Genotyping, sequencing and analysis of 140,000 adults from Mexico City.

The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City1. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. We describe high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Indigenous American, European and African ancestry, with extensive admixture from Indigenous populations in central, southern and southeastern Mexico. Indigenous Mexican segments of the genome had lower levels of coding variation but an excess of homozygous loss-of-function variants compared with segments of African and European origin. We estimated ancestry-specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Indigenous Mexican ancestry at exome variants, all available through a public browser. Using whole-genome sequencing, we developed an imputation reference panel that outperforms existing panels at common variants in individuals with high proportions of central, southern and southeastern Indigenous Mexican ancestry. Our work illustrates the value of genetic studies in diverse populations and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States, where the Hispanic/Latino population is predominantly of Mexican descent.

Rare variant contribution to human disease in 281,104 UK Biobank exomes.

Genome-wide association studies have uncovered thousands of common variants associated with human disease, but the contribution of rare variants to common disease remains relatively unexplored. The UK Biobank contains detailed phenotypic data linked to medical records for approximately 500,000 participants, offering an unprecedented opportunity to evaluate the effect of rare variation on a broad collection of traits1,2. Here we study the relationships between rare protein-coding variants and 17,361 binary and 1,419 quantitative phenotypes using exome sequencing data from 269,171 UK Biobank participants of European ancestry. Gene-based collapsing analyses revealed 1,703 statistically significant gene-phenotype associations for binary traits, with a median odds ratio of 12.4. Furthermore, 83% of these associations were undetectable via single-variant association tests, emphasizing the power of gene-based collapsing analysis in the setting of high allelic heterogeneity. Gene-phenotype associations were also significantly enriched for loss-of-function-mediated traits and approved drug targets. Finally, we performed ancestry-specific and pan-ancestry collapsing analyses using exome sequencing data from 11,933 UK Biobank participants of African, East Asian or South Asian ancestry. Our results highlight a significant contribution of rare variants to common disease. Summary statistics are publicly available through an interactive portal ( http://azphewas.com/ ).

Effects of protein-coding variants on blood metabolite measurements and clinical biomarkers in the UK Biobank.

Genome-wide association studies (GWASs) have established the contribution of common and low-frequency variants to metabolic blood measurements in the UK Biobank (UKB). To complement existing GWAS findings, we assessed the contribution of rare protein-coding variants in relation to 355 metabolic blood measurements-including 325 predominantly lipid-related nuclear magnetic resonance (NMR)-derived blood metabolite measurements (Nightingale Health Plc) and 30 clinical blood biomarkers-using 412,393 exome sequences from four genetically diverse ancestries in the UKB. Gene-level collapsing analyses were conducted to evaluate a diverse range of rare-variant architectures for the metabolic blood measurements. Altogether, we identified significant associations (p < 1 × 10-8) for 205 distinct genes that involved 1,968 significant relationships for the Nightingale blood metabolite measurements and 331 for the clinical blood biomarkers. These include associations for rare non-synonymous variants in PLIN1 and CREB3L3 with lipid metabolite measurements and SYT7 with creatinine, among others, which may not only provide insights into novel biology but also deepen our understanding of established disease mechanisms. Of the study-wide significant clinical biomarker associations, 40% were not previously detected on analyzing coding variants in a GWAS in the same cohort, reinforcing the importance of studying rare variation to fully understand the genetic architecture of metabolic blood measurements.

Superstructure control of first-cycle voltage hysteresis in oxygen-redox cathodes.

In conventional intercalation cathodes, alkali metal ions can move in and out of a layered material with the charge being compensated for by reversible reduction and oxidation of the transition metal ions. If the cathode material used in a lithium-ion or sodium-ion battery is alkali-rich, this can increase the battery's energy density by storing charge on the oxide and the transition metal ions, rather than on the transition metal alone1-10. There is a high voltage associated with oxidation of O2- during the first charge, but this is not recovered on discharge, resulting in reduced energy density11. Displacement of transition metal ions into the alkali metal layers has been proposed to explain the first-cycle voltage loss (hysteresis)9,12-16. By comparing two closely related intercalation cathodes, Na0.75[Li0.25Mn0.75]O2 and Na0.6[Li0.2Mn0.8]O2, here we show that the first-cycle voltage hysteresis is determined by the superstructure in the cathode, specifically the local ordering of lithium and transition metal ions in the transition metal layers. The honeycomb superstructure of Na0.75[Li0.25Mn0.75]O2, present in almost all oxygen-redox compounds, is lost on charging, driven in part by formation of molecular O2 inside the solid. The O2 molecules are cleaved on discharge, reforming O2-, but the manganese ions have migrated within the plane, changing the coordination around O2- and lowering the voltage on discharge. The ribbon superstructure in Na0.6[Li0.2Mn0.8]O2 inhibits manganese disorder and hence O2 formation, suppressing hysteresis and promoting stable electron holes on O2- that are revealed by X-ray absorption spectroscopy. The results show that voltage hysteresis can be avoided in oxygen-redox cathodes by forming materials with a ribbon superstructure in the transition metal layers that suppresses migration of the transition metal.

Coherent many-body exciton in van der Waals antiferromagnet NiPS3.

An exciton is the bosonic quasiparticle of electron-hole pairs bound by the Coulomb interaction1. Bose-Einstein condensation of this exciton state has long been the subject of speculation in various model systems2,3, and examples have been found more recently in optical lattices and two-dimensional materials4-9. Unlike these conventional excitons formed from extended Bloch states4-9, excitonic bound states from intrinsically many-body localized states are rare. Here we show that a spin-orbit-entangled exciton state appears below the Néel temperature of 150 kelvin in NiPS3, an antiferromagnetic van der Waals material. It arises intrinsically from the archetypal many-body states of the Zhang-Rice singlet10,11, and reaches a coherent state assisted by the antiferromagnetic order. Using configuration-interaction theory, we determine the origin of the coherent excitonic excitation to be a transition from a Zhang-Rice triplet to a Zhang-Rice singlet. We combine three spectroscopic tools-resonant inelastic X-ray scattering, photoluminescence and optical absorption-to characterize the exciton and to demonstrate an extremely narrow excitonic linewidth below 50 kelvin. The discovery of the spin-orbit-entangled exciton in antiferromagnetic NiPS3 introduces van der Waals magnets as a platform to study coherent many-body excitons.

Gene-SCOUT: identifying genes with similar continuous trait fingerprints from phenome-wide association analyses.

Large-scale phenome-wide association studies performed using densely-phenotyped cohorts such as the UK Biobank (UKB), reveal many statistically robust gene-phenotype relationships for both clinical and continuous traits. Here, we present Gene-SCOUT, a tool used to identify genes with similar continuous trait fingerprints to a gene of interest. A fingerprint reflects the continuous traits identified to be statistically associated with a gene of interest based on multiple underlying rare variant genetic architectures. Similarities between genes are evaluated by the cosine similarity measure, to capture concordant effect directionality, elucidating clusters of genes in a high dimensional space. The underlying gene-biomarker population-scale association statistics were obtained from a gene-level rare variant collapsing analysis performed on over 1500 continuous traits using 394 692 UKB participant exomes, with additional metabolomic trait associations provided through Nightingale Health's recent study of 121 394 of these participants. We demonstrate that gene similarity estimates from Gene-SCOUT provide stronger enrichments for clinical traits compared to existing methods. Furthermore, we provide a fully interactive web-resource (http://genescout.public.cgr.astrazeneca.com) to explore the pre-calculated exome-wide similarities. This resource enables a user to examine the biological relevance of the most similar genes for Gene Ontology (GO) enrichment and UKB clinical trait enrichment statistics, as well as a detailed breakdown of the traits underpinning a given fingerprint.

Charge density waves in infinite-layer NdNiO2 nickelates.

In materials science, much effort has been devoted to the reproduction of superconductivity in chemical compositions, analogous to cuprate superconductors since their discovery over 30 years ago. This approach was recently successful in realising superconductivity in infinite-layer nickelates1-6. Although differing from cuprates in electronic and magnetic properties, strong Coulomb interactions suggest that infinite-layer nickelates have a propensity towards various symmetry-breaking orders that populate cuprates7-10. Here we report the observation of charge density waves (CDWs) in infinite-layer NdNiO2 films using Ni L3 resonant X-ray scattering. Remarkably, CDWs form in Nd 5d and Ni 3d orbitals at the same commensurate wavevector (0.333, 0) reciprocal lattice units, with non-negligible out-of-plane dependence and an in-plane correlation length of up to ~60 Å. Spectroscopic studies reveal a strong connection between CDWs and Nd 5d-Ni 3d orbital hybridization. Upon entering the superconducting state at 20% Sr doping, the CDWs disappear. Our work demonstrates the existence of CDWs in infinite-layer nickelates with a multiorbital character distinct from cuprates, which establishes their low-energy physics.

Multiorbital charge-density wave excitations and concomitant phonon anomalies in Bi2Sr2LaCuO6+δ.

Charge-density waves (CDWs) are ubiquitous in underdoped cuprate superconductors. As a modulation of the valence electron density, CDWs in hole-doped cuprates possess both Cu-3d and O-2p orbital character owing to the strong hybridization of these orbitals near the Fermi level. Here, we investigate underdoped Bi2Sr1.4La0.6CuO6+δ using resonant inelastic X-ray scattering (RIXS) and find that a short-range CDW exists at both Cu and O sublattices in the copper-oxide (CuO2) planes with a comparable periodicity and correlation length. Furthermore, we uncover bond-stretching and bond-buckling phonon anomalies concomitant to the CDWs. Comparing to slightly overdoped Bi2Sr1.8La0.2CuO6+δ, where neither CDWs nor phonon anomalies appear, we highlight that a sharp intensity anomaly is induced in the proximity of the CDW wavevector (QCDW) for the bond-buckling phonon, in concert with the diffused intensity enhancement of the bond-stretching phonon at wavevectors much greater than QCDW Our results provide a comprehensive picture of the quasistatic CDWs, their dispersive excitations, and associated electron-phonon anomalies, which are key for understanding the competing electronic instabilities in cuprates.

Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels.

Saliva, as a biofluid, is inexpensive and non-invasive to obtain, and provides a vital tool to investigate oral health and its interaction with systemic health conditions. There is growing interest in salivary biomarkers for systemic diseases, notably cardiovascular disease. Whereas hundreds of genetic loci have been shown to be involved in the regulation of blood metabolites, leading to significant insights into the pathogenesis of complex human diseases, little is known about the impact of host genetics on salivary metabolites. Here we report the first genome-wide association study exploring 476 salivary metabolites in 1419 subjects from the TwinsUK cohort (discovery phase), followed by replication in the Study of Health in Pomerania (SHIP-2) cohort. A total of 14 distinct locus-metabolite associations were identified in the discovery phase, most of which were replicated in SHIP-2. While only a limited number of the loci that are known to regulate blood metabolites were also associated with salivary metabolites in our study, we identified several novel saliva-specific locus-metabolite associations, including associations for the AGMAT (with the metabolites 4-guanidinobutanoate and beta-guanidinopropanoate), ATP13A5 (with the metabolite creatinine) and DPYS (with the metabolites 3-ureidopropionate and 3-ureidoisobutyrate) loci. Our study suggests that there may be regulatory pathways of particular relevance to the salivary metabolome. In addition, some of our findings may have clinical significance, such as the utility of the pyrimidine (uracil) degradation metabolites in predicting 5-fluorouracil toxicity and the role of the agmatine pathway metabolites as biomarkers of oral health.

I21: an advanced high-resolution resonant inelastic X-ray scattering beamline at Diamond Light Source.

The I21 beamline at Diamond Light Source is dedicated to advanced resonant inelastic X-ray scattering (RIXS) for probing charge, orbital, spin and lattice excitations in materials across condensed matter physics, applied sciences and chemistry. Both the beamline and the RIXS spectrometer employ divergent variable-line-spacing gratings covering a broad energy range of 280-3000 eV. A combined energy resolution of ∼35 meV (16 meV) is readily achieved at 930 eV (530 eV) owing to the optimized optics and the mechanics. Considerable efforts have been paid to the design of the entire beamline, particularly the implementation of the collection mirrors, to maximize the X-ray photon throughput. The continuous rotation of the spectrometer over 150° under ultra high vacuum and a cryogenic manipulator with six degrees of freedom allow accurate mappings of low-energy excitations from solid state materials in momentum space. Most importantly, the facility features a unique combination of the high energy resolution and the high photon throughput vital for advanced RIXS applications. Together with its stability and user friendliness, I21 has become one of the most sought after RIXS beamlines in the world.

Unraveling the Orbital Physics in a Canonical Orbital System KCuF_{3}.

We explore the existence of the collective orbital excitations, orbitons, in the canonical orbital system KCuF_{3} using the Cu L_{3}-edge resonant inelastic x-ray scattering. We show that the nondispersive high-energy peaks result from the Cu^{2+} dd orbital excitations. These high-energy modes display good agreement with the ab initio quantum chemistry calculation, indicating that the dd excitations are highly localized. At the same time, the low-energy excitations present clear dispersion. They match extremely well with the two-spinon continuum following the comparison with Müller ansatz calculations. The localized dd excitations and the observation of the strongly dispersive magnetic excitations suggest that the orbiton dispersion is below the resolution detection limit. Our results can reconcile with the strong local Jahn-Teller effect in KCuF_{3}, which predominantly drives orbital ordering.

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of 12 anthropometric traits associated with height, body mass, and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates. Of the 106 signals, 6 are in genomic regions that have not been implicated with related traits before, 28 are independent signals at previously reported regions, and 72 represent previously reported signals for a different anthropometric trait. 71% of signals reside within genes and fine mapping resolves 23 signals to one or two likely causal variants. We confirm genetic overlap between human monogenic and polygenic anthropometric traits and find signal enrichment in cis expression QTLs in relevant tissues. Our results highlight the potential of WGS strategies to enhance biologically relevant discoveries across the frequency spectrum.

Many-Body Physics of Single and Double Spin-Flip Excitations in NiO.

Understanding many-body physics of elementary excitations has advanced our control over material properties. Here, we study spin-flip excitations in NiO using Ni L_{3}-edge resonant inelastic x-ray scattering (RIXS) and present a strikingly different resonant energy behavior between single and double spin-flip excitations. Comparing our results with single-site full-multiplet ligand field theory calculations we find that the spectral weight of the double-magnon excitations originates primarily from the double spin-flip transition of the quadrupolar RIXS process within a single magnetic site. Quadrupolar spin-flip processes are among the least studied excitations, despite being important for multiferroic or spin-nematic materials due to their difficult detection. We identify intermediate state multiplets and intra-atomic core-valence exchange interactions as the key many-body factors determining the fate of such excitations. RIXS resonant energy dependence can act as a convincing proof of existence of nondipolar higher-ranked magnetic orders in systems for which, only theoretical predictions are available.

Detection of Acoustic Plasmons in Hole-Doped Lanthanum and Bismuth Cuprate Superconductors Using Resonant Inelastic X-Ray Scattering.

High T_{c} superconductors show a rich variety of phases associated with their charge degrees of freedom. Valence charges can give rise to charge ordering or acoustic plasmons in these layered cuprate superconductors. While charge ordering has been observed for both hole- and electron-doped cuprates, acoustic plasmons have only been found in electron-doped materials. Here, we use resonant inelastic x-ray scattering to observe the presence of acoustic plasmons in two families of hole-doped cuprate superconductors (La_{1.84}Sr_{0.16}CuO_{4} and Bi_{2}Sr_{1.6}La_{0.4}CuO_{6+δ}), crucially completing the picture. Interestingly, in contrast to the quasistatic charge ordering which manifests at both Cu and O sites, the observed acoustic plasmons are predominantly associated with the O sites, revealing a unique dichotomy in the behavior of valence charges in hole-doped cuprates.

New insights into the genetics of primary open-angle glaucoma based on meta-analyses of intraocular pressure and optic disc characteristics.

Primary open-angle glaucoma (POAG), the most common optic neuropathy, is a heritable disease. Siblings of POAG cases have a ten-fold increased risk of developing the disease. Intraocular pressure (IOP) and optic nerve head characteristics are used clinically to predict POAG risk. We conducted a genome-wide association meta-analysis of IOP and optic disc parameters and validated our findings in multiple sets of POAG cases and controls. Using imputation to the 1000 genomes (1000G) reference set, we identified 9 new genomic regions associated with vertical cup-disc ratio (VCDR) and 1 new region associated with IOP. Additionally, we found 5 novel loci for optic nerve cup area and 6 for disc area. Previously it was assumed that genetic variation influenced POAG either through IOP or via changes to the optic nerve head; here we present evidence that some genomic regions affect both IOP and the disc parameters. We characterized the effect of the novel loci through pathway analysis and found that pathways involved are not entirely distinct as assumed so far. Further, we identified a novel association between CDKN1A and POAG. Using a zebrafish model we show that six6b (associated with POAG and optic nerve head variation) alters the expression of cdkn1a. In summary, we have identified several novel genes influencing the major clinical risk predictors of POAG and showed that genetic variation in CDKN1A is important in POAG risk.

Genome-wide association study of primary open-angle glaucoma in continental and admixed African populations.

Primary open angle glaucoma (POAG) is a complex disease with a major genetic contribution. Its prevalence varies greatly among ethnic groups, and is up to five times more frequent in black African populations compared to Europeans. So far, worldwide efforts to elucidate the genetic complexity of POAG in African populations has been limited. We conducted a genome-wide association study in 1113 POAG cases and 1826 controls from Tanzanian, South African and African American study samples. Apart from confirming evidence of association at TXNRD2 (rs16984299; OR[T] 1.20; P = 0.003), we found that a genetic risk score combining the effects of the 15 previously reported POAG loci was significantly associated with POAG in our samples (OR 1.56; 95% CI 1.26-1.93; P = 4.79 × 10-5). By genome-wide association testing we identified a novel candidate locus, rs141186647, harboring EXOC4 (OR[A] 0.48; P = 3.75 × 10-8), a gene transcribing a component of the exocyst complex involved in vesicle transport. The low frequency and high degree of genetic heterogeneity at this region hampered validation of this finding in predominantly West-African replication sets. Our results suggest that established genetic risk factors play a role in African POAG, however, they do not explain the higher disease load. The high heterogeneity within Africans remains a challenge to identify the genetic commonalities for POAG in this ethnicity, and demands studies of extremely large size.

Haplotype reference consortium panel: Practical implications of imputations with large reference panels.

Recently, the Haplotype Reference Consortium (HRC) released a large imputation panel that allows more accurate imputation of genetic variants. In this study, we compared a set of directly assayed common and rare variants from an exome array to imputed genotypes, that is, 1000 genomes project (1000GP) and HRC. We showed that imputation using the HRC panel improved the concordance between assayed and imputed genotypes at common, and especially, low-frequency variants. Furthermore, we performed a genome-wide association meta-analysis of vertical cup-disc ratio, a highly heritable endophenotype of glaucoma, in four cohorts using 1000GP and HRC imputations. We compared the results of the meta-analysis using 1000GP to the meta-analysis results using HRC. Overall, we found that using HRC imputation significantly improved P values (P = 3.07 × 10-61 ), particularly for suggestive variants. Both meta-analyses were performed in the same sample size, yet we found eight genome-wide significant loci in the HRC-based meta-analysis versus seven genome-wide significant loci in the 1000GP-based meta-analysis. This study provides supporting evidence of the new avenues for gene discovery and fine mapping that the HRC imputation panel offers.

Evaluation of the Myocilin Mutation Gln368Stop Demonstrates Reduced Penetrance for Glaucoma in European Populations.

PURPOSE: Sequence variations in the myocilin (MYOC) gene account for approximately 2% to 4% of glaucoma cases. One particular MYOC mutation, Gln368Stop (dbSNP accession number: rs74315329), is the most common genetic mutation causing glaucoma by increasing intraocular pressure (IOP). The objective of this study was to evaluate the effect of this MYOC mutation on IOP using data from large-scale European population panels (directly sequenced and imputation based). DESIGN: Cross-sectional, cohort study. PARTICIPANTS: For this study, the penetrance of the variant rs74315329 was estimated in 2 population-based cohorts, the TwinsUK (N = 6092) and the Rotterdam Study (RS) (N =11 189). METHODS: Carriers of the risk allele for rs74315329 were identified using whole-genome sequencing and imputation data (based on 1000 Genomes Project and Haplotype Reference Consortium panels). The penetrance of this variant was evaluated using IOP measurements and data on visual field testing/a diagnosis of glaucoma (if available). MAIN OUTCOME MEASURES: The penetrance of the variant rs74315329 was estimated from the percentage of the carriers of the risk allele of the variant who had high IOP (ocular hypertension) or glaucoma. RESULTS: In our study, the observed penetrance of the variant rs74315329 in relation to increased IOP was 12.5% and 19.4% in the TwinsUK and the RS, respectively. Thus, our study suggests a much lower penetrance for rs74315329 for ocular hypertension (and thus glaucoma), in comparison with that reported previously. CONCLUSIONS: The significance of this finding is that higher numbers of healthy individuals in the population are expected to be carriers of this mutation, which in turn reduces the utility of identifying carriers of this mutation as a screening tool for glaucoma.

Meta-analysis of Genome-Wide Association Studies Identifies Novel Loci Associated With Optic Disc Morphology.

Primary open-angle glaucoma is the most common optic neuropathy and an important cause of irreversible blindness worldwide. The optic nerve head or optic disc is divided in two parts: a central cup (without nerve fibers) surrounded by the neuroretinal rim (containing axons of the retinal ganglion cells). The International Glaucoma Genetics Consortium conducted a meta-analysis of genome-wide association studies consisting of 17,248 individuals of European ancestry and 6,841 individuals of Asian ancestry. The outcomes of the genome-wide association studies were disc area and cup area. These specific measurements describe optic nerve morphology in another way than the vertical cup-disc ratio, which is a clinically used measurement, and may shed light on new glaucoma mechanisms. We identified 10 new loci associated with disc area (CDC42BPA, F5, DIRC3, RARB, ABI3BP, DCAF4L2, ELP4, TMTC2, NR2F2, and HORMAD2) and another 10 new loci associated with cup area (DHRS3, TRIB2, EFEMP1, FLNB, FAM101, DDHD1, ASB7, KPNB1, BCAS3, and TRIOBP). The new genes participate in a number of pathways and future work is likely to identify more functions related to the pathogenesis of glaucoma.