Stratified genome-wide association analysis of type 2 diabetes reveals subgroups with genetic and environmental heterogeneity

Type 2 diabetes (T2D) is a heterogeneous illness caused by genetic and environmental factors. Previous genome wide association studies (GWAS) have identified many genetic variants associated with T2D and found evidence of differing genetic profiles by age-at-onset. This study seeks to explore further the genetic and environmental drivers of T2D by analysing subgroups based on age-at-onset of diabetes and body mass index (BMI). In UK Biobank, 36 494 T2D cases were stratified into 3 subgroups and GWAS performed for all T2D cases and for each subgroup relative to 421 021 controls. Altogether, 18 SNPs significantly associated genome-wide with T2D in one or more subgroups also showed evidence of heterogeneity between the subgroups, (Cochrane's Q p < 0.01) with 2 remaining significant after multiple testing (in CDKN2B and CYTIP). Combined risk scores, based on genetic profile, BMI and age, resulted in excellent diabetes prediction (AUC = 0.92). A modest improvement in prediction (AUC = 0.93) was seen when the contribution of genetic and environmental factors was evaluated separately for each subgroup. Increasing sample sizes of genetic studies enables us to stratify disease cases into subgroups which have sufficient power to highlight areas of genetic heterogeneity. Despite some evidence that optimising combined risk scores by subgroup improves prediction, larger sample sizes are likely needed for prediction when using a stratification approach

Stratified genome-wide association analysis of Type 2 Diabetes reveals subgroups with genetic and environmental heterogeneity

Type 2 diabetes (T2D) is a heterogeneous illness caused by genetic and environmental factors. Previous genome wide association studies (GWAS) have identified many genetic variants associated with T2D and found evidence of differing genetic profiles by age-at-onset. This study seeks to explore further the genetic and environmental drivers of T2D by analysing subgroups based on age-at-onset of diabetes and body mass index (BMI). In UK Biobank, 36 494 T2D cases were stratified into 3 subgroups and GWAS performed for all T2D cases and for each subgroup relative to 421 021 controls. Altogether, 18 SNPs significantly associated genome-wide with T2D in one or more subgroups also showed evidence of heterogeneity between the subgroups, (Cochrane’s Q p < 0.01) with 2 remaining significant after multiple testing (in CDKN2B and CYTIP). Combined risk scores, based on genetic profile, BMI and age, resulted in excellent diabetes prediction (AUC = 0.92). A modest improvement in prediction (AUC = 0.93) was seen when the contribution of genetic and environmental factors was evaluated separately for each subgroup. Increasing sample sizes of genetic studies enables us to stratify disease cases into subgroups which have sufficient power to highlight areas of genetic heterogeneity. Despite some evidence that optimising combined risk scores by subgroup improves prediction, larger sample sizes are likely needed for prediction when using a stratification approach

Stratified genome-wide association analysis of type 2 diabetes reveals subgroups with genetic and environmental heterogeneity

Type 2 diabetes (T2D) is a heterogeneous illness caused by genetic and environmental factors. Previous genome wide association studies (GWAS) have identified many genetic variants associated with T2D and found evidence of differing genetic profiles by age-at-onset. This study seeks to explore further the genetic and environmental drivers of T2D by analysing subgroups based on age-at-onset of diabetes and body mass index (BMI). In UK Biobank, 36 494 T2D cases were stratified into 3 subgroups and GWAS performed for all T2D cases and for each subgroup relative to 421 021 controls. Altogether, 18 SNPs significantly associated genome-wide with T2D in one or more subgroups also showed evidence of heterogeneity between the subgroups, (Cochrane’s Q p < 0.01) with 2 remaining significant after multiple testing (in CDKN2B and CYTIP). Combined risk scores, based on genetic profile, BMI and age, resulted in excellent diabetes prediction (AUC = 0.92). A modest improvement in prediction (AUC = 0.93) was seen when the contribution of genetic and environmental factors was evaluated separately for each subgroup. Increasing sample sizes of genetic studies enables us to stratify disease cases into subgroups which have sufficient power to highlight areas of genetic heterogeneity. Despite some evidence that optimising combined risk scores by subgroup improves prediction, larger sample sizes are likely needed for prediction when using a stratification approach

A diamond nanophotonic interface with an optically accessible deterministic electronuclear spin register

A contemporary challenge for the scalability of quantum networks is developing quantum nodes with simultaneous high photonic efficiency and long-lived qubits. Here, we present a fibre-packaged nanophotonic diamond waveguide hosting a tin-vacancy centre with a spin-1/2 $^{117}$Sn nucleus. The interaction between the electronic and nuclear spins results in a signature 452(7) MHz hyperfine splitting. This exceeds the natural optical linewidth by a factor of 16, enabling direct optical nuclear-spin initialisation with 98.6(3)% fidelity and single-shot readout with 80(1)% fidelity. The waveguide-to-fibre extraction efficiency of our device of 57(6)% enables the practical detection of 5-photon events. Combining the photonic performance with the optically initialised nuclear spin, we demonstrate a spin-gated single-photon nonlinearity with 11(1)% contrast in the absence of an external magnetic field. These capabilities position our nanophotonic interface as a versatile quantum node in the pursuit of scalable quantum networks

Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria.

Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community

Methylome-wide association study of early life stressors and adult mental health

The environment and events that we are exposed to in utero, during birth and in early childhood influence our future physical and mental health. The underlying mechanisms that lead to these outcomes are unclear, but long-term changes in epigenetic marks, such as DNA methylation, could act as a mediating factor or biomarker. DNA methylation data were assayed at 713 522 CpG sites from 9537 participants of the Generation Scotland: Scottish Family Health Study, a family-based cohort with extensive genetic, medical, family history and lifestyle information. Methylome-wide association studies of eight early life environment phenotypes and two adult mental health phenotypes (major depressive disorder and brief resilience scale) were conducted using DNA methylation data collected from adult whole blood samples. Two genes involved with different developmental pathways (PRICKLE2, Prickle Planar Cell Polarity Protein 2 and ABI1, Abl-Interactor-1) were annotated to CpG sites associated with preterm birth (P < 1.27 × 10(−9)). A further two genes important to the development of sensory pathways (SOBP, Sine Oculis Binding Protein Homolog and RPGRIP1, Retinitis Pigmentosa GTPase Regulator Interacting Protein) were annotated to sites associated with low birth weight (P < 4.35 × 10(−8)). The examination of methylation profile scores and genes and gene-sets annotated from associated CpGs sites found no evidence of overlap between the early life environment and mental health conditions. Birth date was associated with a significant difference in estimated lymphocyte and neutrophil counts. Previous studies have shown that early life environments influence the risk of developing mental health disorders later in life; however, this study found no evidence that this is mediated by stable changes to the methylome detectable in peripheral blood

Hyperfine Spectroscopy of Isotopically Engineered Group-IV Color Centers in Diamond

A quantum register coupled to a spin-photon interface is a key component in quantum communication and information processing. Group-IV color centers in diamond (SiV, GeV, and SnV) are promising candidates for this application, comprising an electronic spin with optical transitions coupled to a nuclear spin as the quantum register. However, the creation of a quantum register for these color centers with deterministic and strong coupling to the spin-photon interface remains challenging. Here, we make first-principles predictions of the hyperfine parameters of the group-IV color centers, which we verify experimentally with a comprehensive comparison between the spectra of spin active and spin neutral intrinsic dopant nuclei in single GeV and SnV emitters. In line with the theoretical predictions, detailed spectroscopy on large sample sizes reveals that hyperfine coupling causes a splitting of the optical transition of SnV an order of magnitude larger than the optical linewidth and provides a magnetic-field insensitive transition. This strong coupling provides access to a new regime for quantum registers in diamond color centers, opening avenues for novel spin-photon entanglement and quantum sensing schemes for these well-studied emitters

Microwave-based quantum control and coherence protection of tin-vacancy spin qubits in a strain-tuned diamond membrane heterostructure

Robust spin-photon interfaces in solids are essential components in quantum networking and sensing technologies. Ideally, these interfaces combine a long-lived spin memory, coherent optical transitions, fast and high-fidelity spin manipulation, and straightforward device integration and scaling. The tin-vacancy center (SnV) in diamond is a promising spin-photon interface with desirable optical and spin properties at 1.7 K. However, the SnV spin lacks efficient microwave control and its spin coherence degrades with higher temperature. In this work, we introduce a new platform that overcomes these challenges - SnV centers in uniformly strained thin diamond membranes. The controlled generation of crystal strain introduces orbital mixing that allows microwave control of the spin state with 99.36(9) % gate fidelity and spin coherence protection beyond a millisecond. Moreover, the presence of crystal strain suppresses temperature dependent dephasing processes, leading to a considerable improvement of the coherence time up to 223(10) ${\mu}$s at 4 K, a widely accessible temperature in common cryogenic systems. Critically, the coherence of optical transitions is unaffected by the elevated temperature, exhibiting nearly lifetime-limited optical linewidths. Combined with the compatibility of diamond membranes with device integration, the demonstrated platform is an ideal spin-photon interface for future quantum technologies