Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.

Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.

Mental Effort in Elite and Nonelite Rowers.

Mental effort (intensity of attention) in elite sports has remained a debated topic and a challenging phenomenon to measure. Thus, a quasi-ecological laboratory study was conducted to investigate mental effort in elite rowers as compared with a group of nonelites. Findings suggest that eye-tracking measures-specifically, blink rates and pupil size-can serve as valid indicators of mental effort in physically demanding sport tasks. Furthermore, findings contradict the notion that elite athletes spend less cognitive effort than their lower-level peers. Specifically, elites displayed similar levels of self-reported effort and performance decrement with increasing mental load and significantly more mental effort overall as measured by pupil-size increase (relative to baseline) during rowing trials as compared with the nonelites in the sample. Future studies on eye tracking in sports may include investigations of mental effort in addition to selective attention during physically demanding tasks.

Deep neural networks learn general and clinically relevant representations of the ageing brain.

The discrepancy between chronological age and the apparent age of the brain based on neuroimaging data - the brain age delta - has emerged as a reliable marker of brain health. With an increasing wealth of data, approaches to tackle heterogeneity in data acquisition are vital. To this end, we compiled raw structural magnetic resonance images into one of the largest and most diverse datasets assembled (n=53542), and trained convolutional neural networks (CNNs) to predict age. We achieved state-of-the-art performance on unseen data from unknown scanners (n=2553), and showed that higher brain age delta is associated with diabetes, alcohol intake and smoking. Using transfer learning, the intermediate representations learned by our model complemented and partly outperformed brain age delta in predicting common brain disorders. Our work shows we can achieve generalizable and biologically plausible brain age predictions using CNNs trained on heterogeneous datasets, and transfer them to clinical use cases.

Pleiotropic Meta-Analysis of Cognition, Education, and Schizophrenia Differentiates Roles of Early Neurodevelopmental and Adult Synaptic Pathways.

Susceptibility to schizophrenia is inversely correlated with general cognitive ability at both the phenotypic and the genetic level. Paradoxically, a modest but consistent positive genetic correlation has been reported between schizophrenia and educational attainment, despite the strong positive genetic correlation between cognitive ability and educational attainment. Here we leverage published genome-wide association studies (GWASs) in cognitive ability, education, and schizophrenia to parse biological mechanisms underlying these results. Association analysis based on subsets (ASSET), a pleiotropic meta-analytic technique, allowed jointly associated loci to be identified and characterized. Specifically, we identified subsets of variants associated in the expected ("concordant") direction across all three phenotypes (i.e., greater risk for schizophrenia, lower cognitive ability, and lower educational attainment); these were contrasted with variants that demonstrated the counterintuitive ("discordant") relationship between education and schizophrenia (i.e., greater risk for schizophrenia and higher educational attainment). ASSET analysis revealed 235 independent loci associated with cognitive ability, education, and/or schizophrenia at p < 5 × 10-8. Pleiotropic analysis successfully identified more than 100 loci that were not significant in the input GWASs. Many of these have been validated by larger, more recent single-phenotype GWASs. Leveraging the joint genetic correlations of cognitive ability, education, and schizophrenia, we were able to dissociate two distinct biological mechanisms-early neurodevelopmental pathways that characterize concordant allelic variation and adulthood synaptic pruning pathways-that were linked to the paradoxical positive genetic association between education and schizophrenia. Furthermore, genetic correlation analyses revealed that these mechanisms contribute not only to the etiopathogenesis of schizophrenia but also to the broader biological dimensions implicated in both general health outcomes and psychiatric illness.

Effects of copy number variations on brain structure and risk for psychiatric illness: Large-scale studies from the ENIGMA working groups on CNVs.

The Enhancing NeuroImaging Genetics through Meta-Analysis copy number variant (ENIGMA-CNV) and 22q11.2 Deletion Syndrome Working Groups (22q-ENIGMA WGs) were created to gain insight into the involvement of genetic factors in human brain development and related cognitive, psychiatric and behavioral manifestations. To that end, the ENIGMA-CNV WG has collated CNV and magnetic resonance imaging (MRI) data from ~49,000 individuals across 38 global research sites, yielding one of the largest studies to date on the effects of CNVs on brain structures in the general population. The 22q-ENIGMA WG includes 12 international research centers that assessed over 533 individuals with a confirmed 22q11.2 deletion syndrome, 40 with 22q11.2 duplications, and 333 typically developing controls, creating the largest-ever 22q11.2 CNV neuroimaging data set. In this review, we outline the ENIGMA infrastructure and procedures for multi-site analysis of CNVs and MRI data. So far, ENIGMA has identified effects of the 22q11.2, 16p11.2 distal, 15q11.2, and 1q21.1 distal CNVs on subcortical and cortical brain structures. Each CNV is associated with differences in cognitive, neurodevelopmental and neuropsychiatric traits, with characteristic patterns of brain structural abnormalities. Evidence of gene-dosage effects on distinct brain regions also emerged, providing further insight into genotype-phenotype relationships. Taken together, these results offer a more comprehensive picture of molecular mechanisms involved in typical and atypical brain development. This "genotype-first" approach also contributes to our understanding of the etiopathogenesis of brain disorders. Finally, we outline future directions to better understand effects of CNVs on brain structure and behavior.

Genetic control of variability in subcortical and intracranial volumes.

Sensitivity to external demands is essential for adaptation to dynamic environments, but comes at the cost of increased risk of adverse outcomes when facing poor environmental conditions. Here, we apply a novel methodology to perform genome-wide association analysis of mean and variance in ten key brain features (accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus, intracranial volume, cortical surface area, and cortical thickness), integrating genetic and neuroanatomical data from a large lifespan sample (n = 25,575 individuals; 8-89 years, mean age 51.9 years). We identify genetic loci associated with phenotypic variability in thalamus volume and cortical thickness. The variance-controlling loci involved genes with a documented role in brain and mental health and were not associated with the mean anatomical volumes. This proof-of-principle of the hypothesis of a genetic regulation of brain volume variability contributes to establishing the genetic basis of phenotypic variance (i.e., heritability), allows identifying different degrees of brain robustness across individuals, and opens new research avenues in the search for mechanisms controlling brain and mental health.

Functional connectivity in multiple sclerosis modelled as connectome stability: A 5-year follow-up study.

BACKGROUND: Brain functional connectivity (FC) in multiple sclerosis (MS) is abnormal compared to healthy controls (HCs). More longitudinal studies in MS are needed to evaluate whether FC stability is clinically relevant. OBJECTIVE: To compare functional magnetic resonance imaging (fMRI)-based FC between MS and HC, and to determine the relationship between longitudinal FC changes and structural brain damage, cognitive performance and physical disability. METHODS: T1-weighted MPRAGE and resting-state fMRI (1.5T) were acquired from 70 relapsing-remitting MS patients and 94 matched HC at baseline (mean months since diagnosis 14.0 ± 11) and from 60 MS patients after 5 years. Independent component analysis and network modelling were used to measure longitudinal FC stability and cross-sectional comparisons with HC. Linear mixed models, adjusted for age and sex, were used to calculate correlations. RESULTS: At baseline, patients with MS showed FC abnormalities both within networks and in single connections compared to HC. Longitudinal analyses revealed functional stability and no significant relationships with clinical disability, cognitive performance, lesion or brain volume. CONCLUSION: FC abnormalities occur already at the first decade of MS, yet we found no relevant clinical correlations for these network deviations. Future large-scale longitudinal fMRI studies across a range of MS subtypes and outcomes are required.

Uncovering the locus coeruleus: Comparison of localization methods for functional analysis.

Functional neuroimaging of small brainstem structures in humans is gaining interest due to their potential importance in aging and many clinical conditions. Researchers have used different methods to measure activity in the locus coeruleus (LC), the main noradrenergic nucleus in the brain. However, the extent to which these different LC localization methods yield similar results is unclear. In the present article, we compared four different approaches to estimate localization of the LC in a large sample (N = 98): 1) a probabilistic map from a previous study, 2) masks segmented from neuromelanin-sensitive scans, both manually and semi-automatically, 3) components from a masked-independent components analysis of the functional data, and 4) a mask from pupil regression of the functional data. The four methods have all been used previously in the imaging community to localize the LC in vivo in humans. We report several measures of similarity between the LC masks obtained from the different methods. In addition, we compare functional connectivity maps obtained from the different masks. We conclude that sample-specific masks appear more suitable than masks obtained from an independent sample, that masks based on structural versus functional methods may capture different portions of LC, and that, at the group level, the creation of a "consensus" mask using more than one approach may give a better estimate of LC localization.

Correction: Dose response of the 16p11.2 distal copy number variant on intracranial volume and basal ganglia.

Prior to and following the publication of this article the authors noted that the complete list of authors was not included in the main article and was only present in Supplementary Table 1. The author list in the original article has now been updated to include all authors, and Supplementary Table 1 has been removed. All other supplementary files have now been updated accordingly. Furthermore, in Table 1 of this Article, the replication cohort for the row Close relative in data set, n (%) was incorrect. All values have now been corrected to 0(0%). The publishers would like to apologise for this error and the inconvenience it may have caused.

Brain scans from 21,297 individuals reveal the genetic architecture of hippocampal subfield volumes.

The hippocampus is a heterogeneous structure, comprising histologically distinguishable subfields. These subfields are differentially involved in memory consolidation, spatial navigation and pattern separation, complex functions often impaired in individuals with brain disorders characterized by reduced hippocampal volume, including Alzheimer's disease (AD) and schizophrenia. Given the structural and functional heterogeneity of the hippocampal formation, we sought to characterize the subfields' genetic architecture. T1-weighted brain scans (n = 21,297, 16 cohorts) were processed with the hippocampal subfields algorithm in FreeSurfer v6.0. We ran a genome-wide association analysis on each subfield, co-varying for whole hippocampal volume. We further calculated the single-nucleotide polymorphism (SNP)-based heritability of 12 subfields, as well as their genetic correlation with each other, with other structural brain features and with AD and schizophrenia. All outcome measures were corrected for age, sex and intracranial volume. We found 15 unique genome-wide significant loci across six subfields, of which eight had not been previously linked to the hippocampus. Top SNPs were mapped to genes associated with neuronal differentiation, locomotor behaviour, schizophrenia and AD. The volumes of all the subfields were estimated to be heritable (h2 from 0.14 to 0.27, all p < 1 × 10-16) and clustered together based on their genetic correlations compared with other structural brain features. There was also evidence of genetic overlap of subicular subfield volumes with schizophrenia. We conclude that hippocampal subfields have partly distinct genetic determinants associated with specific biological processes and traits. Taking into account this specificity may increase our understanding of hippocampal neurobiology and associated pathologies.

Dose response of the 16p11.2 distal copy number variant on intracranial volume and basal ganglia.

Carriers of large recurrent copy number variants (CNVs) have a higher risk of developing neurodevelopmental disorders. The 16p11.2 distal CNV predisposes carriers to e.g., autism spectrum disorder and schizophrenia. We compared subcortical brain volumes of 12 16p11.2 distal deletion and 12 duplication carriers to 6882 non-carriers from the large-scale brain Magnetic Resonance Imaging collaboration, ENIGMA-CNV. After stringent CNV calling procedures, and standardized FreeSurfer image analysis, we found negative dose-response associations with copy number on intracranial volume and on regional caudate, pallidum and putamen volumes (ß = -0.71 to -1.37; P < 0.0005). In an independent sample, consistent results were obtained, with significant effects in the pallidum (ß = -0.95, P = 0.0042). The two data sets combined showed significant negative dose-response for the accumbens, caudate, pallidum, putamen and ICV (P = 0.0032, 8.9 × 10-6, 1.7 × 10-9, 3.5 × 10-12 and 1.0 × 10-4, respectively). Full scale IQ was lower in both deletion and duplication carriers compared to non-carriers. This is the first brain MRI study of the impact of the 16p11.2 distal CNV, and we demonstrate a specific effect on subcortical brain structures, suggesting a neuropathological pattern underlying the neurodevelopmental syndromes.

Distinct Neural Mechanisms Meet Challenges in Dynamic Visual Attention due to Either Load or Object Spacing.

When engaged in dynamic visuospatial tasks, the brain copes with perceptual and cognitive processing challenges. During multiple-object tracking (MOT), the number of objects to be tracked (i.e., load) imposes attentional demands, but so does spatial interference from irrelevant objects (i.e., close encounters). Presently, it is not clear whether the effect of load on accuracy solely depends on the number of close encounters. If so, the same cognitive and physiological mechanisms deal with increasing load by preparing for and dealing with spatial interference. However, this has never been directly tested. Such knowledge is important to understand the neurophysiology of dynamic visual attention and resolve conflicting views within visual cognition concerning sources of capacity limitations. We varied the processing challenge in MOT task in two ways: the number of targets and the minimum spatial proximity between targets and distractors. In a first experiment, we measured task-induced pupil dilations and saccades during MOT. In a separate cohort, we measured fMRI activity. In both cohorts, increased load and close encounters (i.e., close spatial proximity) led to reduced accuracy in an additive manner. Load was associated with pupil dilations, whereas close encounters were not. Activity in dorsal attentional areas and frequency of saccades were proportionally larger both with higher levels of load and close encounters. Close encounters recruited additionally ventral attentional areas that may reflect orienting mechanisms. The activity in two brainstem nuclei, ventral tegmental area/substantia nigra and locus coeruleus, showed clearly dissociated patterns. Our results constitute convergent evidence indicating that different mechanisms underlie processing challenges due to load and object spacing.

Pupillary and behavioral markers of alerting and orienting: An individual difference approach.

Measuring task-evoked pupillary (TEP) responses as an index of phasic activity in the locus coeruleus (LC), we examined two competing hypotheses regarding the alerting and orienting mechanisms of attention. According to a dual mechanism account (Fernandez-Duque & Posner, 1997), two separate noradrenergic and cholinergic mechanisms modulate, respectively, the alerting and orienting effects. However, Corbetta and colleagues (2008) proposed that LC phasic activity may also be involved in orienting effect through its functional relationship with the ventral attentional network. We recruited seventy-five healthy Norwegian participants to perform a Posner cueing task. Both behavioral and pupillary responses revealed the alerting effect. Also, both behavioral and pupillary responses indicated that cued attention is affected by age. Behavioral responses also revealed orienting effect However, we found no TEP differences between valid, invalid, and neutral conditions, suggesting that TEP effects were driven by the alerting effect of cue presentation. Moreover, both behavioral and pupillary estimates of alertness and orienting were uncorrelated. Finally, individual differences in general cognitive abilities did not appear to affect the orienting and alerting mechanisms. This pattern of results is consistent with the dual mechanism account of attention. However, the LC involvement in the (re)orienting attention may be driven by state-specific factors.

Task context load induces reactive cognitive control: An fMRI study on cortical and brain stem activity.

Cognitive control is a highly dynamic process that relies on flexible engagement of prefrontal areas and of neuromodulatory systems in order to adapt to changing demands. A range of internal and external factors come into play when individuals engage in a task requiring cognitive control. Here we investigated whether increased working memory (WM) demands would induce a flexible change in cognitive control mode in young healthy individuals. We developed a novel variant of the well-known AX-continuous performance task (AX-CPT). We manipulated the cognitive demands of maintaining task-relevant contextual information and studied the impact of this manipulation on behavior and brain activity. We expected that low WM load would allow for a more effortful, proactive strategy, while high WM load would induce a strategy of less effortful, stimulus-driven reactive control. In line with our hypothesis, a web-based experiment revealed that increased load was associated with more reactive behavioral responses, and this finding was independently replicated in behavioral data acquired in the MRI scanner. The results from brain activity showed that the right dorsolateral prefrontal cortex was activated by cues in the proactive mode and by probes in the reactive mode. The analysis of task-induced brain stem activity indicated that both the dopaminergic and noradrenergic systems are involved in updating context representations, and that, respectively, these systems mediate a gating signal to the control network and are involved in the dynamic regulation of task engagement.

Correction to: Task context load induces reactive cognitive control: An fMRI study on cortical and brain stem activity.

The article Task context load induces reactive cognitive control.

Conservation of Distinct Genetically-Mediated Human Cortical Pattern.

The many subcomponents of the human cortex are known to follow an anatomical pattern and functional relationship that appears to be highly conserved between individuals. This suggests that this pattern and the relationship among cortical regions are important for cortical function and likely shaped by genetic factors, although the degree to which genetic factors contribute to this pattern is unknown. We assessed the genetic relationships among 12 cortical surface areas using brain images and genotype information on 2,364 unrelated individuals, brain images on 466 twin pairs, and transcriptome data on 6 postmortem brains in order to determine whether a consistent and biologically meaningful pattern could be identified from these very different data sets. We find that the patterns revealed by each data set are highly consistent (p<10-3), and are biologically meaningful on several fronts. For example, close genetic relationships are seen in cortical regions within the same lobes and, the frontal lobe, a region showing great evolutionary expansion and functional complexity, has the most distant genetic relationship with other lobes. The frontal lobe also exhibits the most distinct expression pattern relative to the other regions, implicating a number of genes with known functions mediating immune and related processes. Our analyses reflect one of the first attempts to provide an assessment of the biological consistency of a genetic phenomenon involving the brain that leverages very different types of data, and therefore is not just statistical replication which purposefully use very similar data sets.

Ocular signatures of proactive versus reactive cognitive control in young adults.

During the execution of a cognitive task, the brain maintains contextual information to guide behavior and achieve desired goals. The AX-Continuous Performance Task is used to study proactive versus reactive cognitive control. Young adults tend to behave proactively in standard testing conditions. However, it remains unclear how interindividual variability (e.g., in cognitive and motivational factors) may drive people into more reactive or proactive control under the same task demands. We investigated the use of control strategies in a large population of healthy young adults. We computed the proactive behavioral index and consequently divided participants into proactive, reactive, and intermediate groups. We found that reactive participants were generally slower, presented lower context sensitivity, and larger response variability. Pupillary changes and blink rate index cognitive effort allocation. We measured, concomitantly to the task, the pupil size and frequency of blinks associated with the cue maintenance and response intervals. During the cue period, nonfrequent, nontarget cues led to increased pupil dilation and number of blinks in all participants. During the response interval, we found more errors and increased pupil dilation to the probe when all participants had to overcome a response bias generated by the frequent cue. Only reactive participants showed larger response-related pupil when they had to overcome a response bias related to the frequent probe. Contrary to expectations, groups did not differ in ocular measures in the cue period. In conclusion, interindividual differences in cognitive control between healthy adults can be mapped onto different patterns of effort allocation indexed by the pupil.

Multi-Trait Analysis of GWAS and Biological Insights Into Cognition: A Response to Hill (2018).

Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84-88) presented a critique of our recently published paper in Cell Reports entitled 'Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets' (Lam et al., Cell Reports, Vol. 21, 2017, 2597-2613). Specifically, Hill offered several interrelated comments suggesting potential problems with our use of a new analytic method called Multi-Trait Analysis of GWAS (MTAG) (Turley et al., Nature Genetics, Vol. 50, 2018, 229-237). In this brief article, we respond to each of these concerns. Using empirical data, we conclude that our MTAG results do not suffer from 'inflation in the FDR [false discovery rate]', as suggested by Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84-88), and are not 'more relevant to the genetic contributions to education than they are to the genetic contributions to intelligence'.

A genetic association study of CSMD1 and CSMD2 with cognitive function.

The complement cascade plays a role in synaptic pruning and synaptic plasticity, which seem to be involved in cognitive functions and psychiatric disorders. Genetic variants in the closely related CSMD1 and CSMD2 genes, which are implicated in complement regulation, are associated with schizophrenia. Since patients with schizophrenia often show cognitive impairments, we tested whether variants in CSMD1 and CSMD2 are also associated with cognitive functions per se. We took a discovery-replication approach, using well-characterized Scandinavian cohorts. A total of 1637 SNPs in CSMD1 and 206 SNPs in CSMD2 were tested for association with cognitive functions in the NCNG sample (Norwegian Cognitive NeuroGenetics; n=670). Replication testing of SNPs with p-value<0.001 (7 in CSMD1 and 3 in CSMD2) was carried out in the TOP sample (Thematically Organized Psychosis; n=1025) and the BETULA sample (Betula Longitudinal Study on aging, memory and dementia; n=1742). Finally, we conducted a meta-analysis of these SNPs using all three samples. The previously identified schizophrenia marker in CSMD1 (SNP rs10503253) was also included. The strongest association was observed between the CSMD1 SNP rs2740931 and performance in immediate episodic memory (p-value=5×10-6, minor allele A, MAF 0.48-0.49, negative direction of effect). This association reached the study-wide significance level (p⩽1.2×10-5). SNP rs10503253 was not significantly associated with cognitive functions in our samples. In conclusion, we studied n=3437 individuals and found evidence that a variant in CSMD1 is associated with cognitive function. Additional studies of larger samples with cognitive phenotypes will be needed to further clarify the role of CSMD1 in cognitive phenotypes in health and disease.

High-expanding cortical regions in human development and evolution are related to higher intellectual abilities.

Cortical surface area has tremendously expanded during human evolution, and similar patterns of cortical expansion have been observed during childhood development. An intriguing hypothesis is that the high-expanding cortical regions also show the strongest correlations with intellectual function in humans. However, we do not know how the regional distribution of correlations between intellectual function and cortical area maps onto expansion in development and evolution. Here, in a sample of 1048 participants, we show that regions in which cortical area correlates with visuospatial reasoning abilities are generally high expanding in both development and evolution. Several regions in the frontal cortex, especially the anterior cingulate, showed high expansion in both development and evolution. The area of these regions was related to intellectual functions in humans. Low-expanding areas were not related to cognitive scores. These findings suggest that cortical regions involved in higher intellectual functions have expanded the most during development and evolution. The radial unit hypothesis provides a common framework for interpretation of the findings in the context of evolution and prenatal development, while additional cellular mechanisms, such as synaptogenesis, gliogenesis, dendritic arborization, and intracortical myelination, likely impact area expansion in later childhood.