Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia.

This corrects the article DOI: 10.1038/mp.2016.97.

The iPSYCH2012 case-cohort sample: new directions for unravelling genetic and environmental architectures of severe mental disorders.

The Integrative Psychiatric Research (iPSYCH) consortium has established a large Danish population-based Case-Cohort sample (iPSYCH2012) aimed at unravelling the genetic and environmental architecture of severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born between 1981 and 2005, including 1 472 762 persons. This paper introduces the iPSYCH2012 sample and outlines key future research directions. Cases were identified as persons with schizophrenia (N=3540), autism (N=16 146), attention-deficit/hyperactivity disorder (N=18 726) and affective disorder (N=26 380), of which 1928 had bipolar affective disorder. Controls were randomly sampled individuals (N=30 000). Within the sample of 86 189 individuals, a total of 57 377 individuals had at least one major mental disorder. DNA was extracted from the neonatal dried blood spot samples obtained from the Danish Neonatal Screening Biobank and genotyped using the Illumina PsychChip. Genotyping was successful for 90% of the sample. The assessments of exome sequencing, methylation profiling, metabolome profiling, vitamin-D, inflammatory and neurotrophic factors are in progress. For each individual, the iPSYCH2012 sample also includes longitudinal information on health, prescribed medicine, social and socioeconomic information, and analogous information among relatives. To the best of our knowledge, the iPSYCH2012 sample is the largest and most comprehensive data source for the combined study of genetic and environmental aetiologies of severe mental disorders.

Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia.

The antipsychotic clozapine is uniquely effective in the management of schizophrenia; however, its use is limited by its potential to induce agranulocytosis. The causes of this, and of its precursor neutropenia, are largely unknown, although genetic factors have an important role. We sought risk alleles for clozapine-associated neutropenia in a sample of 66 cases and 5583 clozapine-treated controls, through a genome-wide association study (GWAS), imputed human leukocyte antigen (HLA) alleles, exome array and copy-number variation (CNV) analyses. We then combined associated variants in a meta-analysis with data from the Clozapine-Induced Agranulocytosis Consortium (up to 163 cases and 7970 controls). In the largest combined sample to date, we identified a novel association with rs149104283 (odds ratio (OR)=4.32, P=1.79 × 10-8), intronic to transcripts of SLCO1B3 and SLCO1B7, members of a family of hepatic transporter genes previously implicated in adverse drug reactions including simvastatin-induced myopathy and docetaxel-induced neutropenia. Exome array analysis identified gene-wide associations of uncommon non-synonymous variants within UBAP2 and STARD9. We additionally provide independent replication of a previously identified variant in HLA-DQB1 (OR=15.6, P=0.015, positive predictive value=35.1%). These results implicate biological pathways through which clozapine may act to cause this serious adverse effect.

Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia.

This corrects the article DOI: 10.1038/mp.2016.97.

Detecting large copy number variants using exome genotyping arrays in a large Swedish schizophrenia sample.

Although copy number variants (CNVs) are important in genomic medicine, CNVs have not been systematically assessed for many complex traits. Several large rare CNVs increase risk for schizophrenia (SCZ) and autism and often demonstrate pleiotropic effects; however, their frequencies in the general population and other complex traits are unknown. Genotyping large numbers of samples is essential for progress. Large cohorts from many different diseases are being genotyped using exome-focused arrays designed to detect uncommon or rare protein-altering sequence variation. Although these arrays were not designed for CNV detection, the hybridization intensity data generated in each experiment could, in principle, be used for gene-focused CNV analysis. Our goal was to evaluate the extent to which CNVs can be detected using data from one particular exome array (the Illumina Human Exome Bead Chip). We genotyped 9100 Swedish subjects (3962 cases with SCZ and 5138 controls) using both standard genome-wide association study (GWAS) and exome arrays. In comparison with CNVs detected using GWAS arrays, we observed high sensitivity and specificity for detecting genic CNVs 400 kb including known pathogenic CNVs along with replicating the literature finding that cases with SCZ had greater enrichment for genic CNVs. Our data confirm the association of SCZ with 16p11.2 duplications and 22q11.2 deletions, and suggest a novel association with deletions at 11q12.2. Our results suggest the utility of exome-focused arrays in surveying large genic CNVs in very large samples; and thereby open the door for new opportunities such as conducting well-powered CNV assessment and comparisons between different diseases. The use of a single platform also minimizes potential confounding factors that could impact accurate detection.

Intracellular pH regulation in neurons from chemosensitive and nonchemosensitive regions of Helix aspersa.

We used 2',7'-bis(carboxyethyl)-5(6)-carboxyflourescein (BCECF), a pH-sensitive fluorescent dye, to study intracellular pH (pH(i)) regulation in neurons in CO(2) chemoreceptor and nonchemoreceptor regions in the pulmonate, terrestrial snail, Helix aspersa. We studied pH(i) during hypercapnic acidosis, after ammonia prepulse, and during isohydric hypercapnia. In all treatment conditions, pH(i) fell to similar levels in chemoreceptor and nonchemoreceptor regions. However, pH(i) recovery was consistently slower in chemoreceptor regions compared with nonchemoreceptor regions, and pH(i) recovery was slower in all regions when extracellular pH (pH(e)) was also reduced. We also studied the effect of amiloride and DIDS on pH(i) regulation during isohydric hypercapnia. An amiloride-sensitive mechanism was the dominant pH(i) regulatory process during acidosis. We conclude that pH(e) modulates and slows pH(i) regulation in chemoreceptor regions to a greater extent than in nonchemoreceptor regions by inhibiting an amiloride-sensitive Na(+)/H(+) exchanger. Although the phylogenetic distance between vertebrates and invertebrates is large, similar results have been reported in CO(2)-sensitive regions within the rat brain stem.

EXAFS comparison of the dimanganese core structures of manganese catalase, arginase, and manganese-substituted ribonucleotide reductase and hemerythrin.

The solution structures of the binuclear Mn centers in arginase, Mn catalase, and the Mn-substituted forms of the Fe enzymes ribonucleotide reductase and hemerythrin have been determined using X-ray absorption spectroscopy (XAS). X-ray absorption near edge structure (XANES) spectra for these proteins were compared to those obtained for Mn(II) models. The Mn model spectra show an inverse correlation between the XANES peak maximum and the root-mean-square (RMS) deviation in metal-ligand bond lengths. For these complexes, the XANES maxima appear to be more effective than the 1s --> 3d areas as an indicator of metal-site symmetry. Arginase and Mn-substituted ribonucleotide reductase have symmetric nearest neighbor environments with low RMS deviation in bond length, while Mn catalase and Mn-substituted hemerythrin appear to have a larger RMS bond length deviation. The 1s --> 3d areas for arginase and Mn-substituted ribonucleotide reductase are consistent with six coordinate Mn, while the 1s --> 3d areas for Mn catalase and Mn-substituted hemerythrin are larger, suggesting that one or both of the Mn ions are five-coordinate in these proteins. Extended x-ray absorption fine structure (EXAFS) spectra were used to determine the Mn2 core structure for the four proteins. In order to quantitate the number of histidine residues bound to the Mn2 centers, EXAFS data for the crystallographically characterized model hexakis-imidazole Mn(II) dichloride tetrahydrate were used to calibrate the Mn-imidazole multiple scattering interactions. These calibrated parameters allowed the outer shell EXAFS to be fit to give a lower limit on the number of bound histidine residues. The EXAFS spectra for Mn-substituted ribonucleotide reductase and arginase are nearly identical, with symmetric Mn-nearest neighbor environments and outer shell scattering consistent with a lower limit of one histidine per Mn2 core. In contrast, the EXAFS data for Mn catalase and Mn-substituted hemerythrin show two distinct Mn-nearest neighbor shells, modeled as Mn-O at ca. 2.1 A and Mn-N at ca. 2.3 A, and outer shell carbon scattering consistent with a lower limit of ca. 2-3 His residues per Mn2 core. Only Mn catalase shows clear evidence for Mn...Mn scattering. The observed Mn...Mn distance is 3.53 A, which is significantly longer than the approximately 3.3 A distances that are typically observed for Mn(II)2 cores with two single atom bridges, but which is typical of the distances seen in Mn(II)2 cores having one single atom bridge (e.g., aqua or hydroxo) together with one or two carboxylate bridges. The absence of EXAFS-detectable Mn...Mn interactions for the other three proteins suggests either that there are no single atom bridges in these cases or that the Mn...Mn interactions are more disordered.

Thin foil preparation of metal particles in brittle ceramic matrices.

Thin foil preparation for metal particles in brittle ceramic matrices is particularly difficult, due to differential thinning of the component materials. This paper considers the preparation of thin foils of stony meteorites. Stony meteorites have a composite nature consisting of small metal particles (< 200 microns) embedded in an inherently brittle silicate matrix. Specimens of this type are difficult to prepare as thin foils because the area of interest is limited to specific regions within the metal particles. The problems of thin foil preparation of metal particles in the stony meteorites were overcome by developing a technique involving electrochemical polishing prior to ion beam thinning. The metal particles were first separated from the silicate matrix and then embedded in Epo-Tek H20E silver epoxy. This specific epoxy was selected for its good electron conductivity which allowed the specimen to be thinned by the electrochemical polishing technique. Specimens prepared by this technique have permitted the direct observation and characterization of the metallic phases in stony meteorites.

On the use of ionization cross sections in analytical electron microscopy.

There are two approaches to the utilization of the ionization cross section, Q, for use in the determination of kappa AB factors for quantitative microanalysis in the analytical electron microscope. The first approach is to interpolate a value of Q from experimentally determined kappa AB factors at a fixed accelerating voltage (kV). The second approach uses a theoretical parameterization of Q generated by fitting the fundamental Bethe expression to selected experimental values of Q over a wide range of kV. This paper discusses the relative merits of the two approaches.

Electron microprobe analysis of lunar samples.

Plagioclase feldspar, clinopyroxene, and ilmenite in a polished thin section of a type A crystalline rock were analyzed. The clinopyroxene grains are compositionally variable, and both high Ca and low Ca phases are present. The plagioclase is compositionally homogeneous. The ilmenite is chemically homogeneous except for occasional, small areas of high local chromium concentration. Accessory minerals are: apatite (containing Cl, F, Y, and Ce), troilite, and metallic iron. Glassy spherules from the lunar soil are for the most part similar in composition to the crystalline rocks; however, some appear to have been monomineralic. The crystalline rock has apparently formed by relatively rapid cooling of a silicate melt under conditions of low oxygen partial pressure. Many components of the soil appear to have formed by meteoritic impact.

Pallasitic meteorites: implications regarding the deep structure of asteroids.

Olivine compositions in pallasites exhibit a bimodal distribution and indicate a high degree of internal equilibrium. Cooling rates measured in the metal phases are uniform and consistently lower than those of most iron meteorites. These factors suggest that the pallasites were derived from few parent bodies, and that they crystallized in a highly insulated site-presumably the core of their parent body. Most iron meteorites were derived either from isolated areas closer to the surface or from other parent bodies.

Rapid methods of determining cooling rates of iron and stony iron meteorites.

Two rapid and simple methods have been developed for determining the approximate cooling rates of iron and stony-iron meteorites in which kamacite formed by diffusion-controlled growth along planar fronts. The first method requires only measurements of the mean kamacite bandwidth and the bulk nickel content. The second method requires the determination of the nickel composition near the taenite-kamacite interface with an electron microprobe.

Butler, missouri: an unusual iron meteorite.

The Butler iron meteorite has been found to have, with respect to other iron meteorites, an unusually high cobalt content (1.4 percent by weight), unusually high germanium contents in the kamacite and the taenite phases, and an unusually low cooling rate (0.5 degrees C/10(6) years). It is suggested that Butler formed in a different environment from that of the rest of the iron meteorites.