Mitigating type 1 error inflation and power loss in GxE PRS: Genotype-environment interaction in polygenic risk score models.

The use of polygenic risk score (PRS) models has transformed the field of genetics by enabling the prediction of complex traits and diseases based on an individual's genetic profile. However, the impact of genotype-environment interaction (GxE) on the performance and applicability of PRS models remains a crucial aspect to be explored. Currently, existing genotype-environment interaction polygenic risk score (GxE PRS) models are often inappropriately used, which can result in inflated type 1 error rates and compromised results. In this study, we propose novel GxE PRS models that jointly incorporate additive and interaction genetic effects although also including an additional quadratic term for nongenetic covariates, enhancing their robustness against model misspecification. Through extensive simulations, we demonstrate that our proposed models outperform existing models in terms of controlling type 1 error rates and enhancing statistical power. Furthermore, we apply the proposed models to real data, and report significant GxE effects. Specifically, we highlight the impact of our models on both quantitative and binary traits. For quantitative traits, we uncover the GxE modulation of genetic effects on body mass index by alcohol intake frequency. In the case of binary traits, we identify the GxE modulation of genetic effects on hypertension by waist-to-hip ratio. These findings underscore the importance of employing a robust model that effectively controls type 1 error rates, thus preventing the occurrence of spurious GxE signals. To facilitate the implementation of our approach, we have developed an innovative R software package called GxEprs, specifically designed to detect and estimate GxE effects. Overall, our study highlights the importance of accurate GxE modeling and its implications for genetic risk prediction, although providing a practical tool to support further research in this area.

Unraveling phenotypic variance in metabolic syndrome through multi-omics.

Complex multi-omics effects drive the clustering of cardiometabolic risk factors, underscoring the imperative to comprehend how individual and combined omics shape phenotypic variation. Our study partitions phenotypic variance in metabolic syndrome (MetS), blood glucose (GLU), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and blood pressure through genome, transcriptome, metabolome, and exposome (i.e., lifestyle exposome) analyses. Our analysis included a cohort of 62,822 unrelated individuals with white British ancestry, sourced from the UK biobank. We employed linear mixed models to partition phenotypic variance using the restricted maximum likelihood (REML) method, implemented in MTG2 (v2.22). We initiated the analysis by individually modeling omics, followed by subsequent integration of pairwise omics in a joint model that also accounted for the covariance and interaction between omics layers. Finally, we estimated the correlations of various omics effects between the phenotypes using bivariate REML. Significant proportions of the MetS variance were attributed to distinct data sources: genome (9.47%), transcriptome (4.24%), metabolome (14.34%), and exposome (3.77%). The phenotypic variances explained by the genome, transcriptome, metabolome, and exposome ranged from 3.28% for GLU to 25.35% for HDL-C, 0% for GLU to 19.34% for HDL-C, 4.29% for systolic blood pressure (SBP) to 35.75% for TG, and 0.89% for GLU to 10.17% for HDL-C, respectively. Significant correlations were found between genomic and transcriptomic effects for TG and HDL-C. Furthermore, significant interaction effects between omics data were detected for both MetS and its components. Interestingly, significant correlation of omics effect between the phenotypes was found. This study underscores omics' roles, interaction effects, and random-effects covariance in unveiling phenotypic variation in multi-omics domains.

Cross-ancestry genetic architecture and prediction for cholesterol traits.

While cholesterol is essential, a high level of cholesterol is associated with the risk of cardiovascular diseases. Genome-wide association studies (GWASs) have proven successful in identifying genetic variants that are linked to cholesterol levels, predominantly in white European populations. However, the extent to which genetic effects on cholesterol vary across different ancestries remains largely unexplored. Here, we estimate cross-ancestry genetic correlation to address questions on how genetic effects are shared across ancestries. We find significant genetic heterogeneity between ancestries for cholesterol traits. Furthermore, we demonstrate that single nucleotide polymorphisms (SNPs) with concordant effects across ancestries for cholesterol are more frequently found in regulatory regions compared to other genomic regions. Indeed, the positive genetic covariance between ancestries is mostly driven by the effects of the concordant SNPs, whereas the genetic heterogeneity is attributed to the discordant SNPs. We also show that the predictive ability of the concordant SNPs is significantly higher than the discordant SNPs in the cross-ancestry polygenic prediction. The list of concordant SNPs for cholesterol is available in GWAS Catalog. These findings have relevance for the understanding of shared genetic architecture across ancestries, contributing to the development of clinical strategies for polygenic prediction of cholesterol in cross-ancestral settings.

Uncovering Predictors of Low Hippocampal Volume: Evidence from a Large-Scale Machine-Learning-Based Study in the UK Biobank.

INTRODUCTION: Hippocampal atrophy is an established biomarker for conversion from the normal ageing process to developing cognitive impairment and dementia. This study used a novel hypothesis-free machine-learning approach, to uncover potential risk factors of lower hippocampal volume using information from the world's largest brain imaging study. METHODS: A combination of machine learning and conventional statistical methods were used to identify predictors of low hippocampal volume. We run gradient boosting decision tree modelling including 2,891 input features measured before magnetic resonance imaging assessments (median 9.2 years, range 4.2-13.8 years) using data from 42,152 dementia-free UK Biobank participants. Logistic regression analyses were run on 87 factors identified as important for prediction based on Shapley values. False discovery rate-adjusted p value <0.05 was used to declare statistical significance. RESULTS: Older age, male sex, greater height, and whole-body fat-free mass were the main predictors of low hippocampal volume with the model also identifying associations with lung function and lifestyle factors including smoking, physical activity, and coffee intake (corrected p < 0.05 for all). Red blood cell count and several red blood cell indices such as haemoglobin concentration, mean corpuscular haemoglobin, mean corpuscular volume, mean reticulocyte volume, mean sphered cell volume, and red blood cell distribution width were among many biomarkers associated with low hippocampal volume. CONCLUSION: Lifestyles, physical measures, and biomarkers may affect hippocampal volume, with many of the characteristics potentially reflecting oxygen supply to the brain. Further studies are required to establish causality and clinical relevance of these findings.

LLpowershap: logistic loss-based automated Shapley values feature selection method.

BACKGROUND: Shapley values have been used extensively in machine learning, not only to explain black box machine learning models, but among other tasks, also to conduct model debugging, sensitivity and fairness analyses and to select important features for robust modelling and for further follow-up analyses. Shapley values satisfy certain axioms that promote fairness in distributing contributions of features toward prediction or reducing error, after accounting for non-linear relationships and interactions when complex machine learning models are employed. Recently, feature selection methods using predictive Shapley values and p-values have been introduced, including powershap. METHODS: We present a novel feature selection method, LLpowershap, that takes forward these recent advances by employing loss-based Shapley values to identify informative features with minimal noise among the selected sets of features. We also enhance the calculation of p-values and power to identify informative features and to estimate number of iterations of model development and testing. RESULTS: Our simulation results show that LLpowershap not only identifies higher number of informative features but outputs fewer noise features compared to other state-of-the-art feature selection methods. Benchmarking results on four real-world datasets demonstrate higher or comparable predictive performance of LLpowershap compared to other Shapley based wrapper methods, or filter methods. LLpowershap is also ranked the best in mean ranking among the seven feature selection methods tested on the benchmark datasets. CONCLUSION: Our results demonstrate that LLpowershap is a viable wrapper feature selection method that can be used for feature selection in large biomedical datasets and other settings.

Large-scale analysis to identify risk factors for ovarian cancer.

OBJECTIVE: Ovarian cancer is characterized by late-stage diagnoses and poor prognosis. We aimed to identify factors that can inform prevention and early detection of ovarian cancer. METHODS: We used a data-driven machine learning approach to identify predictors of epithelial ovarian cancer from 2920 input features measured 12.6 years (IQR 11.9 to 13.3 years) before diagnoses. Analyses included 221 732 female participants in the UK Biobank without a history of cancer. During the follow-up 1441 women developed ovarian cancer. For factors that contributed to model prediction, we used multivariate logistic regression to evaluate the association with ovarian cancer, with evidence for causality tested by Mendelian randomization (MR) analyses in the Ovarian Cancer Genetics Consortium (25 509 cases). RESULTS: Greater parity and ever-use of oral contraception were associated with lower ovarian cancer risk (ever vs never OR 0.74, 95% CI 0.66 to 0.84). After adjustment for established risk factors, greater height, weight, and greater red blood cell distribution width were associated with increased ovarian cancer risk, while higher aspartate aminotransferase levels and mean corpuscular volume were associated with lower risk. MR analyses confirmed observational associations with anthropometric/adiposity traits (eg, body fat percentage per standard deviation (SD); OR inverse-variance weighted (ORIVW) 1.28, 95% CI 1.13 to 1.46) and aspartate aminotransferase (ORIVW 0.87, 95% CI 0.78 to 0.98). MR also provided genetic evidence for a protective association of higher total serum protein on ovarian cancer, higher lymphocyte count on serous and endometrioid ovarian cancer, and greater forced expiratory volume in 1 s on serous ovarian cancer among other findings. CONCLUSIONS: This study shows that certain risk factors for ovarian cancer are modifiable, suggesting that weight reduction and interventions to reduce the number of ovulations may provide potential for future prevention. We also identified blood biomarkers associated with ovarian cancer years before diagnoses, warranting further investigation.

Hypothesis-free discovery of novel cancer predictors using machine learning.

BACKGROUND: Cancer is a leading cause of morbidity and mortality worldwide, and better understanding of the risk factors could enhance prevention. METHODS: We conducted a hypothesis-free analysis combining machine learning and statistical approaches to identify cancer risk factors from 2828 potential predictors captured at baseline. There were 459,169 UK Biobank participants free from cancer at baseline and 48,671 new cancer cases during the 10-year follow-up. Logistic regression models adjusted for age, sex, ethnicity, education, material deprivation, smoking, alcohol intake, body mass index and skin colour (as a proxy for sun sensitivity) were used for obtaining adjusted odds ratios, with continuous predictors presented using quintiles (Q). RESULTS: In addition to smoking, older age and male sex, positively associating features included several anthropometric characteristics, whole body water mass, pulse, hypertension and biomarkers such as urinary microalbumin (Q5 vs. Q1 OR 1.16, 95% CI = 1.13-1.19), C-reactive protein (Q5 vs. Q1 OR 1.20, 95% CI = 1.16-1.24) and red blood cell distribution width (Q5 vs. Q1 OR 1.18, 95% CI = 1.14-1.21), among others. High-density lipoprotein cholesterol (Q5 vs. Q1 OR 0.84, 95% CI = 0.81-0.87) and albumin (Q5 vs. Q1 OR 0.84, 95% CI = 0.81-0.87) were inversely associated with cancer. In sex-stratified analyses, higher testosterone increased the risk in females but not in males (Q5 vs. Q1 ORfemales 1.23, 95% CI = 1.17-1.30). Phosphate was associated with a lower risk in females but a higher risk in males (Q5 vs. Q1 ORfemales 0.94, 95% CI = 0.90-0.99 vs. ORmales 1.09, 95% CI 1.04-1.15). CONCLUSIONS: This hypothesis-free analysis suggests personal characteristics, metabolic biomarkers, physical measures and smoking as important predictors of cancer risk, with further studies needed to confirm causality and clinical relevance.

Metabolic profile-based subgroups can identify differences in brain volumes and brain iron deposition.

AIMS: To evaluate associations of metabolic profiles and biomarkers with brain atrophy, lesions, and iron deposition to understand the early risk factors associated with dementia. MATERIALS AND METHODS: Using data from 26 239 UK Biobank participants free from dementia and stroke, we assessed the associations of metabolic subgroups, derived using an artificial neural network approach (self-organizing map), and 39 individual biomarkers with brain MRI measures: total brain volume (TBV), grey matter volume (GMV), white matter volume (WMV), hippocampal volume (HV), white matter hyperintensity (WMH) volume, and caudate iron deposition. RESULTS: In metabolic subgroup analyses, participants characterized by high triglycerides and liver enzymes showed the most adverse brain outcomes compared to the healthy reference subgroup with high-density lipoprotein cholesterol and low body mass index (BMI) including associations with GMV (ßstandardized -0.20, 95% confidence interval [CI] -0.24 to -0.16), HV (ßstandardized -0.09, 95% CI -0.13 to -0.04), WMH volume (ßstandardized 0.22, 95% CI 0.18 to 0.26), and caudate iron deposition (ßstandardized 0.30, 95% CI 0.25 to 0.34), with similar adverse associations for the subgroup with high BMI, C-reactive protein and cystatin C, and the subgroup with high blood pressure (BP) and apolipoprotein B. Among the biomarkers, striking associations were seen between basal metabolic rate (BMR) and caudate iron deposition (ßstandardized 0.23, 95% CI 0.22 to 0.24 per 1 SD increase), GMV (ßstandardized -0.15, 95% CI -0.16 to -0.14) and HV (ßstandardized -0.11, 95% CI -0.12 to -0.10), and between BP and WMH volume (ßstandardized 0.13, 95% CI 0.12 to 0.14 for diastolic BP). CONCLUSIONS: Metabolic profiles were associated differentially with brain neuroimaging characteristics. Associations of BMR, BP and other individual biomarkers may provide insights into actionable mechanisms driving these brain associations.

Do Chronic Low Back Pain and Chronic Widespread Pain differ in their association with Depression Symptoms in the 1958 British Cohort?

OBJECTIVE: Depression frequently coexists with chronic pain. Contemporary models suggest that these conditions share pathobiological mechanisms, prompting a need to investigate their temporal association. This investigation aimed to explore two distinctly different chronic pain conditions, and their cross-sectional and prospective associations with depression. METHODS: Self-reported information was available on chronic widespread pain (CWP), chronic low back pain (CLBP) (45 years), and depression symptoms (45 and 50 years) from up to 9,377 participants in the 1958 British cohort. Depression symptom outcomes were derived by "Clinical Interview Schedule-Revised" (45 years) and "Short Form-36" (50 years). Relationships between both chronic pain conditions and depression symptoms were investigated by fitting four separate logistic regression models, each with varying levels of covariate adjustment, including depression at baseline. RESULTS: CWP was associated with depression symptoms cross-sectionally (odds ratio [OR] = 2.04, 95% confidence interval [CI] 1.65, 2.52; P < 0.001, n = 7,629), and prospectively when fully adjusted for baseline, sociodemographic, lifestyle, and health covariates (OR = 1.45, 95% CI 1.17, 1.80; P = < 0.001, n = 6,275). CLBP was associated with depression symptoms prospectively (full model: OR = 1.28, 95% CI 1.01, 1.61; P = 0.04, n = 6,288). In fully adjusted models the prospective association of CWP with depression symptoms was more heavily influenced by our covariates than CLBP with depression symptoms. CONCLUSION: Pain may be a stressor from which depression can arise. Development of depression may be differentially dependant upon the type of pain experienced. Screening for depression symptoms among individuals with both chronic pain conditions is indicated and should be repeated over time.

Vitamin D Deficiency Increases Mortality Risk in the UK Biobank : A Nonlinear Mendelian Randomization Study.

BACKGROUND: Low vitamin D status is associated with increased mortality, but randomized trials on severely deficient participants are lacking. OBJECTIVE: To assess genetic evidence for the causal role of low vitamin D status in mortality. DESIGN: Nonlinear Mendelian randomization analyses. SETTING: UK Biobank, a large-scale, prospective cohort from England, Scotland, and Wales with participants recruited between March 2006 and July 2010. PARTICIPANTS: 307 601 unrelated UK Biobank participants of White European ancestry (aged 37 to 73 years at recruitment) with available measurements of 25-hydroxyvitamin D (25-(OH)D) and genetic data. MEASUREMENTS: Genetically predicted 25-(OH)D was estimated using 35 confirmed variants of 25-(OH)D. All-cause and cause-specific mortality (cardiovascular disease [CVD], cancer, and respiratory) were recorded up to June 2020. RESULTS: There were 18 700 deaths during the 14 years of follow-up. The association of genetically predicted 25-(OH)D with all-cause mortality was L-shaped (P for nonlinearity < 0.001), and risk for death decreased steeply with increasing concentrations until 50 nmol/L. Evidence for an association was also seen in analyses of mortality from cancer, CVD, and respiratory diseases (P ≤ 0.033 for all outcomes). Odds of all-cause mortality in the genetic analysis were estimated to increase by 25% (odds ratio, 1.25 [95% CI, 1.16 to 1.35]) for participants with a measured 25-(OH)D concentration of 25 nmol/L compared with 50 nmol/L. LIMITATIONS: Analyses were restricted to a White European population. A genetic approach is best suited to providing proof of principle on causality, whereas the strength of the association is approximate. CONCLUSION: Our study supports a causal relationship between vitamin D deficiency and mortality. Additional research needs to identify strategies that meet the National Academy of Medicine's guideline of greater than 50 nmol/L and that reduce the premature risk for death associated with low vitamin D levels. PRIMARY FUNDING SOURCE: National Health and Medical Research Council.

Non-linear Mendelian randomization analyses support a role for vitamin D deficiency in cardiovascular disease risk.

AIMS: Low vitamin D status is associated with a higher risk for cardiovascular diseases (CVDs). Although most existing linear Mendelian randomization (MR) studies reported a null effect of vitamin D on CVD risk, a non-linear effect cannot be excluded. Our aim was to apply the non-linear MR design to investigate the association of serum 25-hydroxyvitamin D [25(OH)D] concentration with CVD risk. METHODS AND RESULTS: The non-linear MR analysis was conducted in the UK Biobank with 44 519 CVD cases and 251 269 controls. Blood pressure (BP) and cardiac-imaging-derived phenotypes were included as secondary outcomes. Serum 25(OH)D concentration was instrumented using 35 confirmed genome-wide significant variants.We also estimated the potential reduction in CVD incidence attributable to correction of low vitamin D status. There was a L-shaped association between genetically predicted serum 25(OH)D and CVD risk (Pnon-linear = 0.007), where CVD risk initially decreased steeply with increasing concentrations and levelled off at around 50 nmol/L. A similar association was seen for systolic (Pnon-linear = 0.03) and diastolic (Pnon-linear = 0.07) BP. No evidence of association was seen for cardiac-imaging phenotypes (P = 0.05 for all). Correction of serum 25(OH)D level below 50 nmol/L was predicted to result in a 4.4% reduction in CVD incidence (95% confidence interval: 1.8- 7.3%). CONCLUSION: Vitamin D deficiency can increase the risk of CVD. Burden of CVD could be reduced by population-wide correction of low vitamin D status.

Estimating the influence of body mass index (BMI) on mortality using offspring BMI as an instrumental variable.

OBJECTIVE: High body mass index (BMI) is an important predictor of mortality but estimating underlying causality is hampered by confounding and pre-existing disease. Here, we use information from the offspring to approximate parental BMIs, with an aim to avoid biased estimation of mortality risk caused by reverse causality. METHODS: The analyses were based on information on 9674 offspring-mother and 9096 offspring-father pairs obtained from the 1958 British birth cohort. Parental BMI-mortality associations were analysed using conventional methods and using offspring BMI as a proxy, or instrument, for their parents' BMI. RESULTS: In the conventional analysis, associations between parental BMI and all-cause mortality were U-shaped (Pcurvature < 0.001), while offspring BMI had linear associations with parental mortality (Ptrend < 0.001, Pcurvature > 0.46). Curvature was particularly pronounced for mortality from respiratory diseases and from lung cancer. Instrumental variable analyses suggested a positive association between BMI and mortality from all causes [mothers: HR per SD of BMI 1.43 (95% CI 1.21-1.69), fathers: HR 1.17 (1.00-1.36)] and from coronary heart disease [mothers: HR 1.65 (1.15-2.36), fathers: HR 1.51 (1.17-1.97)]. These were larger than HR from the equivalent conventional analyses, despite some attenuation by adjustment for social indicators and smoking. CONCLUSIONS: Analyses using offspring BMI as a proxy for parental BMI suggest that the apparent adverse consequences of low BMI are considerably overestimated and adverse consequences of overweight are underestimated in conventional epidemiological studies.

High coffee consumption, brain volume and risk of dementia and stroke.

BACKGROUND: Coffee is a highly popular beverage worldwide, containing caffeine which is a central nervous system stimulant. OBJECTIVES: We examined whether habitual coffee consumption is associated with differences in brain volumes or the odds of dementia or stroke. METHODS: We conducted prospective analyses of habitual coffee consumption on 398,646 UK Biobank participants (age 37-73 years), including 17,702 participants with MRI information. We examined the associations with brain volume using covariate adjusted linear regression, and with odds of dementia (4,333 incident cases) and stroke (6,181 incident cases) using logistic regression. RESULTS: There were inverse linear associations between habitual coffee consumption and total brain (fully adjusted ß per cup -1.42, 95% CI -1.89, -0.94), grey matter (ß -0.91, 95% CI -1.20, -0.62), white matter (ß -0.51, 95% CI -0.83, -0.19) and hippocampal volumes (ß -0.01, 95% CI -0.02, -0.003), but no evidence to support an association with white matter hyperintensity (WMH) volume (ß -0.01, 95% CI -0.07, 0.05). The association between coffee consumption and dementia was non-linear (Pnon-linearity = 0.0001), with evidence for higher odds for non-coffee and decaffeinated coffee drinkers and those drinking >6 cups/day, compared to light coffee drinkers. After full covariate adjustment, consumption of >6 cups/day was associated with 53% higher odds of dementia compared to consumption of 1-2 cups/day (fully adjusted OR 1.53, 95% CI 1.28, 1.83), with less evidence for an association with stroke (OR 1.17, 95% CI 1.00, 1.37, p = 0.055). CONCLUSION: High coffee consumption was associated with smaller total brain volumes and increased odds of dementia.

Evidence for a causal association between milk intake and cardiometabolic disease outcomes using a two-sample Mendelian Randomization analysis in up to 1,904,220 individuals.

BACKGROUND: High milk intake has been associated with cardio-metabolic risk. We conducted a Mendelian Randomization (MR) study to obtain evidence for the causal relationship between milk consumption and cardio-metabolic traits using the lactase persistence (LCT-13910 C > T, rs4988235) variant as an instrumental variable. METHODS: We tested the association of LCT genotype with milk consumption (for validation) and with cardio-metabolic traits (for a possible causal association) in a meta-analysis of the data from three large-scale population-based studies (1958 British Birth Cohort, Health and Retirement study, and UK Biobank) with up to 417,236 participants and using summary statistics from consortia meta-analyses on intermediate traits (N = 123,665-697,307) and extended to cover disease endpoints (N = 86,995-149,821). RESULTS: In the UK Biobank, carriers of 'T' allele of LCT variant were more likely to consume milk (P = 7.02 × 10-14). In meta-analysis including UK Biobank, the 1958BC, the HRS, and consortia-based studies, under an additive model, 'T' allele was associated with higher body mass index (BMI) (Pmeta-analysis = 4.68 × 10-12) and lower total cholesterol (TC) (P = 2.40 × 10-36), low-density lipoprotein cholesterol (LDL-C) (P = 2.08 × 10-26) and high-density lipoprotein cholesterol (HDL-C) (P = 9.40 × 10-13). In consortia meta-analyses, 'T' allele was associated with a lower risk of coronary artery disease (OR:0.86, 95% CI:0.75-0.99) but not with type 2 diabetes (OR:1.06, 95% CI:0.97-1.16). Furthermore, the two-sample MR analysis showed a causal association between genetically instrumented milk intake and higher BMI (P = 3.60 × 10-5) and body fat (total body fat, leg fat, arm fat and trunk fat; P < 1.37 × 10-6) and lower LDL-C (P = 3.60 × 10-6), TC (P = 1.90 × 10-6) and HDL-C (P = 3.00 × 10-5). CONCLUSIONS: Our large-scale MR study provides genetic evidence for the association of milk consumption with higher BMI but lower serum cholesterol levels. These data suggest no need to limit milk intakes with respect to cardiovascular disease risk, with the suggested benefits requiring confirmation in further studies.

Adiposity and cancer: a Mendelian randomization analysis in the UK biobank.

BACKGROUND: Observational and Mendelian randomization (MR) studies link obesity and cancer, but it remains unclear whether these depend upon related metabolic abnormalities. METHODS: We used information from 321,472 participants in the UK biobank, including 30,561 cases of obesity-related cancer. We constructed three genetic instruments reflecting higher adiposity together with either "unfavourable" (82 SNPs), "favourable" (24 SNPs) or "neutral" metabolic profile (25 SNPs). We looked at associations with 14 types of cancer, previously suggested to be associated with obesity. RESULTS: All genetic instruments had a strong association with BMI (p < 1 × 10-300 for all). The instrument reflecting unfavourable adiposity was also associated with higher CRP, HbA1c and adverse lipid profile, while instrument reflecting metabolically favourable adiposity was associated with lower HbA1c and a favourable lipid profile. In MR-inverse-variance weighted analysis unfavourable adiposity was associated with an increased risk of non-hormonal cancers (OR = 1.22, 95% confidence interval [CI]:1.08, 1.38), but a lower risk of hormonal cancers (OR = 0.80, 95%CI: 0.72, 0.89). From individual cancers, MR analyses suggested causal increases in the risk of multiple myeloma (OR = 1.36, 95%CI: 1.09, 1.70) and endometrial cancer (OR = 1.77, 95%CI: 1.16, 2.68) by greater genetically instrumented unfavourable adiposity but lower risks of breast and prostate cancer (OR = 0.72, 95%CI: 0.61, 0.83 and OR = 0.81, 95%CI: 0.68, 0.97, respectively). Favourable or neutral adiposity were not associated with the odds of any individual cancer. CONCLUSIONS: Higher adiposity associated with a higher risk of non-hormonal cancer but a lower risk of some hormone related cancers. Presence of metabolic abnormalities might aggravate the adverse effects of higher adiposity on cancer. Further studies are warranted to investigate whether interventions on adverse metabolic health may help to alleviate obesity-related cancer risk.

Association between major depressive disorder and multiple disease outcomes: a phenome-wide Mendelian randomisation study in the UK Biobank.

Depression affects all aspects of an individual's life but evidence relating to the causal effects on health is limited. We used information from 337,536 UK Biobank participants and performed hypothesis-free phenome-wide association analyses between major depressive disorder (MDD) genetic risk score (GRS) and 925 disease outcomes. GRS-disease outcome associations passing the multiple-testing corrected significance threshold (P < 1.9 × 10-3) were followed by Mendelian randomisation (MR) analyses to test for causality. MDD GRS was associated with 22 distinct diseases in the phenome-wide discovery stage, with the strongest signal observed for MDD diagnosis and related co-morbidities including anxiety and sleep disorders. In inverse-variance weighted MR analyses, MDD was associated with several inflammatory and haemorrhagic gastrointestinal diseases, including oesophagitis (OR 1.32, 95% CI 1.18-1.48), non-infectious gastroenteritis (OR 1.25, 95% CI 1.06-1.48), gastrointestinal haemorrhage (OR 1.26, 95% CI 1.11-1.43) and intestinal E.coli infections (OR 3.24, 95% CI 1.74-6.02). Signals were also observed for symptoms/disorders of the urinary system (OR 1.36, 95% CI 1.19-1.56), asthma (OR 1.23, 95% CI 1.06-1.44), and painful respiration (OR 1.28, 95% CI 1.14-1.44). MDD was associated with disorders of lipid metabolism (OR 1.22, 95% CI 1.12-1.34) and ischaemic heart disease (OR 1.30, 95% CI 1.15-1.47). Sensitivity analyses excluding pleiotropic variants provided consistent associations. Our study indicates a causal link between MDD and a broad range of diseases, suggesting a notable burden of co-morbidity. Early detection and management of MDD is important, and treatment strategies should be selected to also minimise the risk of related co-morbidities.

A Bidirectional Mendelian Randomization Study to evaluate the causal role of reduced blood vitamin D levels with type 2 diabetes risk in South Asians and Europeans.

CONTEXT: Multiple observational studies have reported an inverse relationship between 25-hydroxyvitamin D concentrations (25(OH)D) and type 2 diabetes (T2D). However, the results of short- and long-term interventional trials concerning the relationship between 25(OH)D and T2D risk have been inconsistent. OBJECTIVES AND METHODS: To evaluate the causal role of reduced blood 25(OH)D in T2D, here we have performed a bidirectional Mendelian randomization study using 59,890 individuals (5,862 T2D cases and 54,028 controls) from European and Asian Indian ancestries. We used six known SNPs, including three T2D SNPs and three vitamin D pathway SNPs, as a genetic instrument to evaluate the causality and direction of the association between T2D and circulating 25(OH)D concentration. RESULTS: Results of the combined meta-analysis of eight participating studies showed that a composite score of three T2D SNPs would significantly increase T2D risk by an odds ratio (OR) of 1.24, p = 1.82 × 10-32; Z score 11.86, which, however, had no significant association with 25(OH)D status (Beta -0.02nmol/L ± SE 0.01nmol/L; p = 0.83; Z score -0.21). Likewise, the genetically instrumented composite score of 25(OH)D lowering alleles significantly decreased 25(OH)D concentrations (-2.1nmol/L ± SE 0.1nmol/L, p = 7.92 × 10-78; Z score -18.68) but was not associated with increased risk for T2D (OR 1.00, p = 0.12; Z score 1.54). However, using 25(OH)D synthesis SNP (DHCR7; rs12785878) as an individual genetic instrument, a per allele reduction of 25(OH)D concentration (-4.2nmol/L ± SE 0.3nmol/L) was predicted to increase T2D risk by 5%, p = 0.004; Z score 2.84. This effect, however, was not seen in other 25(OH)D SNPs (GC rs2282679, CYP2R1 rs12794714) when used as an individual instrument. CONCLUSION: Our new data on this bidirectional Mendelian randomization study suggests that genetically instrumented T2D risk does not cause changes in 25(OH)D levels. However, genetically regulated 25(OH)D deficiency due to vitamin D synthesis gene (DHCR7) may influence the risk of T2D.

Associations of genetically determined iron status across the phenome: A mendelian randomization study.

BACKGROUND: Iron is integral to many physiological processes, and variations in its levels, even within the normal range, can have implications for health. The objective of this study was to explore the broad clinical effects of varying iron status. METHODS AND FINDINGS: Genome-wide association study (GWAS) summary data obtained from 48,972 European individuals (55% female) across 19 cohorts in the Genetics of Iron Status Consortium were used to identify 3 genetic variants (rs1800562 and rs1799945 in the hemochromatosis gene [HFE] and rs855791 in the transmembrane protease serine 6 gene [TMPRSS6]) that associate with increased serum iron, ferritin, and transferrin saturation and decreased transferrin levels, thus serving as instruments for systemic iron status. Phenome-wide association study (PheWAS) of these instruments was performed on 424,439 European individuals (54% female) in the UK Biobank who were aged 40-69 years when recruited from 2006 to 2010, with their genetic data linked to Hospital Episode Statistics (HES) from April, 1995 to March, 2016. Two-sample summary data mendelian randomization (MR) analysis was performed to investigate the effect of varying iron status on outcomes across the human phenome. MR-PheWAS analysis for the 3 iron status genetic instruments was performed separately and then pooled by meta-analysis. Correction was made for testing of multiple correlated phenotypes using a 5% false discovery rate (FDR) threshold. Heterogeneity between MR estimates for different instruments was used to indicate possible bias due to effects of the genetic variants through pathways unrelated to iron status. There were 904 distinct phenotypes included in the MR-PheWAS analyses. After correcting for multiple testing, the 3 genetic instruments for systemic iron status demonstrated consistent evidence of a causal effect of higher iron status on decreasing risk of traits related to anemia (iron deficiency anemia: odds ratio [OR] scaled to a standard deviation [SD] increase in genetically determined serum iron levels 0.72, 95% confidence interval [CI] 0.64-0.81, P = 4 × 10-8) and hypercholesterolemia (hypercholesterolemia: OR 0.88, 95% CI 0.83-0.93, P = 2 × 10-5) and increasing risk of traits related to infection of the skin and related structures (cellulitis and abscess of the leg: OR 1.25, 95% CI 1.10-1.42, P = 6 × 10-4). The main limitations of this study relate to possible bias from pleiotropic effects of the considered genetic variants and misclassification of diagnoses in the HES data. Furthermore, this work only investigated participants with European ancestry, and the findings may not be applicable to other ethnic groups. CONCLUSIONS: Our findings offer novel, to our knowledge, insight into previously unreported effects of iron status, highlighting a potential protective effect of higher iron status on hypercholesterolemia and a detrimental role on risk of skin and skin structure infections. Given the modifiable and variable nature of iron status, these findings warrant further investigation.

Depression increases the genetic susceptibility to high body mass index: Evidence from UK Biobank.

BACKGROUND: This study aimed to explore the association between depression and body mass index (BMI), and to investigate whether genetic susceptibility to high BMI is different among individuals with or without depression. METHODS: We used data on 251,125 individuals of white British ancestry from the UK Biobank. We conducted Mendelian randomization (MR) analysis to test for a causal association between depression and BMI using a major depressive disorder (MDD)-related genetic risk score (GRSMDD ) as an instrument for depression. We also examined whether depression modifies genetic susceptibility to high BMI, by investigating the interaction between depression and the BMI-related GRSBMI . RESULTS: We found observational and genetic evidence for an association between depression and BMI (MR beta: 0.09, 95% confidence interval [CI] 0.04-0.13). Further, the contribution of genetic risk to high BMI was higher among individuals with depression compared to controls. Carrying 10 additional BMI increasing alleles was associated with 0.24 standard deviation (SD; 95%CI 0.23-0.25) higher BMI among depressed individuals compared to 0.20 SD (95%CI 0.19-0.21) higher in controls, which corresponds to 3.4 kg and 2.8 kg extra weight for an individual of average height. Amongst the individual loci, the evidence for interaction was most notable for a variant near MC4R, a gene known to affect both appetite regulation and the hypothalamic-pituitary adrenal axis (pinteraction = 5.7 × 10-5 ). CONCLUSION: Genetic predisposition to high BMI was higher among depressed than to nondepressed individuals. This study provides support for a possible role of MC4R in the link between depression and obesity.

Phenome-wide association analysis of LDL-cholesterol lowering genetic variants in PCSK9.

BACKGROUND: We characterised the phenotypic consequence of genetic variation at the PCSK9 locus and compared findings with recent trials of pharmacological inhibitors of PCSK9. METHODS: Published and individual participant level data (300,000+ participants) were combined to construct a weighted PCSK9 gene-centric score (GS). Seventeen randomized placebo controlled PCSK9 inhibitor trials were included, providing data on 79,578 participants. Results were scaled to a one mmol/L lower LDL-C concentration. RESULTS: The PCSK9 GS (comprising 4 SNPs) associations with plasma lipid and apolipoprotein levels were consistent in direction with treatment effects. The GS odds ratio (OR) for myocardial infarction (MI) was 0.53 (95% CI 0.42; 0.68), compared to a PCSK9 inhibitor effect of 0.90 (95% CI 0.86; 0.93). For ischemic stroke ORs were 0.84 (95% CI 0.57; 1.22) for the GS, compared to 0.85 (95% CI 0.78; 0.93) in the drug trials. ORs with type 2 diabetes mellitus (T2DM) were 1.29 (95% CI 1.11; 1.50) for the GS, as compared to 1.00 (95% CI 0.96; 1.04) for incident T2DM in PCSK9 inhibitor trials. No genetic associations were observed for cancer, heart failure, atrial fibrillation, chronic obstructive pulmonary disease, or Alzheimer's disease - outcomes for which large-scale trial data were unavailable. CONCLUSIONS: Genetic variation at the PCSK9 locus recapitulates the effects of therapeutic inhibition of PCSK9 on major blood lipid fractions and MI. While indicating an increased risk of T2DM, no other possible safety concerns were shown; although precision was moderate.