Educational attainment polygenic score predicts inhibitory control and academic skills in early and middle childhood

Inhibitory control skills are important for academic outcomes across childhood, but it is unknown whether inhibitory control is implicated in the association between genetic variation and academic performance. This study examined the relationship between a GWAS-based (EduYears) polygenic score indexing educational attainment (EA PGS) and inhibitory control in early (Mage  = 3.80 years) and middle childhood (Mage  = 9.18 years), and whether inhibitory control in early childhood mediated the relation between EA PGS and academic skills. The sample comprised 731 low-income and racially/ethnically diverse children and their families from the longitudinal early steps multisite study. EA PGS predicted middle childhood inhibitory control (estimate = 0.09, SE = 0.05, p < 0.05) and academic skills (estimate = 0.18, SE = 0.05, p < 0.01) but did not predict early childhood inhibitory control (estimate = 0.08, SE = 0.05, p = 0.11); thus, mediation was not tested. Sensitivity analyses showed that effect sizes were similar across European and African American groups. This study suggests that inhibitory control could serve as a potential mechanism linking genetic differences to educational outcomes.

Risk Prediction Using Polygenic Risk Scores for Prevention of Stroke and Other Cardiovascular Diseases

Early prediction of risk of cardiovascular disease (CVD), including stroke, is a cornerstone of disease prevention. Clinical risk scores have been widely used for predicting CVD risk from known risk factors. Most CVDs have a substantial genetic component, which also has been confirmed for stroke in recent gene discovery efforts. However, the role of genetics in prediction of risk of CVD, including stroke, has been limited to testing for highly penetrant monogenic disorders. In contrast, the importance of polygenic variation, the aggregated effect of many common genetic variants across the genome with individually small effects, has become more apparent in the last 5 to 10 years, and powerful polygenic risk scores for CVD have been developed. Here we review the current state of the field of polygenic risk scores for CVD including stroke, and their potential to improve CVD risk prediction. We present findings and lessons from diseases such as coronary artery disease as these will likely be useful to inform future research in stroke polygenic risk prediction.

A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics

Genetic prediction of complex traits has great promise for disease prevention, monitoring, and treatment. The development of accurate risk prediction models is hindered by the wide diversity of genetic architecture across different traits, limited access to individual level data for training and parameter tuning, and the demand for computational resources. To overcome the limitations of the most existing methods that make explicit assumptions on the underlying genetic architecture and need a separate validation data set for parameter tuning, we develop a summary statistics-based nonparametric method that does not rely on validation datasets to tune parameters. In our implementation, we refine the commonly used likelihood assumption to deal with the discrepancy between summary statistics and external reference panel. We also leverage the block structure of the reference linkage disequilibrium matrix for implementation of a parallel algorithm. Through simulations and applications to twelve traits, we show that our method is adaptive to different genetic architectures, statistically robust, and computationally efficient. Our method is available at https://github.com/eldronzhou/SDPR.

Extended-amygdala intrinsic functional connectivity networks: A population study

Pre-clinical and human neuroimaging research implicates the extended-amygdala (ExtA) (including the bed nucleus of the stria terminalis [BST] and central nucleus of the amygdala [CeA]) in networks mediating negative emotional states associated with stress and substance-use behaviours. The extent to which individual ExtA structures form a functionally integrated unit is controversial. We utilised a large sample (n > 1,000 healthy young adult humans) to compare the intrinsic functional connectivity networks (ICNs) of the BST and CeA using task-free functional magnetic resonance imaging (fMRI) data from the Human Connectome Project. We assessed whether inter-individual differences within these ICNs were related to two principal components representing negative disposition and alcohol use. Building on recent primate evidence, we tested whether within BST-CeA intrinsic functional connectivity (iFC) was heritable and further examined co-heritability with our principal components. We demonstrate the BST and CeA to have discrete, but largely overlapping ICNs similar to previous findings. We found no evidence that within BST-CeA iFC was heritable; however, post hoc analyses found significant BST iFC heritability with the broader superficial and centromedial amygdala regions. There were no significant correlations or co-heritability associations with our principal components either across the ICNs or for specific BST-Amygdala iFC. Possible differences in phenotype associations across task-free, task-based, and clinical fMRI are discussed, along with suggestions for more causal investigative paradigms that make use of the now well-established ExtA ICNs.

Effects of Thyroid Status on Regional Brain Volumes: A Diagnostic and Genetic Imaging Study in UK Biobank

BACKGROUND

Thyroid hormone is essential for optimal human neurodevelopment and may modify the risk of attention-deficit/hyperactivity disorder (ADHD). However, the brain structures involved are unknown and it is unclear if the adult brain is also susceptible to changes in thyroid status.

METHODS

We used International Classification of Disease-10 codes, polygenic thyroid scores at different thresholds of association with thyroid traits (PT-values), and image-derived phenotypes in UK Biobank (n = 18 825) to investigate the effects of a recorded diagnosis of thyroid disease and genetic risk for thyroid status on cerebellar and subcortical gray matter volume. Regional genetic pleiotropy between thyroid status and ADHD was explored using the GWAS-pairwise method.

RESULTS

A recorded diagnosis of hypothyroidism (n = 419) was associated with significant reductions in total cerebellar and pallidum gray matter volumes (β [95% CI] = -0.14[-0.23, -0.06], P = 0.0005 and β [95%CI] = -0.12 [-0.20, -0.04], P = 0.0042, respectively), mediated in part by increases in body mass index. While we found no evidence for total cerebellar volume alterations with increased polygenic scores for any thyroid trait, opposing influences of increased polygenic scores for hypo- and hyperthyroidism were found in the pallidum (PT < 1e-3: β [95% CI] = -0.02 [-0.03, -0.01], P = 0.0003 and PT < 1e-7: β [95% CI] = 0.02 [0.01, 0.03], P = 0.0003, respectively). Neither hypo- nor hyperthyroidism showed evidence of regional genetic pleiotropy with ADHD.

CONCLUSIONS

Thyroid status affects gray matter volume in adults, particularly at the level of the cerebellum and pallidum, with potential implications for the regulation of motor, cognitive, and affective function.

Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease

Polygenic inheritance plays a central role in Parkinson disease (PD). A priority in elucidating PD etiology lies in defining the biological basis of genetic risk. Unraveling how risk leads to disruption will yield disease-modifying therapeutic targets that may be effective. Here, we utilized a high-throughput and hypothesis-free approach to determine biological processes underlying PD using the largest currently available cohorts of genetic and gene expression data from International Parkinson's Disease Genetics Consortium (IPDGC) and the Accelerating Medicines Partnership-Parkinson's disease initiative (AMP-PD), among other sources. We applied large-scale gene-set specific polygenic risk score (PRS) analyses to assess the role of common variation on PD risk focusing on publicly annotated gene sets representative of curated pathways. We nominated specific molecular sub-processes underlying protein misfolding and aggregation, post-translational protein modification, immune response, membrane and intracellular trafficking, lipid and vitamin metabolism, synaptic transmission, endosomal-lysosomal dysfunction, chromatin remodeling and apoptosis mediated by caspases among the main contributors to PD etiology. We assessed the impact of rare variation on PD risk in an independent cohort of whole-genome sequencing data and found evidence for a burden of rare damaging alleles in a range of processes, including neuronal transmission-related pathways and immune response. We explored enrichment linked to expression cell specificity patterns using single-cell gene expression data and demonstrated a significant risk pattern for dopaminergic neurons, serotonergic neurons, hypothalamic GABAergic neurons, and neural progenitors. Subsequently, we created a novel way of building de novo pathways by constructing a network expression community map using transcriptomic data derived from the blood of PD patients, which revealed functional enrichment in inflammatory signaling pathways, cell death machinery related processes, and dysregulation of mitochondrial homeostasis. Our analyses highlight several specific promising pathways and genes for functional prioritization and provide a cellular context in which such work should be done.

Cortical Surfaces Mediate the Relationship Between Polygenic Scores for Intelligence and General Intelligence

Recent large-scale, genome-wide association studies (GWAS) have identified hundreds of genetic loci associated with general intelligence. The cumulative influence of these loci on brain structure is unknown. We examined if cortical morphology mediates the relationship between GWAS-derived polygenic scores for intelligence (PSi) and g-factor. Using the effect sizes from one of the largest GWAS meta-analysis on general intelligence to date, PSi were calculated among 10 P value thresholds. PSi were assessed for the association with g-factor performance, cortical thickness (CT), and surface area (SA) in two large imaging-genetics samples (IMAGEN N = 1651; IntegraMooDS N = 742). PSi explained up to 5.1% of the variance of g-factor in IMAGEN (F1,1640 = 12.2-94.3; P < 0.005), and up to 3.0% in IntegraMooDS (F1,725 = 10.0-21.0; P < 0.005). The association between polygenic scores and g-factor was partially mediated by SA and CT in prefrontal, anterior cingulate, insula, and medial temporal cortices in both samples (PFWER-corrected < 0.005). The variance explained by mediation was up to 0.75% in IMAGEN and 0.77% in IntegraMooDS. Our results provide evidence that cumulative genetic load influences g-factor via cortical structure. The consistency of our results across samples suggests that cortex morphology could be a novel potential biomarker for neurocognitive dysfunction that is among the most intractable psychiatric symptoms.

Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal

Adaptive evolution in humans has rarely been characterized for its whole set of components, i.e. selective pressure, adaptive phenotype, beneficial alleles and realized fitness differential. We combined approaches for detecting polygenic adaptations and for mapping the genetic bases of physiological and fertility phenotypes in approximately 1000 indigenous ethnically Tibetan women from Nepal, adapted to high altitude. The results of genome-wide association analyses and tests for polygenic adaptations showed evidence of positive selection for alleles associated with more pregnancies and live births and evidence of negative selection for those associated with higher offspring mortality. Lower hemoglobin level did not show clear evidence for polygenic adaptation, despite its strong association with an EPAS1 haplotype carrying selective sweep signals.

Genetics of Depression: Progress at Last

PURPOSE OF REVIEW

We will describe the success of recent genome-wide association studies that identify genetic variants associated with depression and outline the strategies used to reduce heterogeneity and increase sample size.

RECENT FINDINGS

The CONVERGE consortium identified two genetic associations by focusing on a sample of Chinese women with recurrent severe depression. Three other loci have been found in Europeans by combining cohorts with clinical diagnosis and measures of depressive symptoms to increase sample size. 23andMe identified 15 loci associated with depression using self-report of clinical diagnosis in a study of over 300,000 individuals. The first genetic associations with depression have been identified, and this number is now expected to increase linearly with sample size, as seen in other polygenic disorders. These loci provide invaluable insights into the biology of depression and exciting opportunities to develop new biomarkers and therapeutic targets.

[Gentetics, environment and determinants of autoimmune diseases]

We initiate this review article by a brief description of a few monogenic autoimmune diseases such as the APECED and the IPEX syndrome because they allow understand the fundamental mechanisms of self tolerance. Next we describe with more details the complex autoimmune diseases and discuss the recent data regarding the associated genetic and environmental factors and their modes of interaction. The conclusion of the article deals with the practical implications of this inherent complexity for the researcher and the clinician.

Genomic tools for characterizing monogenic and polygenic traits in ruminants--using the bovine as an example

Next generation sequencing platforms have democratized genome sequencing. Large genome centers are no longer required to produce genome sequences costing millions. A few lanes of paired-end sequence on an Illumina Genome Analyzer, costing < $10,000, will produce more sequence than generated only a few years ago to produce the human and cow assemblies. The de novo assembly of large numbers of short reads into a high-quality whole-genome sequence is now technically feasible and will allow the whole genome sequencing and assembly of a broad spectrum of ruminant species. Next-generation sequencing instruments are also proving very useful for transcriptome or resequencing projects in which the entire RNA population produced by a tissue, or the entire genomes of individual animals are sequenced, and the produced reads are aligned to a reference assembly. We have used this strategy to examine gene expression differences in tissues from cattle differing in feed efficiency, to perform genome-wide single nucleotide polymorphism discovery for the construction of ultrahigh-density genotyping assays, and in combination with genome-wide association analysis, for the identification of mutations responsible for Mendelian diseases. The new 800K SNP bovine genotyping assays possess the resolution to map trait associations to the locations of individual genes and the 45 million polymorphisms identified in > 180X genome sequence coverage on over 200 animals can be queried to identify the polymorphisms present within positional candidate genes. These new tools should rapidly allow the identification of genes and mutations underlying variation in cattle production and reproductive traits.

[Mitochondrial DNA: properties and applications]

Mitochondria are the intracellular organelle responsible for the production of cellular energy. They play an important role in the regulation of cellular metabolism, apoptosis and oxydative stress control. Mitochondrial DNA (mtDNA) has many special features such as a high copy number in cell, maternal inheritance, and a high mutation rate which have made it attractive to scientists from many fields. In anthropological genetics, mtDNA is useful to trace geographic distribution of genetic variation, for the investigation of expansions, migrations and other pattern of gene flow. mtDNA is widely applicated in forensic science. It is a powerful implement to identify human remains. mtDNA is characterized by the high rate of polymorphisms and mutations. Some of which are increasingly recognized as an important cause of human pathology such as oxidative phosphorylation (OXPHOS) disorders, maternally inherited diabetes and deafness (MIDD), Type 2 diabetes mellitus, neurodegenerative disorders, heart failure and cancer.

POLYGENIC TRAITS AND PARASITE LOCAL ADAPTATION

The extent to which parasites are locally adapted to their hosts has important implications for human health and agriculture. A recently developed conceptual framework--the geographic mosaic theory of coevolution--predicts that local maladaptation should be common and largely determined by the interplay between gene flow and spatially variable reciprocal selection. Previous investigation of this theory has predominately focused on genetic systems of infection and resistance characterized by few genes of major effect and particular forms of epistasis. Here we extend existing theory by analyzing mathematical models of host-parasite interactions in which host resistance to parasites is mediated by quantitative traits with an additive polygenic basis. In contrast to previous theoretical studies predicated upon major gene mechanisms, we find that parasite local maladaptation is quite uncommon and restricted to one specific functional form of host resistance. Furthermore, our results show that local maladaptation should be rare or absent in studies that measure local adaptation using reciprocal transplant designs conducted in natural environments. Our results thus narrow the scope over which the predictions of the geographic mosaic theory are likely to hold and provide novel and readily testable predictions about when and where local maladaptation is expected.

Resemblance for body mass index in families of obese African American and European American women

OBJECTIVE

We determined the levels of resemblance in body mass index (BMI) in large samples of families selected through obese African American and European American women.

RESEARCH METHODS AND PROCEDURES

We examined correlations among relatives in 1,185 European American and African American families ascertained through age-matched obese women (BMI > or = 30 kg/m2). A subset of 801 families were ascertained through extremely obese women (BMI > or = 40 kg/m2).

RESULTS

Parent-offspring and sibling correlations ranged from 0.19 to 0.15, suggesting a moderate level of heritability in both groups. Mean BMI values for female relatives were lower for European Americans than for African Americans even though probands were matched, perhaps because the European American relatives regress to a lower population mean. We found significantly higher family correlations for height in European Americans, suggesting greater environmental variability among African Americans for factors affecting growth and physical development.

DISCUSSION

Our results suggest a similar level of heritability of BMI in families of obese African American and European American women. Other genetic studies will be needed to determine the extent to which the same or different genes and environmental conditions contribute to an overall similar heritability in the two racial groups.