital anomalies (CA). Genome-wide single-nucleotide polymorphism (SNP) array analysis was subsequently implemented as the first line diagnostic test for ID/CA patients in our laboratory in 2009, because its diagnostic yield is significantly higher than that of routine cytogenetic analysis. In addition to the detection of copy number variations, the genotype information obtained with SNP array analysis enables the detection of stretches of homozygosity and thereby the possible identification of recessive disease genes, mosaic aneuploidy, or uniparental disomy. Patient-parent (trio) information analysis is used to screen for the presence of any form of uniparental disomy in the patient and can determine the parental origin of a de novo copy number variation. Moreover, the outcome of a genotype analysis is used as a final quality control by ruling out potential sample mismatches due to non-paternity or sample mix-up. SNP array analysis is now also used in our laboratory for patients with disorders for which locus heterogeneity is known (homozygosity pre-screening), in prenatal diagnosis in case of structural ultrasound anomalies, and for patients with leukemia. In this report, we summarize our array findings and experiences in the various diagnostic applications and demonstrate the power of a SNP-based array platform for molecular karyotyping, because it not only significantly improves the diagnostic yield in both constitutional and cancer genome diagnostics, but it also enhances the quality of the diagnostic laboratory workflow.

Familial Kleefstra syndrome due to maternal somatic mosaicism for interstitial 9q34.3 microdeletions.

The Kleefstra syndrome (Online Mendelian Inheritance in Man 607001) is caused by a submicroscopic 9q34.3 deletion or by intragenic euchromatin histone methyl transferase 1 (EHMT1) mutations. So far only de novo occurrence of mutations has been reported, whereas 9q34.3 deletions can be either de novo or caused by complex chromosomal rearrangements or translocations. Here we give the first descriptions of affected parent-to-child transmission of Kleefstra syndrome caused by small interstitial deletions, approximately 200 kb, involving part of the EHMT1 gene. Additional genome-wide array studies in the parents showed the presence of similar deletions in both mothers who only had mild learning difficulties and minor facial characteristics suggesting either variable clinical expression or somatic mosaicism for these deletions. Further studies showed only one of the maternal deletions resulted in significantly quantitative differences in signal intensity on the array between the mother and her child. But by investigating different tissues with additional fluorescent in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA) analyses, we confirmed somatic mosaicism in both mothers. Careful clinical and cytogenetic assessments of parents of an affected proband with an (interstitial) 9q34.3 microdeletion are merited for accurate estimation of recurrence risk.

Identification of clinically significant, submicroscopic chromosome alterations and UPD in fetuses with ultrasound anomalies using genome-wide 250k SNP array analysis.

BACKGROUND: The implementation of microarray analysis in prenatal diagnostics is a topic of discussion, as rare copy number variants with unknown/uncertain clinical consequences are likely to be found. The application of targeted microarrays limits such findings, but the potential disadvantage is that relevant, so far unknown, aberrations might be overlooked. Therefore, we explore the possibilities for the prenatal application of the genome-wide 250k single nucleotide polymorphism array platform. METHODS: Affymetrix 250k NspI single nucleotide polymorphism array analysis (Affymetrix, Inc., Santa Clara, California, USA) was performed on DNA from 38 prenatally karyotyped fetuses with ultrasound anomalies. Analyses were performed after termination of pregnancy, intrauterine fetal death or birth on DNA isolated from fetal or neonatal material. RESULTS: Aberrations were detected in 17 of 38 fetuses, 6 of whom with a previously identified chromosomal abnormality and 11 with previously normal or balanced karyotypes. Of the latter, the detected aberration occurred de novo and was considered of clinical relevance in five cases (16%), inherited from a healthy parent in four cases (12%), and de novo yet with unclear clinical relevance in two cases (6%). The clinically relevant abnormalities either were novel copy number variants (n=3) or concerned a uniparental disomy (n=2). CONCLUSION: In at least 16% of fetuses with ultrasound anomalies and a normal or balanced karyotype, causal (submicroscopic) aberrations were detected, illustrating the importance of the (careful) implementation of microarray analysis in prenatal diagnosis. The fact that the identified, clinically relevant, aberrations would have gone undetected with most targeted approaches underscores the added value of a genome-wide approach.

Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome.

BACKGROUND: Recurrent 15q13.3 microdeletions were recently identified with identical proximal (BP4) and distal (BP5) breakpoints and associated with mild to moderate mental retardation and epilepsy. METHODS: To assess further the clinical implications of this novel 15q13.3 microdeletion syndrome, 18 new probands with a deletion were molecularly and clinically characterised. In addition, we evaluated the characteristics of a family with a more proximal deletion between BP3 and BP4. Finally, four patients with a duplication in the BP3-BP4-BP5 region were included in this study to ascertain the clinical significance of duplications in this region. RESULTS: The 15q13.3 microdeletion in our series was associated with a highly variable intra- and inter-familial phenotype. At least 11 of the 18 deletions identified were inherited. Moreover, 7 of 10 siblings from four different families also had this deletion: one had a mild developmental delay, four had only learning problems during childhood, but functioned well in daily life as adults, whereas the other two had no learning problems at all. In contrast to previous findings, seizures were not a common feature in our series (only 2 of 17 living probands). Three patients with deletions had cardiac defects and deletion of the KLF13 gene, located in the critical region, may contribute to these abnormalities. The limited data from the single family with the more proximal BP3-BP4 deletion suggest this deletion may have little clinical significance. Patients with duplications of the BP3-BP4-BP5 region did not share a recognisable phenotype, but psychiatric disease was noted in 2 of 4 patients. CONCLUSIONS: Overall, our findings broaden the phenotypic spectrum associated with 15q13.3 deletions and suggest that, in some individuals, deletion of 15q13.3 is not sufficient to cause disease. The existence of microdeletion syndromes, associated with an unpredictable and variable phenotypic outcome, will pose the clinician with diagnostic difficulties and challenge the commonly used paradigm in the diagnostic setting that aberrations inherited from a phenotypically normal parent are usually without clinical consequences.

Clinical and molecular characteristics of 1qter microdeletion syndrome: delineating a critical region for corpus callosum agenesis/hypogenesis.

BACKGROUND: Patients with a microscopically visible deletion of the distal part of the long arm of chromosome 1 have a recognisable phenotype, including mental retardation, microcephaly, growth retardation, a distinct facial appearance and various midline defects including corpus callosum abnormalities, cardiac, gastro-oesophageal and urogenital defects, as well as various central nervous system anomalies. Patients with a submicroscopic, subtelomeric 1qter deletion have a similar phenotype, suggesting that the main phenotype of these patients is caused by haploinsufficiency of genes in this region. OBJECTIVE: To describe the clinical presentation of 13 new patients with a submicroscopic deletion of 1q43q44, of which nine were interstitial, and to report on the molecular characterisation of the deletion size. RESULTS AND CONCLUSIONS: The clinical presentation of these patients has clear similarities with previously reported cases with a terminal 1q deletion. Corpus callosum abnormalities were present in 10 of our patients. The AKT3 gene has been reported as an important candidate gene causing this abnormality. However, through detailed molecular analysis of the deletion sizes in our patient cohort, we were able to delineate the critical region for corpus callosum abnormalities to a 360 kb genomic segment which contains four possible candidate genes, but excluding the AKT3 gene.

Variable phenotypes associated with 10q23 microdeletions involving the PTEN and BMPR1A genes.

Infantile juvenile polyposis is a rare disease with severe gastrointestinal symptoms and a grave clinical course. Recently, 10q23 microdeletions involving the PTEN and BMPR1A genes were found in four patients with infantile juvenile polyposis. It was hypothesized that a combined and synergistic effect of the deletion of both genes would explain the condition. Subsequently, however, a patient with a larger 10q23 deletion including the same genes but with a mild clinical phenotype was identified. Here, we present four additional patients with 10q23 microdeletions involving the PTEN and BMPR1A genes. The sizes of the deletions were analyzed using single nucleotide polymorphism array analysis. All patients had macrocephaly, dysmorphic features, retardation and congenital abnormalities. One patient developed colorectal cancer. However, only one case had disease onset before 2 years of age and severe symptoms requiring colectomy. No clear correlation was found between ages at onset or severity of gastrointestinal symptoms and the sizes of the deletions. We conclude that patients with 10q23 microdeletions involving the PTEN and BMPR1A genes have variable clinical phenotypes, which cannot be explained merely by the deletion sizes. The phenotypes are not restricted to severe infantile juvenile polyposis but include childhood-onset cases with macrocephaly, retardation, mild gastrointestinal symptoms and possibly early-onset colorectal cancer.

Effect on the mechanical properties of type I collagen of intra-molecular lysine-arginine derived advanced glycation end-product cross-linking.

Non-enzymatic advanced glycation end product (AGE) cross-linking of collagen molecules has been hypothesised to result in significant changes to the mechanical properties of the connective tissues within the body, potentially resulting in a number of age related diseases. We have investigated the effect of two of these cross-links, glucosepane and DOGDIC, on the tensile and lateral moduli of the collagen molecule through the use of a steered molecular dynamics approach, using previously identified preferential formation sites for intra-molecular cross-links. Our results show that the presence of intra-molecular AGE cross-links increases the tensile and lateral Young's moduli in the low strain domain by between 3.0-8.5% and 2.9-60.3% respectively, with little effect exhibited at higher strains.