The UK Biobank resource with deep phenotyping and genomic data.

The UK Biobank project is a prospective cohort study with deep genetic and phenotypic data collected on approximately 500,000 individuals from across the United Kingdom, aged between 40 and 69 at recruitment. The open resource is unique in its size and scope. A rich variety of phenotypic and health-related information is available on each participant, including biological measurements, lifestyle indicators, biomarkers in blood and urine, and imaging of the body and brain. Follow-up information is provided by linking health and medical records. Genome-wide genotype data have been collected on all participants, providing many opportunities for the discovery of new genetic associations and the genetic bases of complex traits. Here we describe the centralized analysis of the genetic data, including genotype quality, properties of population structure and relatedness of the genetic data, and efficient phasing and genotype imputation that increases the number of testable variants to around 96 million. Classical allelic variation at 11 human leukocyte antigen genes was imputed, resulting in the recovery of signals with known associations between human leukocyte antigen alleles and many diseases.

Significance of atomic-scale defects in flexible surfaces on local solvent and ion behaviour.

Many factors can affect the course of heterogeneous nucleation, such as surface chemistry, flexibility and topology, substrate concentration and solubility. Atomic-scale defects are rarely investigated in detail and are often considered to be unimportant surface features. In this work, we set out to investigate the significance of atomic-scale defects in a flexible self-assembled monolayer surface for the behaviour of clusters of Ca2+ and CO32- ions in water. To this end, we use molecular dynamics simulations to estimate the diffusion coefficients of ion clusters at different topological surface features and obtain ionic radial distribution functions around features of interest. Well-tempered metadynamics is used to gain insight into the free energy of ions around selected surface defects. We find that certain defects, which we refer to as active defects, can impair ionic surface diffusion, as well as affect the diffusion of ions in close proximity to the surface feature in question. Our findings suggest that this effect can result in an ability of such topological features to promote ion clustering and increase local ionic concentration at specific surface sites. The work reported here shows how the presence of small atomic-scale defects can affect the role of a surface in the process of heterogeneous nucleation and contributes towards a rational definition of surfaces as effective nucleating agents.

A general method for calculating solid/liquid interfacial free energies from atomistic simulations: Application to CaSO4·xH2O.

We present a general method for computing interfacial free energies from atomistic simulations, which is particularly suitable for solid/liquid interfaces. Our method uses an Einstein crystal as a universal reference state and is more flexible than previous approaches. Surfaces with dipoles, complex reconstructions, and miscible species are all easily accommodated within the framework. It may also be extended to calculating the relative free energies of different phases and other types of defect. We have applied our method to interfaces of bassanite and gypsum with water and obtained interfacial free energies of the order of 0.12 J/m2, of which ∼45% is due to entropic contributions. Our calculations of the interfacial free energy of NaCl with water obtained a value of 0.13 J/m2, of which only 19% is from entropic contributions. We have also predicted equilibrium morphologies for bassanite and gypsum that compare well with experiments and previous calculations.

The Role of Extracellular DNA in Microbial Attachment to Oxidized Silicon Surfaces in the Presence of Ca2+ and Na.

Attachment assays of a Pseudomonas isolate to fused silica slides showed that treatment with DNaseI significantly inhibited cellular adsorption, which was restored upon DNA treatment. These assays confirmed the important role of extracellular DNA (eDNA) adsorption to a surface. To investigate the eDNA adsorption mechanism, single-molecule force spectroscopy (SMFS) was used to measure the adsorption of eDNA to silicon surfaces in the presence of different concentrations of sodium and calcium ions. SMFS reveals that the work of adhesion required to remove calcium-bound eDNA from the silicon oxide surface is substantially greater than that for sodium. Molecular dynamics simulations were also performed, and here, it was shown that the energy gain in eDNA adsorption to a silicon oxide surface in the presence of calcium ions is small and much less than that in the presence of sodium. The simulations show that the length scales involved in eDNA adsorption are less in the presence of sodium ions than those in the presence of calcium. In the presence of calcium, eDNA is pushed above the surface cations, whereas in the presence of sodium ions, short-range interactions with the surface dominate. Moreover, SMFS data show that increasing [Ca2+] from 1 to 10 mM increases the adsorption of the cations to the silicon oxide surface and consequently enhances the Stern layer, which in turn increases the length scale associated with eDNA adsorption.

The fine-scale genetic structure of the British population.

Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom. This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to southeastern England from Anglo-Saxon migrations to be under half, and identify the regions not carrying genetic material from these migrations. We suggest significant pre-Roman but post-Mesolithic movement into southeastern England from continental Europe, and show that in non-Saxon parts of the United Kingdom, there exist genetically differentiated subgroups rather than a general 'Celtic' population.

Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children.

Bacteremia (bacterial bloodstream infection) is a major cause of illness and death in sub-Saharan Africa but little is known about the role of human genetics in susceptibility. We conducted a genome-wide association study of bacteremia susceptibility in more than 5,000 Kenyan children as part of the Wellcome Trust Case Control Consortium 2 (WTCCC2). Both the blood-culture-proven bacteremia case subjects and healthy infants as controls were recruited from Kilifi, on the east coast of Kenya. Streptococcus pneumoniae is the most common cause of bacteremia in Kilifi and was thus the focus of this study. We identified an association between polymorphisms in a long intergenic non-coding RNA (lincRNA) gene (AC011288.2) and pneumococcal bacteremia and replicated the results in the same population (p combined = 1.69 × 10(-9); OR = 2.47, 95% CI = 1.84-3.31). The susceptibility allele is African specific, derived rather than ancestral, and occurs at low frequency (2.7% in control subjects and 6.4% in case subjects). Our further studies showed AC011288.2 expression only in neutrophils, a cell type that is known to play a major role in pneumococcal clearance. Identification of this novel association will further focus research on the role of lincRNAs in human infectious disease.

Ion Association in Lanthanide Chloride Solutions.

A better understanding of the solution chemistry of the lanthanide (Ln) salts in water would have wide ranging implications in materials processing, waste management, element tracing, medicine and many more fields. This is particularly true for minerals processing, given governmental concerns about lanthanide security of supply and the drive to identify environmentally sustainable processing routes. Despite much effort, even in simple systems, the mechanisms and thermodynamics of LnIII association with small anions remain unclear. In the present study, molecular dynamics (MD), using a newly developed force field, provide new insights into LnCl3 (aq) solutions. The force field accurately reproduces the structure and dynamics of Nd3+ , Gd3+ and Er3+ in water when compared to calculations using density functional theory (DFT). Adaptive-bias MD simulations show that the mechanisms for ion pairing change from dissociative to associative exchange depending upon cation size. Thermodynamics of association reveal that whereas ion pairing is favourable, the equilibrium distribution of species at low concentration is dominated by weakly bound solvent-shared and solvent-separated ion pairs, rather than contact ion pairs, reconciling a number of contrasting observations of LnIII -Cl association in the literature. In addition, we show that the thermodynamic stabilities of a range of inner sphere and outer sphere LnCl x ( 3 - x ) + coordination complexes are comparable and that the kinetics of anion binding to cations may control solution speciation distributions beyond ion pairs. The techniques adopted in this work provide a framework with which to investigate more complex solution chemistries of cations in water.

Tuning hardness in calcite by incorporation of amino acids.

Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit-mineral single crystals containing embedded macromolecules-remain poorly understood. Here, by means of a model biomineral made from calcite single crystals containing glycine (0-7 mol%) or aspartic acid (0-4 mol%), we elucidate the origin of the superior hardness of biogenic calcite. We analysed lattice distortions in these model crystals by using X-ray diffraction and molecular dynamics simulations, and by means of solid-state nuclear magnetic resonance show that the amino acids are incorporated as individual molecules. We also demonstrate that nanoindentation hardness increased with amino acid content, reaching values equivalent to their biogenic counterparts. A dislocation pinning model reveals that the enhanced hardness is determined by the force required to cut covalent bonds in the molecules.

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis.

A common sequence motif associated with recombination hot spots and genome instability in humans.

In humans, most meiotic crossover events are clustered into short regions of the genome known as recombination hot spots. We have previously identified DNA motifs that are enriched in hot spots, particularly the 7-mer CCTCCCT. Here we use the increased hot-spot resolution afforded by the Phase 2 HapMap and novel search methods to identify an extended family of motifs based around the degenerate 13-mer CCNCCNTNNCCNC, which is critical in recruiting crossover events to at least 40% of all human hot spots and which operates on diverse genetic backgrounds in both sexes. Furthermore, these motifs are found in hypervariable minisatellites and are clustered in the breakpoint regions of both disease-causing nonallelic homologous recombination hot spots and common mitochondrial deletion hot spots, implicating the motif as a driver of genome instability.

The Effect of Additives on the Early Stages of Growth of Calcite Single Crystals.

As crystallization processes are often rapid, it can be difficult to monitor their growth mechanisms. In this study, we made use of the fact that crystallization proceeds more slowly in small volumes than in bulk solution to investigate the effects of the soluble additives Mg2+ and poly(styrene sulfonate) (PSS) on the early stages of growth of calcite crystals. Using a "Crystal Hotel" microfluidic device to provide well-defined, nanoliter volumes, we observed that calcite crystals form via an amorphous precursor phase. Surprisingly, the first calcite crystals formed are perfect rhombohedra, and the soluble additives have no influence on the morphology until the crystals reach sizes of 0.1-0.5 µm for Mg2+ and 1-2 µm for PSS. The crystals then continue to grow to develop morphologies characteristic of these additives. These results can be rationalized by considering additive binding to kink sites, which is consistent with crystal growth by a classical mechanism.

An inherited duplication at the gene p21 Protein-Activated Kinase 7 (PAK7) is a risk factor for psychosis.

Identifying rare, highly penetrant risk mutations may be an important step in dissecting the molecular etiology of schizophrenia. We conducted a gene-based analysis of large (>100 kb), rare copy-number variants (CNVs) in the Wellcome Trust Case Control Consortium 2 (WTCCC2) schizophrenia sample of 1564 cases and 1748 controls all from Ireland, and further extended the analysis to include an additional 5196 UK controls. We found association with duplications at chr20p12.2 (P = 0.007) and evidence of replication in large independent European schizophrenia (P = 0.052) and UK bipolar disorder case-control cohorts (P = 0.047). A combined analysis of Irish/UK subjects including additional psychosis cases (schizophrenia and bipolar disorder) identified 22 carriers in 11 707 cases and 10 carriers in 21 204 controls [meta-analysis Cochran-Mantel-Haenszel P-value = 2 × 10(-4); odds ratio (OR) = 11.3, 95% CI = 3.7, ∞]. Nineteen of the 22 cases and 8 of the 10 controls carried duplications starting at 9.68 Mb with similar breakpoints across samples. By haplotype analysis and sequencing, we identified a tandem ~149 kb duplication overlapping the gene p21 Protein-Activated Kinase 7 (PAK7, also called PAK5) which was in linkage disequilibrium with local haplotypes (P = 2.5 × 10(-21)), indicative of a single ancestral duplication event. We confirmed the breakpoints in 8/8 carriers tested and found co-segregation of the duplication with illness in two additional family members of one of the affected probands. We demonstrate that PAK7 is developmentally co-expressed with another known psychosis risk gene (DISC1) suggesting a potential molecular mechanism involving aberrant synapse development and plasticity.

How does an amorphous surface influence molecular binding?--ovocleidin-17 and amorphous calcium carbonate.

Atomistic molecular dynamics simulations of dehydrated amorphous calcium carbonate interacting with the protein ovocleidin-17 are presented. These simulations demonstrate that the amorphisation of the calcium carbonate surface removes water structure from the surface. This reduction of structure allows the protein to bind with many residues, unlike on crystalline surfaces where binding is strongest when only a few residues are attached to the surface. Basic residues are observed to dominate the binding interactions. The implications for protein control over crystallisation are discussed.

Adsorption of poly acrylic acid onto the surface of calcite: an experimental and simulation study.

Macromolecular binding to minerals is of great importance in the formation of biofilms, and carboxylate functional groups have been found to play a pivotal role in the functioning of these macromolecules. Here we present both fluorescence time-resolved anisotropy measurements and simulation data on the conformational behaviour and binding of a poly acrylic acid polymer. In solution the polymer exhibits a pH dependent behaviour, with a coiled conformation at a low pH and extended conformation at higher pH values. The polymer is readily adsorbed on the surface of calcite, preferring to bind in an extended conformation, with the strength of the adsorption dependent on the pH and presence of counter ions. We discuss the reasons why the calculated adsorption free energy differs from that obtained from a Langmuir isotherm analysis, showing that they refer to different quantities. The enhanced binding of the extended conformations shows the importance of flexibility in the binding of macromolecules.

Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population.

In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10-20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions.

Dissection of the genetics of Parkinson's disease identifies an additional association 5' of SNCA and multiple associated haplotypes at 17q21.

We performed a genome-wide association study (GWAS) in 1705 Parkinson's disease (PD) UK patients and 5175 UK controls, the largest sample size so far for a PD GWAS. Replication was attempted in an additional cohort of 1039 French PD cases and 1984 controls for the 27 regions showing the strongest evidence of association (P< 10(-4)). We replicated published associations in the 4q22/SNCA and 17q21/MAPT chromosome regions (P< 10(-10)) and found evidence for an additional independent association in 4q22/SNCA. A detailed analysis of the haplotype structure at 17q21 showed that there are three separate risk groups within this region. We found weak but consistent evidence of association for common variants located in three previously published associated regions (4p15/BST1, 4p16/GAK and 1q32/PARK16). We found no support for the previously reported SNP association in 12q12/LRRK2. We also found an association of the two SNPs in 4q22/SNCA with the age of onset of the disease.

A robust clustering algorithm for identifying problematic samples in genome-wide association studies.

SUMMARY: High-throughput genotyping arrays provide an efficient way to survey single nucleotide polymorphisms (SNPs) across the genome in large numbers of individuals. Downstream analysis of the data, for example in genome-wide association studies (GWAS), often involves statistical models of genotype frequencies across individuals. The complexities of the sample collection process and the potential for errors in the experimental assay can lead to biases and artefacts in an individual's inferred genotypes. Rather than attempting to model these complications, it has become a standard practice to remove individuals whose genome-wide data differ from the sample at large. Here we describe a simple, but robust, statistical algorithm to identify samples with atypical summaries of genome-wide variation. Its use as a semi-automated quality control tool is demonstrated using several summary statistics, selected to identify different potential problems, and it is applied to two different genotyping platforms and sample collections. AVAILABILITY: The algorithm is written in R and is freely available at www.well.ox.ac.uk/chris-spencer CONTACT: chris.spencer@well.ox.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dynamic tilting in perovskites.

A new computational analysis of tilt behaviour in perovskites is presented. This includes the development of a computational program - PALAMEDES - to extract tilt angles and the tilt phase from molecular dynamics simulations. The results are used to generate simulated selected-area electron and neutron diffraction patterns which are compared with experimental patterns for CaTiO3. The simulations not only reproduced all symmetrically allowed superlattice reflections associated with tilt but also showed local correlations that give rise to symmetrically forbidden reflections and the kinematic origin of diffuse scattering.

Electron transparent nanotubes reveal crystallization pathways in confinement.

The cylindrical pores of track-etched membranes offer excellent environments for studying the effects of confinement on crystallization as the pore diameter is readily varied and the anisotropic morphologies can direct crystal orientation. However, the inability to image individual crystals in situ within the pores in this system has prevented many of the underlying mechanisms from being characterized. Here, we study the crystallization of calcium sulfate within track-etched membranes and reveal that oriented gypsum forms in 200 nm diameter pores, bassanite in 25-100 nm pores and anhydrite in 10 nm pores. The crystallization pathways are then studied by coating the membranes with an amorphous titania layer prior to mineralization to create electron transparent nanotubes that protect fragile precursor materials. By visualizing the evolutionary pathways of the crystals within the pores we show that the product single crystals derive from multiple nucleation events and that orientation is determined at early reaction times. Finally, the transformation of bassanite to gypsum within the membrane pores is studied using experiment and potential mean force calculations and is shown to proceed by localized dissolution/reprecipitation. This work provides insight into the effects of confinement on crystallization processes, which is relevant to mineral formation in many real-world environments.