Polygenic architecture of brain structure and function, behaviors, and psychopathologies in children.

The human brain undergoes structural and functional changes during childhood, a critical period in cognitive and behavioral development. Understanding the genetic architecture of the brain development in children can offer valuable insights into the development of the brain, cognition, and behaviors. Here, we integrated brain imaging-genetic-phenotype data from over 8,600 preadolescent children of diverse ethnic backgrounds using multivariate statistical techniques. We found a low-to-moderate level of SNP-based heritability in most IDPs, which is lower compared to the adult brain. Using sparse generalized canonical correlation analysis (SGCCA), we identified several covariation patterns among genome-wide polygenic scores (GPSs) of 29 traits, 7 different modalities of brain imaging-derived phenotypes (IDPs), and 266 cognitive and psychological phenotype data. In structural MRI, significant positive associations were observed between total grey matter volume, left ventral diencephalon volume, surface area of right accumbens and the GPSs of cognition-related traits. Conversely, negative associations were found with the GPSs of ADHD, depression and neuroticism. Additionally, we identified a significant positive association between educational attainment GPS and regional brain activation during the N-back task. The BMI GPS showed a positive association with fractional anisotropy (FA) of connectivity between the cerebellum cortex and amygdala in diffusion MRI, while the GPSs for educational attainment and cannabis use were negatively associated with the same IDPs. Our GPS-based prediction models revealed substantial genetic contributions to cognitive variability, while the genetic basis for many mental and behavioral phenotypes remained elusive. This study delivers a comprehensive map of the relationships between genetic profiles, neuroanatomical diversity, and the spectrum of cognitive and behavioral traits in preadolescence.

Gene-environment pathways to cognitive intelligence and psychotic-like experiences in children.

In children, psychotic-like experiences (PLEs) are related to risk of psychosis, schizophrenia, and other mental disorders. Maladaptive cognitive functioning, influenced by genetic and environmental factors, is hypothesized to mediate the relationship between these factors and childhood PLEs. Using large-scale longitudinal data, we tested the relationships of genetic and environmental factors (such as familial and neighborhood environment) with cognitive intelligence and their relationships with current and future PLEs in children. We leveraged large-scale multimodal data of 6,602 children from the Adolescent Brain and Cognitive Development Study. Linear mixed model and a novel structural equation modeling (SEM) method that allows estimation of both components and factors were used to estimate the joint effects of cognitive phenotypes polygenic scores (PGSs), familial and neighborhood socioeconomic status (SES), and supportive environment on NIH Toolbox cognitive intelligence and PLEs. We adjusted for ethnicity (genetically defined), schizophrenia PGS, and additionally unobserved confounders (using computational confound modeling). Our findings indicate that lower cognitive intelligence and higher PLEs are significantly associated with lower PGSs for cognitive phenotypes, lower familial SES, lower neighborhood SES, and less supportive environments. Specifically, cognitive intelligence mediates the effects of these factors on PLEs, with supportive parenting and positive school environments showing the strongest impact on reducing PLEs. This study underscores the influence of genetic and environmental factors on PLEs through their effects on cognitive intelligence. Our findings have policy implications in that improving school and family environments and promoting local economic development may enhance cognitive and mental health in children.

Childhood is a critical period for brain development. Difficult experiences during this developmental phase may contribute to reduced intelligence and poorer mental health later in life. Genetics and environmental factors also play roles. For example, having family support or a higher family income has been linked to better brain health outcomes for children. Delusions or hallucinations, or other psychotic-like experiences during childhood, are linked with poor mental health later in life. Children who experience psychotic-like episodes between the ages of nine and eleven have a higher risk of developing schizophrenia or related conditions. Environmental circumstances during childhood also appear to play a crucial role in shaping the risk of schizophrenia or related conditions. Park, Lee et al. show that positive parenting and supportive school and neighborhood environments boost child intelligence and mental health. In the experiments, Park, Lee et al. analyzed data on 6,602 children to determine how genetics and environmental factors shaped their intelligence and mental health. The models show that children with higher intelligence have a lower risk of psychosis. Both genetics and supportive environments contribute to higher intelligence. Complex interactions between biology and social factors shape children's intelligence and mental health. Beneficial genetics and coming from a family with more financial resources are helpful. Yet, social environments, such as having parents who use positive child-rearing practices, or having supportive schools or neighborhoods, have protective effects that can offset other disadvantages. Policies that help parents, encourage supportive school environments, and strengthen neighborhoods may boost children's intelligence and mental health later in life.

Multimodal integration of neuroimaging and genetic data for the diagnosis of mood disorders based on computer vision models.

Mood disorders, particularly major depressive disorder (MDD) and bipolar disorder (BD), are often underdiagnosed, leading to substantial morbidity. Harnessing the potential of emerging methodologies, we propose a novel multimodal fusion approach that integrates patient-oriented brain structural magnetic resonance imaging (sMRI) scans with DNA whole-exome sequencing (WES) data. Multimodal data fusion aims to improve the detection of mood disorders by employing established deep-learning architectures for computer vision and machine-learning strategies. We analyzed brain imaging genetic data of 321 East Asian individuals, including 147 patients with MDD, 78 patients with BD, and 96 healthy controls. We developed and evaluated six fusion models by leveraging common computer vision models in image classification: Vision Transformer (ViT), Inception-V3, and ResNet50, in conjunction with advanced machine-learning techniques (XGBoost and LightGBM) known for high-dimensional data analysis. Model validation was performed using a 10-fold cross-validation. Our ViT ⊕ XGBoost fusion model with MRI scans, genomic Single Nucleotide polymorphism (SNP) data, and unweighted polygenic risk score (PRS) outperformed baseline models, achieving an incremental area under the curve (AUC) of 0.2162 (32.03% increase) and 0.0675 (+8.19%) and incremental accuracy of 0.1455 (+25.14%) and 0.0849 (+13.28%) compared to SNP-only and image-only baseline models, respectively. Our findings highlight the opportunity to refine mood disorder diagnostics by demonstrating the transformative potential of integrating diverse, yet complementary, data modalities and methodologies.

Early life stress modulates the genetic influence on brain structure and cognitive function in children.

The enduring influence of early life stress (ELS) on brain and cognitive development has been widely acknowledged, yet the precise mechanisms underlying this association remain elusive. We hypothesize that ELS might disrupt the genome-wide influence on brain morphology and connectivity development, consequently exerting a detrimental impact on children's cognitive ability. We analyzed the multimodal data of DNA genotypes, brain imaging (structural and diffusion MRI), and neurocognitive battery (NIH Toolbox) of 4276 children (ages 9-10 years, European ancestry) from the Adolescent Brain Cognitive Development (ABCD) study. The genome-wide influence on cognitive function was estimated using the polygenic score (GPS). By using brain morphometry and tractography, we identified the brain correlates of the cognition GPSs. Statistical analyses revealed relationships for the gene-brain-cognition pathway. The brain structural variance significantly mediated the genetic influence on cognition (indirect effect = 0.016, PFDR < 0.001). Of note, this gene-brain relationship was significantly modulated by abuse, resulting in diminished cognitive capacity (Index of Moderated Mediation = -0.007; 95 % CI = -0.012 âˆ¼ -0.002). Our results support a novel gene-brain-cognition model likely elucidating the long-lasting negative impact of ELS on children's cognitive development.

Overestimated prediction using polygenic prediction derived from summary statistics.

BACKGROUND: When polygenic risk score (PRS) is derived from summary statistics, independence between discovery and test sets cannot be monitored. We compared two types of PRS studies derived from raw genetic data (denoted as rPRS) and the summary statistics for IGAP (sPRS). RESULTS: Two variables with the high heritability in UK Biobank, hypertension, and height, are used to derive an exemplary scale effect of PRS. sPRS without APOE is derived from International Genomics of Alzheimer's Project (IGAP), which records ΔAUC and ΔR2 of 0.051 ± 0.013 and 0.063 ± 0.015 for Alzheimer's Disease Sequencing Project (ADSP) and 0.060 and 0.086 for Accelerating Medicine Partnership - Alzheimer's Disease (AMP-AD). On UK Biobank, rPRS performances for hypertension assuming a similar size of discovery and test sets are 0.0036 ± 0.0027 (ΔAUC) and 0.0032 ± 0.0028 (ΔR2). For height, ΔR2 is 0.029 ± 0.0037. CONCLUSION: Considering the high heritability of hypertension and height of UK Biobank and sample size of UK Biobank, sPRS results from AD databases are inflated. Independence between discovery and test sets is a well-known basic requirement for PRS studies. However, a lot of PRS studies cannot follow such requirements because of impossible direct comparisons when using summary statistics. Thus, for sPRS, potential duplications should be carefully considered within the same ethnic group.

Topical Ozone Accelerates Diabetic Wound Healing by Promoting Re-Epithelialization through the Activation of IGF1R-EGFR Signaling.

Ozonated oil increases the healing of chronic diabetic wounds, but the underlying mechanisms remain unclear. We investigated the effect of topical ozonated oil on wound healing in mice with diabetes with diet-induced obesity and further elucidated the role of EGFR and IGF1R signaling in diabetic wound healing. We found that topical ozonated oil accelerated wound healing; increased phosphorylation of IGF1R, EGFR, and VEGFR; and improved vascularization at the wound leading edge in mice with diabetes with diet-induced obesity. Exposure of normal epidermal keratinocytes to ozonated medium (20 µM for 2 hours daily) increased cell proliferation and migration distance by increasing phosphorylation of IGF1R and EGFR and downstream phosphoinositide 3-kinase, protein kinase B, and extracellular signal-regulated kinase. These findings shed light on the mechanism for topical ozone action in chronic wounds and support its potential therapeutic application.

Multi-ancestry genome- and phenome-wide association studies of diverticular disease in electronic health records with natural language processing enriched phenotyping algorithm.

OBJECTIVE: Diverticular disease (DD) is one of the most prevalent conditions encountered by gastroenterologists, affecting ~50% of Americans before the age of 60. Our aim was to identify genetic risk variants and clinical phenotypes associated with DD, leveraging multiple electronic health record (EHR) data sources of 91,166 multi-ancestry participants with a Natural Language Processing (NLP) technique. MATERIALS AND METHODS: We developed a NLP-enriched phenotyping algorithm that incorporated colonoscopy or abdominal imaging reports to identify patients with diverticulosis and diverticulitis from multicenter EHRs. We performed genome-wide association studies (GWAS) of DD in European, African and multi-ancestry participants, followed by phenome-wide association studies (PheWAS) of the risk variants to identify their potential comorbid/pleiotropic effects in clinical phenotypes. RESULTS: Our developed algorithm showed a significant improvement in patient classification performance for DD analysis (algorithm PPVs ≥ 0.94), with up to a 3.5 fold increase in terms of the number of identified patients than the traditional method. Ancestry-stratified analyses of diverticulosis and diverticulitis of the identified subjects replicated the well-established associations between ARHGAP15 loci with DD, showing overall intensified GWAS signals in diverticulitis patients compared to diverticulosis patients. Our PheWAS analyses identified significant associations between the DD GWAS variants and circulatory system, genitourinary, and neoplastic EHR phenotypes. DISCUSSION: As the first multi-ancestry GWAS-PheWAS study, we showcased that heterogenous EHR data can be mapped through an integrative analytical pipeline and reveal significant genotype-phenotype associations with clinical interpretation. CONCLUSION: A systematic framework to process unstructured EHR data with NLP could advance a deep and scalable phenotyping for better patient identification and facilitate etiological investigation of a disease with multilayered data.

Maternal age at birth and child attention-deficit hyperactivity disorder: causal association or familial confounding?

BACKGROUND: Causal explanations for the association of young motherhood with increased risk for child attention-deficit hyperactivity disorder (ADHD) remain unclear. METHODS: The ABCD Study recruited 11,878 youth from 22 sites across the United States between June 1, 2016 and October 15, 2018. This cross-sectional analysis of 8,514 children aged 8-11 years excluded 2,260 twins/triplets, 265 adopted children, and 839 younger siblings. We examined associations of maternal age with ADHD clinical range diagnoses based on the Child Behavior Checklist and NIH Toolbox Flanker Attention Scores using mixed logistic and linear regression models, respectively. We conducted confounding and causal mediation analyses using genotype array, demographic, socioeconomic, and prenatal environment data to investigate which genetic and environmental variables may explain the association between young maternal age and child ADHD. RESULTS: In crude models, each 10-year increase in maternal age was associated with 32% decreased odds of ADHD clinical range diagnosis (OR = 0.68; 95% CI [0.59, 0.78]) and 1.09-points increased NIH Flanker Attention Scores (ß = 1.09; 95% CI [0.76, 1.41]), indicating better child visual selective attention. However, adjustment for confounders weakened these associations. The strongest confounders were family income, caregiver education, and ADHD polygenic risk score for ADHD clinical range diagnoses, and family income, caregiver education, and race/ethnicity for NIH Flanker Attention Scores. Breastfeeding duration, prenatal alcohol exposure, and prenatal tobacco exposure were responsible for up to 18%, 6%, and 4% mediation, respectively. CONCLUSIONS: Socioeconomic disadvantages were likely the primary explanation for the association of young maternal age with child ADHD, although genetics and modifiable environmental factors also played a role. Public policies aimed at reducing the burden of ADHD associated with young motherhood should target socioeconomic inequalities and support young pregnant women by advocating for reduced prenatal tobacco exposure and healthy breastfeeding practices after childbirth.

Statin use in patients with hormone receptor-positive metastatic breast cancer treated with everolimus and exemestane.

BACKGROUND: We analyzed the effect of statins in patients with hormone receptor-positive (HR+) metastatic breast cancer treated with everolimus + exemestane (EverX). MATERIALS AND METHODS: We conducted a nationwide retrospective cohort study using the National Health Insurance database with patients who received EverX for metastatic breast cancer between 2011 and 2019. RESULTS: Of 224,948 patients diagnosed with breast cancer, 1749 patients who received EverX for at least 30 days were included. Among them, 500 (28.6%) patients were found to take statins with EverX treatment (statin group), and the median duration of this combination was 5.36 months. The median time to treatment duration (TTD) for EverX and the overall survival (OS) were significantly higher in the statin group than in the no-statin group [7.69 vs. 5.06 months, p < 0.001; 45.7 vs. 26.0 months, p < 0.001, respectively]. Multivariable Cox analysis revealed that the use of statins was associated with prolonged TTD [HR = 0.67 (95% CI, 0.59-0.77)] and OS [HR = 0.57 (95% CI, 0.46-0.70)] for EverX even after adjustment for other covariates. CONCLUSION: Statins may have synergistic effects with endocrine therapy with the mTOR inhibitor everolimus, and improve survival in patients with HR+ metastatic breast cancer.

Cognitive Capacity Genome-Wide Polygenic Scores Identify Individuals with Slower Cognitive Decline in Aging.

The genetic protective factors for cognitive decline in aging remain unknown. Predicting an individual's rate of cognitive decline-or with better cognitive resilience-using genetics will allow personalized intervention for cognitive enhancement and the optimal selection of target samples in clinical trials. Here, using genome-wide polygenic scores (GPS) of cognitive capacity as the genomic indicators for variations of human intelligence, we analyzed the 18-year records of cognitive and behavioral data of 8511 European-ancestry adults from the Wisconsin Longitudinal Study (WLS), specifically focusing on the cognitive assessments that were repeatedly administered to the participants with their average ages of 64.5 and 71.5. We identified a significant interaction effect between age and cognitive capacity GPS, which indicated that a higher cognitive capacity GPS significantly correlated with a slower cognitive decline in the domain of immediate memory recall (ß = 1.86 × 10-1, p-value = 1.79 × 10-3). The additional phenome-wide analyses identified several associations between cognitive capacity GPSs and cognitive/behavioral phenotypes, such as similarities task (ß = 1.36, 95% CI = (1.22, 1.51), p-value = 3.59 × 10-74), number series task (ß = 0.94, 95% CI = (0.85, 1.04), p-value = 2.55 × 10-78), IQ scores (ß = 1.42, 95% CI = (1.32, 1.51), p-value = 7.74 × 10-179), high school classrank (ß = 1.86, 95% CI = (1.69, 2.02), p-value = 3.07 × 10-101), Openness from the BIG 5 personality factor (p-value = 2.19 × 10-14, ß = 0.57, 95% CI = (0.42, 0.71)), and leisure activity of reading books (ß = 0.50, 95% CI = (0.40, 0.60), p-value = 2.03 × 10-21), attending cultural events, such as concerts, plays, or museums (ß = 0.60, 95% CI = (0.49, 0.72), p-value = 2.06 × 10-23), and watching TV (ß = -0.48, 95% CI = (-0.59, -0.37), p-value = 4.16 × 10-18). As the first phenome-wide analysis of cognitive and behavioral phenotypes, this study presents the novel genetic protective effects of cognitive ability on the decline of memory recall in an aging population.

The sexual brain, genes, and cognition: A machine-predicted brain sex score explains individual differences in cognitive intelligence and genetic influence in young children.

Sex impacts the development of the brain and cognition differently across individuals. However, the literature on brain sex dimorphism in humans is mixed. We aim to investigate the biological underpinnings of the individual variability of sexual dimorphism in the brain and its impact on cognitive performance. To this end, we tested whether the individual difference in brain sex would be linked to that in cognitive performance that is influenced by genetic factors in prepubertal children (N = 9,658, ages 9-10 years old; the Adolescent Brain Cognitive Development study). To capture the interindividual variability of the brain, we estimated the probability of being male or female based on the brain morphometry and connectivity features using machine learning (herein called a brain sex score). The models accurately classified the biological sex with a test ROC-AUC of 93.32%. As a result, a greater brain sex score correlated significantly with greater intelligence (pfdr < .001, ηp2  = .011-.034; adjusted for covariates) and higher cognitive genome-wide polygenic scores (GPSs) (pfdr < .001, ηp2 < .005). Structural equation models revealed that the GPS-intelligence association was significantly modulated by the brain sex score, such that a brain with a higher maleness score (or a lower femaleness score) mediated a positive GPS effect on intelligence (indirect effects = .006-.009; p = .002-.022; sex-stratified analysis). The finding of the sex modulatory effect on the gene-brain-cognition relationship presents a likely biological pathway to the individual and sex differences in the brain and cognitive performance in preadolescence.

Association of Genome-Wide Polygenic Scores for Multiple Psychiatric and Common Traits in Preadolescent Youths at Risk of Suicide.

Importance: Suicide is the second leading cause of death among youths worldwide, but no available means exist to identify the risk of suicide in this population. Objective: To assess whether genome-wide polygenic scores for psychiatric and common traits are associated with the risk of suicide among preadolescent children and to investigate whether and to what extent the interaction between early life stress (a major environmental risk factor) and polygenic factors is associated with suicidal thoughts and behaviors among youths. Design, Setting, and Participants: This cohort study analyzed the genotype-phenotype data of 11 869 preadolescent children aged 9 to 10 years from the Adolescent Brain and Cognitive Development study. Data were collected from September 1, 2016, to October 21, 2018, and analyzed from August 1, 2020, to January 3, 2021. Using machine learning approaches, genome-wide polygenic scores of 24 complex traits were estimated to investigate their phenome-wide associations and utility for assessing risk of suicidal thoughts and behaviors (suicidal ideation [active, passive, and overall] and suicide attempt). Main Outcomes and Measures: Genome-wide polygenic scores were used to measure 24 traits, including psychiatric disorders, cognitive capacity, and personality and psychological characteristics. The Child Behavior Checklist was used to measure early life stress, and the Family Environment Scale was used to assess family environment. Suicidal ideation and suicide attempts were derived from the computerized version of the Kiddie Schedule for Affective Disorders and Schizophrenia. Results: Among 11 869 preadolescent children in the US, complete data for phenotypic outcomes, genotypes, and covariates were available for 7140 participants in the multiethnic cohort (mean [SD] age, 9.9 [0.6] years; 3588 girls [50.3%]), including 925 participants with suicidal ideation and 63 participants with suicide attempts. Among those 7140 participants, 729 had African ancestry (self-reported race or ethnicity: 569 Black, 71 Hispanic, and 89 other), 276 had admixed American ancestry (self-reported race or ethnicity: 265 Hispanic, 3 White, and 8 other), 150 had East Asian ancestry (self-reported race or ethnicity: 67 Asian, 18 Hispanic, and 65 other), 5718 had European ancestry (self-reported race or ethnicity: 7 Asian, 39 Black, 1142 Hispanic, 3934 White, and 596 other), and 267 had other ancestries (self-reported race or ethnicity: 70 Asian, 13 Black, 126 Hispanic, 48 White, and 10 other). Three genome-wide polygenic scores were significantly associated (false discovery rate P < .05) with suicidal thoughts and behaviors among all participants: attention-deficit/hyperactivity disorder (odds ratio [OR], 1.12; 95% CI, 1.05-1.21; P = .001), schizophrenia (OR, 1.50; 95% CI, 1.17-1.93; P = .002), and general happiness (OR, 0.89; 95% CI, 0.83-0.96; P = .002). In the analysis including only children with European ancestry, 3 additional genome-wide polygenic scores with false discovery rate significance were associated with suicidal thoughts and behaviors: autism spectrum disorder (OR, 1.18; 95% CI, 1.06-1.31; P = .002), major depressive disorder (OR, 1.12; 95% CI, 1.04-1.21; P = .003), and posttraumatic stress disorder (OR, 1.12; 95% CI, 1.04-1.21; P = .004). A significant interaction between genome-wide polygenic scores and environment was found, with genetic risk factors for autism spectrum disorder and the level of early life stress associated with increases in the risk of overall suicidal ideation and overall suicidal thoughts and behaviors (OR, 1.20; 95% CI, 1.07-1.35; P = .002). A machine learning model using multitrait genome-wide polygenic scores and additional self-reported questionnaire data (Child Behavior Checklist and Family Environment Scale) produced a moderately accurate estimate of overall suicidal thoughts and behaviors (area under the receiver operating characteristic curve [AUROC], 0.77; 95% CI, 0.73-0.81; accuracy, 0.67) and suicidal ideation (AUROC, 0.76; 95% CI, 0.72-0.80; accuracy, 0.66) among children with European ancestry only. Among all children in the multiethnic cohort, the integrated model also outperformed the baseline model in estimating the risk of overall suicidal thoughts and behaviors (AUROC, 0.71; 95% CI, 0.67-0.75; accuracy, 0.68) and suicidal ideation (AUROC, 0.75; 95% CI, 0.71-0.78; accuracy, 0.67). Conclusions and Relevance: In this cohort study of preadolescent youths in the US, higher genome-wide polygenic scores for psychiatric disorders, such as attention-deficit/hyperactivity disorder, autism spectrum disorder, posttraumatic stress disorder, and schizophrenia, were significantly associated with a greater risk of suicidal ideation and suicide attempt. The findings and quantitative models from this study may help to identify children with a high risk of suicide, potentially assisting with early screening, intervention, and prevention.

Misperception of body weight and associated socioeconomic and health-related factors among Korean female adults: A nationwide population-based study.

Background: Misperception of body weight is associated with various psychological and health problems, including obesity, eating disorders, and mental problems. To date, female-specific risk factors, including socioeconomic or health-related lifestyle features, or their indicative performance for the misperception in Asian women according to age groups remain unknown. Objectives: To investigate the prevalence and associated risk factors for the mismatch in self-perceived body weight and evaluated the classification performance of the identified risk factors across age groups in female adults. Methods: We analyzed data of 22,121 women (age 19-97 years) from the 7-year Korea National Health and Nutrition Examination Survey dataset (2010-2016). We evaluated self-perceived body weight of the participants with their actual weight using the body mass index cut-off and grouped them by age: early adulthood (19-45), middle adulthood (46-59), and late adulthood (≥60). Logistic regression was conducted in each age group based on their weight misperception. The classification performance of the identified risk factors was evaluated with a bagging tree ensemble model with 5-fold cross-validation. Results: 22.2% (n=4,916) of the study participants incorrectly perceived their body weight, of which 14.1% (n=3,110) and 8.2% (n=1,806) were in the underestimated and overestimated groups. Among the age groups, the proportion of participants who misperceived their body weight was highest in late adulthood (31.8%) and the rate of overestimation was highest in early adulthood (14.1%). We found that a lower education level, absence of menopause, perception of themselves as unhealthy, and efforts for weight management were significantly associated with the overall misperception (overestimation or underestimation) of body weight across age groups. Based on the identified risk factors, the highest area under the receiver operating curve (AUROC) and accuracy of the best classification model (weight overestimation in all participants) were 0.758 and 0.761, respectively. Adding various associated lifestyle factors to the baseline model resulted in an average increase of 0.159 and 0.135 in AUROC for classifying weight underestimation and overestimation, respectively. Conclusions: Age, education level, marital status, absence of menopause, amount of exercise, efforts for weight management (gain, loss, and maintenance), and self-perceived health status were significantly associated with the mismatch of body weight.

Genetic discovery and risk characterization in type 2 diabetes across diverse populations.

Genomic discovery and characterization of risk loci for type 2 diabetes (T2D) have been conducted primarily in individuals of European ancestry. We conducted a multiethnic genome-wide association study of T2D among 53,102 cases and 193,679 control subjects from African, Hispanic, Asian, Native Hawaiian, and European population groups in the Population Architecture Genomics and Epidemiology (PAGE) and Diabetes Genetics Replication and Meta-analysis (DIAGRAM) Consortia. In individuals of African ancestry, we discovered a risk variant in the TGFB1 gene (rs11466334, risk allele frequency (RAF) = 6.8%, odds ratio [OR] = 1.27, p = 2.06 × 10-8), which replicated in independent studies of African ancestry (p = 6.26 × 10-23). We identified a multiethnic risk variant in the BACE2 gene (rs13052926, RAF = 14.1%, OR = 1.08, p = 5.75 × 10-9), which also replicated in independent studies (p = 3.45 × 10-4). We also observed a significant difference in the performance of a multiethnic genetic risk score (GRS) across population groups (pheterogeneity = 3.85 × 10-20). Comparing individuals in the top GRS risk category (40%-60%), the OR was highest in Asians (OR = 3.08) and European (OR = 2.94) ancestry populations, followed by Hispanic (OR = 2.39), Native Hawaiian (OR = 2.02), and African ancestry (OR = 1.57) populations. These findings underscore the importance of genetic discovery and risk characterization in diverse populations and the urgent need to further increase representation of non-European ancestry individuals in genetics research to improve genetic-based risk prediction across populations.

Secular trends in postpartum weight retention from 2003 to 2012: a nationwide, population-based, retrospective, longitudinal study in South Korea.

OBJECTIVE: To assess the secular trends in postpartum weight retention (PWR) over a decade with the population-based risk factors. DESIGN: Retrospective cohort study. SETTING: A national health screening examination data provided by the National Health Insurance Service in South Korea. PARTICIPANTS: 130 551 women who delivered babies between 1 January 2003 and 31 December 2012 and who underwent a national health screening examination 1 to 2 years prior to delivery and within 1 year after delivery. METHODS: Their PWR were determined during the study period of 2003-2012. We fitted logistic regression and linear mixed models to assess the independent contribution of PWR to obesity after adjusting for potential confounders. PRIMARY AND SECONDARY OUTCOME MEASURES: Prepregnancy and postpartum weight and body mass index (BMI). RESULTS: The adjusted PWR increased from mean value of 2.02 kg in 2003 (95% CI 1.88 to 2.15) to 2.79 kg in 2012 (95% CI 2.73 to 2.84) (p value for trend <0.01), after adjusting potential confounders including age, prepregnancy time, postpartum time, prepregnancy BMI, income and smoking status. The risk for a PWR of more than 5 kg also increased over the study period. CONCLUSIONS: Secular increases in PWR have been significantly observed between 2003 and 2012 for childbearing women. It is necessary to identify risk factors contributing to the observed increase and develop effective strategies to address the heightened risk for PWR.

A Polygenic and Phenotypic Risk Prediction for Polycystic Ovary Syndrome Evaluated by Phenome-Wide Association Studies.

CONTEXT: As many as 75% of patients with polycystic ovary syndrome (PCOS) are estimated to be unidentified in clinical practice. OBJECTIVE: Utilizing polygenic risk prediction, we aim to identify the phenome-wide comorbidity patterns characteristic of PCOS to improve accurate diagnosis and preventive treatment. DESIGN, PATIENTS, AND METHODS: Leveraging the electronic health records (EHRs) of 124 852 individuals, we developed a PCOS risk prediction algorithm by combining polygenic risk scores (PRS) with PCOS component phenotypes into a polygenic and phenotypic risk score (PPRS). We evaluated its predictive capability across different ancestries and perform a PRS-based phenome-wide association study (PheWAS) to assess the phenomic expression of the heightened risk of PCOS. RESULTS: The integrated polygenic prediction improved the average performance (pseudo-R2) for PCOS detection by 0.228 (61.5-fold), 0.224 (58.8-fold), 0.211 (57.0-fold) over the null model across European, African, and multi-ancestry participants respectively. The subsequent PRS-powered PheWAS identified a high level of shared biology between PCOS and a range of metabolic and endocrine outcomes, especially with obesity and diabetes: "morbid obesity", "type 2 diabetes", "hypercholesterolemia", "disorders of lipid metabolism", "hypertension", and "sleep apnea" reaching phenome-wide significance. CONCLUSIONS: Our study has expanded the methodological utility of PRS in patient stratification and risk prediction, especially in a multifactorial condition like PCOS, across different genetic origins. By utilizing the individual genome-phenome data available from the EHR, our approach also demonstrates that polygenic prediction by PRS can provide valuable opportunities to discover the pleiotropic phenomic network associated with PCOS pathogenesis.

The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype.

The Electronic Medical Records and Genomics (eMERGE) network is a network of medical centers with electronic medical records linked to existing biorepository samples for genomic discovery and genomic medicine research. The network sought to unify the genetic results from 78 Illumina and Affymetrix genotype array batches from 12 contributing medical centers for joint association analysis of 83,717 human participants. In this report, we describe the imputation of eMERGE results and methods to create the unified imputed merged set of genome-wide variant genotype data. We imputed the data using the Michigan Imputation Server, which provides a missing single-nucleotide variant genotype imputation service using the minimac3 imputation algorithm with the Haplotype Reference Consortium genotype reference set. We describe the quality control and filtering steps used in the generation of this data set and suggest generalizable quality thresholds for imputation and phenotype association studies. To test the merged imputed genotype set, we replicated a previously reported chromosome 6 HLA-B herpes zoster (shingles) association and discovered a novel zoster-associated loci in an epigenetic binding site near the terminus of chromosome 3 (3p29).