The sequences of 150,119 genomes in the UK Biobank.

Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data1,2. Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank3. This constitutes a set of high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% of all possible human single-nucleotide polymorphisms, and 58,707,036 indels. This large set of variants allows us to characterize selection based on sequence variation within a population through a depletion rank score of windows along the genome. Depletion rank analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UK Biobank: a large British Irish cohort, a smaller African cohort and a South Asian cohort. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large-scale whole-genome sequencing studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on whole-exome sequencing and/or imputation.

Actionable Genotypes and Their Association with Life Span in Iceland.

BACKGROUND: In 2021, the American College of Medical Genetics and Genomics (ACMG) recommended reporting actionable genotypes in 73 genes associated with diseases for which preventive or therapeutic measures are available. Evaluations of the association of actionable genotypes in these genes with life span are currently lacking. METHODS: We assessed the prevalence of coding and splice variants in genes on the ACMG Secondary Findings, version 3.0 (ACMG SF v3.0), list in the genomes of 57,933 Icelanders. We assigned pathogenicity to all reviewed variants using reported evidence in the ClinVar database, the frequency of variants, and their associations with disease to create a manually curated set of actionable genotypes (variants). We assessed the relationship between these genotypes and life span and further examined the specific causes of death among carriers. RESULTS: Through manual curation of 4405 sequence variants in the ACMG SF v3.0 genes, we identified 235 actionable genotypes in 53 genes. Of the 57,933 participants, 2306 (4.0%) carried at least one actionable genotype. We found shorter median survival among persons carrying actionable genotypes than among noncarriers. Specifically, we found that carrying an actionable genotype in a cancer gene was associated with survival that was 3 years shorter than that among noncarriers, with causes of death among carriers attributed primarily to cancer-related conditions. Furthermore, we found evidence of association between carrying an actionable genotype in certain genes in the cardiovascular disease group and a reduced life span. CONCLUSIONS: On the basis of the ACMG SF v3.0 guidelines, we found that approximately 1 in 25 Icelanders carried an actionable genotype and that carrying such a genotype was associated with a reduced life span. (Funded by deCODE Genetics-Amgen.).

NCOurd: modelling length distributions of NCO events and gene conversion tracts.

MOTIVATION: Meiotic recombination is the main driving force of human genetic diversity, along with mutations. Recombinations split into crossovers, separating large chromosomal regions originating from different homologous chromosomes, and non-crossovers (NCOs), where a small segment from one chromosome is embedded in a region originating from the homologous chromosome. NCOs are much less studied than mutations and crossovers as NCOs are short and can only be detected at markers heterozygous in the transmitting parent, leaving most of them undetectable. RESULTS: The detectable NCOs, known as gene conversions, hide information about NCOs, including their number and length, waiting to be unveiled. We introduce NCOurd, software, and algorithm, based on an expectation-maximization algorithm, to estimate the number of NCOs and their length distribution from gene conversion data. AVAILABILITY AND IMPLEMENTATION: https://github.com/DecodeGenetics/NCOurd.

Interstitial Hydrogen in Fe/V Superstructures: Lattice Site Location and Thermal Vibration.

We report real space location of hydrogen in single crystalline Fe/V superstructures. Anisotropic strain is quantified versus hydrogen concentration by using the yield of backscattered primary 2 MeV ^{4}He ions for incidence in different crystallographic directions. From a comparison of ion channeling in combination with ^{1}H(^{15}N,αγ)^{12}C nuclear reaction analysis and Monte Carlo simulations we show that hydrogen is located in octahedral z sites and quantify its vibrational amplitude of 0.2 Å.

On the interaction of softwood hemicellulose with cellulose surfaces in relation to molecular structure and physicochemical properties of hemicellulose.

The substantial part of the water-soluble hemicellulose fraction, obtained when processing cellulose to produce paper and other products, has so far been discarded. The aim of this work is to reveal the interfacial properties of softwood hemicellulose (galactoglucomannan, GGM) in relation to their molecular and solution structure. In this study the sugar composition of GGM was characterised by chemical analysis as well as 1D and 2D NMR spectroscopy. Previously it has been demonstrated that hemicellulose has high affinity towards cellulose and has the ability to alter the properties of cellulose based products. This study is focused on the interactions between hemicellulose and the cellulose surface. Therefore, adsorption to hydrophobized silica and cellulose surfaces of two softwood hemicellulose samples and structurally similar seed hemicelluloses (galactomannans, GMs) was studied with ellipsometry, QCM-D and neutron reflectometry. Aqueous solutions of all samples were characterized with light scattering to determine how the degree of side-group substitution and molecular weight affect the conformation and aggregation of these polymers in the bulk. In addition, hemicellulose samples were studied with SAXS to investigate backbone flexibility. Light scattering results indicated that GM polymers form globular particles while GGMs were found to form rod-like aggregates in the solution. The polysaccharides exhibit higher adsorption to cellulose than on hydrophobic surfaces. A clear correlation between the increase in molecular weight of polysaccharides and increasing adsorbed amount on cellulose was observed, while the adsorbed amount on the hydrophobic surface was fairly independent of the molecular weight. The obtained layer thickness was compared with bulk scattering data and the results indicated flat conformation of the polysaccharides on the surface.

Nuclear Spin Incoherent Neutron Scattering from Quantum Well Resonators.

We report the detection and quantification of nuclear spin incoherent scattering from hydrogen occupying interstitial sites in a thin film of vanadium. The neutron wave field is enhanced in a quantum resonator with magnetically switchable boundaries. Our results provide a pathway for the study of dynamics at surfaces and in ultrathin films using inelastic and/or quasielastic neutron scattering methods.

Interfacial properties of lipid sponge-like nanoparticles and the role of stabilizer on particle structure and surface interactions.

The advantage of using nonlamellar lipid liquid crystalline phases has been demonstrated in many applications, such as drug delivery, protein encapsulation and crystallisation. We have recently reported that a mixture of mono- and diglycerides is able to form sponge-like nanoparticles (L3-NPs) with large enough aqueous pores to encapsulate macromolecules such as proteins. Here we use small angle neutron scattering (SANS) to reveal morphology, structural and chemical composition of these polysorbate 80 (P80) stabilized sponge phase nanoparticles, not previously known. Our results suggest that L3-NPs have a core-shell sphere structure, with a shell rich in P80. It was also found that even if P80 is mostly located on the surface, it also contributes to the formation of the inner sponge phase structure. An important aspect for the application and colloidal stability of these particles is their interfacial properties. Therefore, the interfacial behaviour of the nanoparticles on hydrophilic silica was revealed by Quartz crystal microbalance with dissipation (QCM-D) and neutron reflectivity (NR). Adsorption experiments reveal the formation of a thin lipid layer, with the dimension corresponding to a lipid bilayer after L3-NPs are in contact with hydrophilic silica. This suggests that the diglycerol monoleate/Capmul GMO-50/P80 particles reorganize themselves on this surface, probably due to interactions between P80 head group and SiO2.

Electro-responsivity of ionic liquid boundary layers in a polar solvent revealed by neutron reflectance.

Using neutron reflectivity, the electro-responsive structuring of the non-halogenated ionic liquid (IL) trihexyl(tetradecyl)phosphonium-bis(mandelato)borate, [P6,6,6,14][BMB], has been studied at a gold electrode surface in a polar solvent. For a 20% w/w IL mixture, contrast matched to the gold surface, distinct Kiessig fringes were observed for all potentials studied, indicative of a boundary layer of different composition to that of the bulk IL-solvent mixture. With applied potential, the amplitudes of the fringes from the gold-boundary layer interface varied systematically. These changes are attributable to the differing ratios of cations and anions in the boundary layer, leading to a greater or diminished contrast with the gold electrode, depending on the individual ion scattering length densities. Such electro-responsive changes were also evident in the reflectivities measured for the pure IL and a less concentrated (5% w/w) IL-solvent mixture at the same applied potentials, but gave rise to less pronounced changes. These measurements, therefore, demonstrate the enhanced sensitivity achieved by contrast matching the bulk solution and that the structure of the IL boundary layers formed in mixtures is strongly influenced by the bulk concentration. Together these results represent an important step in characterising IL boundary layers in IL-solvent mixtures and provide clear evidence of electro-responsive structuring of IL ions in their solutions with applied potential.

Strong interlayer coupling in van der Waals heterostructures built from single-layer chalcogenides.

Semiconductor heterostructures are the fundamental platform for many important device applications such as lasers, light-emitting diodes, solar cells, and high-electron-mobility transistors. Analogous to traditional heterostructures, layered transition metal dichalcogenide heterostructures can be designed and built by assembling individual single layers into functional multilayer structures, but in principle with atomically sharp interfaces, no interdiffusion of atoms, digitally controlled layered components, and no lattice parameter constraints. Nonetheless, the optoelectronic behavior of this new type of van der Waals (vdW) semiconductor heterostructure is unknown at the single-layer limit. Specifically, it is experimentally unknown whether the optical transitions will be spatially direct or indirect in such hetero-bilayers. Here, we investigate artificial semiconductor heterostructures built from single-layer WSe2 and MoS2. We observe a large Stokes-like shift of ∼ 100 meV between the photoluminescence peak and the lowest absorption peak that is consistent with a type II band alignment having spatially direct absorption but spatially indirect emission. Notably, the photoluminescence intensity of this spatially indirect transition is strong, suggesting strong interlayer coupling of charge carriers. This coupling at the hetero-interface can be readily tuned by inserting dielectric layers into the vdW gap, consisting of hexagonal BN. Consequently, the generic nature of this interlayer coupling provides a new degree of freedom in band engineering and is expected to yield a new family of semiconductor heterostructures having tunable optoelectronic properties with customized composite layers.

Depth profiling charge accumulation from a ferroelectric into a doped Mott insulator.

The electric field control of functional properties is a crucial goal in oxide-based electronics. Nonvolatile switching between different resistivity or magnetic states in an oxide channel can be achieved through charge accumulation or depletion from an adjacent ferroelectric. However, the way in which charge distributes near the interface between the ferroelectric and the oxide remains poorly known, which limits our understanding of such switching effects. Here, we use a first-of-a-kind combination of scanning transmission electron microscopy with electron energy loss spectroscopy, near-total-reflection hard X-ray photoemission spectroscopy, and ab initio theory to address this issue. We achieve a direct, quantitative, atomic-scale characterization of the polarization-induced charge density changes at the interface between the ferroelectric BiFeO3 and the doped Mott insulator Ca(1-x)Ce(x)MnO3, thus providing insight on how interface-engineering can enhance these switching effects.

Finite-size effects: hydrogen in Fe/V(001) superlattices.

We investigate the effect of finite size on phase boundaries of hydride formation in ultrathin metallic films, using Fe/V(001) superlattices as a model system. The critical temperature is determined to scale linearly with the inverse thickness of the V layers. The decrease of the ordering temperature with decreasing layer thickness arises from the missing H neighbors at the interfaces, analogous to observed finite-size effects in magnetic layers and nanosized ice crystals.

Determining pair distribution functions of thin films using laboratory-based X-ray sources.

This article demonstrates the feasibility of obtaining accurate pair distribution functions of thin amorphous films down to 80 nm, using modern laboratory-based X-ray sources. The pair distribution functions are obtained using a single diffraction scan without the requirement of additional scans of the substrate or of the air. By using a crystalline substrate combined with an oblique scattering geometry, most of the Bragg scattering of the substrate is avoided, rendering the substrate Compton scattering the primary contribution. By utilizing a discriminating energy filter, available in the latest generation of modern detectors, it is demonstrated that the Compton intensity can further be reduced to negligible levels at higher wavevector values. Scattering from the sample holder and the air is minimized by the systematic selection of pixels in the detector image based on the projected detection footprint of the sample and the use of a 3D-printed sample holder. Finally, X-ray optical effects in the absorption factors and the ratios between the Compton intensity of the substrate and film are taken into account by using a theoretical tool that simulates the electric field inside the film and the substrate, which aids in planning both the sample design and the measurement protocol.

Variant in the synaptonemal complex protein SYCE2 associates with pregnancy loss through effect on recombination.

Two-thirds of all human conceptions are lost, in most cases before clinical detection. The lack of detailed understanding of the causes of pregnancy losses constrains focused counseling for future pregnancies. We have previously shown that a missense variant in synaptonemal complex central element protein 2 (SYCE2), in a key residue for the assembly of the synaptonemal complex backbone, associates with recombination traits. Here we show that it also increases risk of pregnancy loss in a genome-wide association analysis on 114,761 women with reported pregnancy loss. We further show that the variant associates with more random placement of crossovers and lower recombination rate in longer chromosomes but higher in the shorter ones. These results support the hypothesis that some pregnancy losses are due to failures in recombination. They further demonstrate that variants with a substantial effect on the quality of recombination can be maintained in the population.

Sequence variants affecting the genome-wide rate of germline microsatellite mutations.

Microsatellites are polymorphic tracts of short tandem repeats with one to six base-pair (bp) motifs and are some of the most polymorphic variants in the genome. Using 6084 Icelandic parent-offspring trios we estimate 63.7 (95% CI: 61.9-65.4) microsatellite de novo mutations (mDNMs) per offspring per generation, excluding one bp repeats motifs (homopolymers) the estimate is 48.2 mDNMs (95% CI: 46.7-49.6). Paternal mDNMs occur at longer repeats than maternal ones, which are in turn larger with a mean size of 3.4 bp vs 3.1 bp for paternal ones. mDNMs increase by 0.97 (95% CI: 0.90-1.04) and 0.31 (95% CI: 0.25-0.37) per year of father's and mother's age at conception, respectively. Here, we find two independent coding variants that associate with the number of mDNMs transmitted to offspring; The minor allele of a missense variant (allele frequency (AF) = 1.9%) in MSH2, a mismatch repair gene, increases transmitted mDNMs from both parents (effect: 13.1 paternal and 7.8 maternal mDNMs). A synonymous variant (AF = 20.3%) in NEIL2, a DNA damage repair gene, increases paternally transmitted mDNMs (effect: 4.4 mDNMs). Thus, the microsatellite mutation rate in humans is in part under genetic control.

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits.

Long-read sequencing (LRS) promises to improve the characterization of structural variants (SVs). We generated LRS data from 3,622 Icelanders and identified a median of 22,636 SVs per individual (a median of 13,353 insertions and 9,474 deletions). We discovered a set of 133,886 reliably genotyped SV alleles and imputed them into 166,281 individuals to explore their effects on diseases and other traits. We discovered an association of a rare deletion in PCSK9 with lower low-density lipoprotein (LDL) cholesterol levels, compared to the population average. We also discovered an association of a multiallelic SV in ACAN with height; we found 11 alleles that differed in the number of a 57-bp-motif repeat and observed a linear relationship between the number of repeats carried and height. These results show that SVs can be accurately characterized at the population scale using LRS data in a genome-wide non-targeted approach and demonstrate how SVs impact phenotypes.

Significance of self-trapping on hydrogen diffusion.

The diffusion rate of hydrogen in Nb was calculated using ab initio molecular dynamics simulations. At low temperatures the hydrogen is strongly trapped in a local strain field which is caused by the elastic response of the lattice. At elevated temperatures, the residence time (τ) of hydrogen in an interstitial site is not sufficient for fully developing the local strain field. This unbinding of the interstitial hydrogen and the strain field increases the hopping rate (1/τ) at elevated temperatures (>400 K). These results call for a revision of the conceptual framework of diffusion of hydrogen in transition metals at elevated temperatures.

Characterizing mutagenic effects of recombination through a sequence-level genetic map.

Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.

Interactions of perfluoroalkyl substances with a phospholipid bilayer studied by neutron reflectometry.

The interactions between perfluoroalkyl substances (PFASs) and a phospholipid bilayer (1,2-dimyristoyl-sn-glycero-3-phosphocholine) were investigated at the molecular level using neutron reflectometry. Representative PFASs with different chain length and functional groups were selected in this study including: perfluorobutane sulfonate (PFBS), perfluorohexanoate (PFHxA), perfluorohexane sulfonate (PFHxS), perfluorononanoate (PFNA), perfluorooctane sulfonate (PFOS), and perfluorooctane sulfonamide (FOSA). All PFASs were found to interact with the bilayer by incorporation, indicating PFAS ability to accumulate once ingested or taken up by organisms. The interactions were observed to increase with chain length and vary with the functional group as SO2NH2(FOSA)>SO2O-(PFOS)>COO-(PFNA). The PFAS hydrophobicity, which is strongly correlated with perfluorocarbon chain length, was found to strongly influence the interactions. Longer chain PFASs showed higher tendency to penetrate into the bilayer compared to the short-chain compounds. The incorporated PFASs could for all substances but one (PFNA) be removed from the lipid membrane by gentle rinsing with water (2mLmin-1). Although short-chain PFASs have been suggested to be the potentially less bioaccumulative alternative, we found that in high enough concentrations they can also disturb the bilayer. The roughness and disorder of the bilayer was observed to increase as the concentration of PFASs increased (in particular for the high concentrations of short-chain substances i.e. PFHxA and PFBS), which can be an indication of aggregation of PFASs in the bilayer.

Depth resolved grazing incidence neutron scattering experiments from semi-infinite interfaces: a statistical analysis of the scattering contributions.

Grazing incidence neutron scattering experiments offer surface sensitivity by reflecting from an interface at momentum transfers close to total external reflection. Under these conditions the penetration depth is strongly non-linear and may change by many orders of magnitude. This fact imposes severe challenges for depth resolved experiments, since the brilliance of neutron beams is relatively low in comparison to e.g. synchrotron radiation. In this article we use probability density functions to calculate the contribution of scattering at different distances from an interface to the intensities registered on the detector. Our method has the particular advantage that the depth sensitivity is directly extracted from the scattering pattern itself. Hence for perfectly known samples exact resolution functions can be calculated and visa versa. We show that any tails in the resolution function, e.g. Gaussian shaped, hinders depth resolved experiments. More importantly we provide means for a descriptive statistical analysis of detector images with respect to the scattering contributions and show that even for perfect resolution near surface scattering is hardly accessible.

Multiple transmissions of de novo mutations in families.

De novo mutations (DNMs) cause a large proportion of severe rare diseases of childhood. DNMs that occur early may result in mosaicism of both somatic and germ cells. Such early mutations can cause recurrence of disease. We scanned 1,007 sibling pairs from 251 families and identified 878 DNMs shared by siblings (ssDNMs) at 448 genomic sites. We estimated DNM recurrence probability based on parental mosaicism, sharing of DNMs among siblings, parent-of-origin, mutation type and genomic position. We detected 57.2% of ssDNMs in the parental blood. The recurrence probability of a DNM decreases by 2.27% per year for paternal DNMs and 1.78% per year for maternal DNMs. Maternal ssDNMs are more likely to be T>C mutations than paternal ssDNMs, and less likely to be C>T mutations. Depending on the properties of the DNM, the recurrence probability ranges from 0.011% to 28.5%. We have launched an online calculator to allow estimation of DNM recurrence probability for research purposes.