scholarly journals The genetic architecture of the human cerebral cortex

2018 ◽  
Author(s):  
Katrina L. Grasby ◽  
Neda Jahanshad ◽  
Jodie N. Painter ◽  
Lucía Colodro-Conde ◽  
Janita Bralten ◽  
...  
Keyword(s):  
Cerebral Cortex ◽  
Surface Area ◽  
Multiple Testing ◽  
Meta Analysis ◽  
Brain Mri ◽  
Regulatory Elements ◽  
Total Surface Area ◽  
Multiple Testing Correction ◽  
Cortical Structure ◽  
A Genome

The cerebral cortex underlies our complex cognitive capabilities, yet we know little about the specific genetic loci influencing human cortical structure. To identify genetic variants, including structural variants, impacting cortical structure, we conducted a genome-wide association meta-analysis of brain MRI data from 51,662 individuals. We analysed the surface area and average thickness of the whole cortex and 34 regions with known functional specialisations. We identified 255 nominally significant loci (P≤ 5 × 10−8); 199 survived multiple testing correction (P≤ 8.3 × 10−10; 187 surface area; 12 thickness). We found significant enrichment for loci influencing total surface area within regulatory elements active during prenatal cortical development, supporting the radial unit hypothesis. Loci impacting regional surface area cluster near genes in Wnt signalling pathways, known to influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson’s disease, insomnia, depression and ADHD.One Sentence SummaryCommon genetic variation is associated with inter-individual variation in the structure of the human cortex, both globally and within specific regions, and is shared with genetic risk factors for some neuropsychiatric disorders.

scholarly journals The genetic architecture of the human cerebral cortex

Science ◽  
2020 ◽  
Vol 367 (6484) ◽  
pp. eaay6690 ◽  
Author(s):  
Katrina L. Grasby ◽  
Neda Jahanshad ◽  
Jodie N. Painter ◽  
Lucía Colodro-Conde ◽  
Janita Bralten ◽  
...  
Keyword(s):  
Cerebral Cortex ◽  
Surface Area ◽  
Meta Analysis ◽  
Brain Magnetic Resonance Imaging ◽  
Regulatory Elements ◽  
Total Surface Area ◽  
Imaging Data ◽  
Cortical Structure ◽  
A Genome ◽  
Significant Enrichment

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson’s disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder.

scholarly journals Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions

2018 ◽  
Author(s):  
David M. Howard ◽  
Mark J. Adams ◽  
Toni-Kim Clarke ◽  
Jonathan D. Hafferty ◽  
Jude Gibson ◽  
...  
Keyword(s):  
Multiple Testing ◽  
Drug Repositioning ◽  
Association Studies ◽  
Meta Analysis ◽  
Enrichment Analysis ◽  
Brain Regions ◽  
Genome Wide Association Studies ◽  
Multiple Testing Correction ◽  
Synaptic Structure ◽  
Genome Wide

AbstractMajor depression is a debilitating psychiatric illness that is typically associated with low mood, anhedonia and a range of comorbidities. Depression has a heritable component that has remained difficult to elucidate with current sample sizes due to the polygenic nature of the disorder. To maximise sample size, we meta-analysed data on 807,553 individuals (246,363 cases and 561,190 controls) from the three largest genome-wide association studies of depression. We identified 102 independent variants, 269 genes, and 15 gene-sets associated with depression, including both genes and gene-pathways associated with synaptic structure and neurotransmission. Further evidence of the importance of prefrontal brain regions in depression was provided by an enrichment analysis. In an independent replication sample of 1,306,354 individuals (414,055 cases and 892,299 controls), 87 of the 102 associated variants were significant following multiple testing correction. Based on the putative genes associated with depression this work also highlights several potential drug repositioning opportunities. These findings advance our understanding of the complex genetic architecture of depression and provide several future avenues for understanding aetiology and developing new treatment approaches.

scholarly journals Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 87
Author(s):  
Sean M. Burnard ◽  
Rodney A. Lea ◽  
Miles Benton ◽  
David Eccles ◽  
Daniel W. Kennedy ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Complex Traits ◽  
Multiple Testing ◽  
Large Scale ◽  
Disease Risk ◽  
Association Studies ◽  
Meta Analysis ◽  
Elastic Net ◽  
Genome Wide Association Studies ◽  
Multiple Testing Correction

Conventional genome-wide association studies (GWASs) of complex traits, such as Multiple Sclerosis (MS), are reliant on per-SNP p-values and are therefore heavily burdened by multiple testing correction. Thus, in order to detect more subtle alterations, ever increasing sample sizes are required, while ignoring potentially valuable information that is readily available in existing datasets. To overcome this, we used penalised regression incorporating elastic net with a stability selection method by iterative subsampling to detect the potential interaction of loci with MS risk. Through re-analysis of the ANZgene dataset (1617 cases and 1988 controls) and an IMSGC dataset as a replication cohort (1313 cases and 1458 controls), we identified new association signals for MS predisposition, including SNPs above and below conventional significance thresholds while targeting two natural killer receptor loci and the well-established HLA loci. For example, rs2844482 (98.1% iterations), otherwise ignored by conventional statistics (p = 0.673) in the same dataset, was independently strongly associated with MS in another GWAS that required more than 40 times the number of cases (~45 K). Further comparison of our hits to those present in a large-scale meta-analysis, confirmed that the majority of SNPs identified by the elastic net model reached conventional statistical GWAS thresholds (p < 5 × 10−8) in this much larger dataset. Moreover, we found that gene variants involved in oxidative stress, in addition to innate immunity, were associated with MS. Overall, this study highlights the benefit of using more advanced statistical methods to (re-)analyse subtle genetic variation among loci that have a biological basis for their contribution to disease risk.

scholarly journals Cortical structure and the risk for Alzheimer’s disease: a bidirectional Mendelian randomization study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bang-Sheng Wu ◽  
Ya-Ru Zhang ◽  
Hong-Qi Li ◽  
Kevin Kuo ◽  
Shi-Dong Chen ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Causal Relationship ◽  
Surface Area ◽  
Mendelian Randomization ◽  
Brain Area ◽  
Meta Analysis ◽  
European Ancestry ◽  
Cortical Structure ◽  
Temporal Pole

AbstractProgressive loss of neurons in a specific brain area is one of the manifestations of Alzheimer’s disease (AD). Much effort has been devoted to investigating brain atrophy and AD. However, the causal relationship between cortical structure and AD is not clear. We conducted a bidirectional two-sample Mendelian randomization analysis to investigate the causal relationship between cortical structure (surface area and thickness of the whole cortex and 34 cortical regions) and AD risk. Genetic variants used as instruments came from a large genome-wide association meta-analysis of cortical structure (33,992 participants of European ancestry) and AD (AD and AD-by-proxy, 71,880 cases, 383,378 controls). We found suggestive associations of the decreased surface area of the temporal pole (OR (95% CI): 0.95 (0.9, 0.997), p = 0.04), and decreased thickness of cuneus (OR (95% CI): 0.93 (0.89, 0.98), p = 0.006) with higher AD risk. We also found a suggestive association of vulnerability to AD with the decreased surface area of precentral (β (SE): –43.4 (21.3), p = 0.042) and isthmus cingulate (β (SE): –18.5 (7.3), p = 0.011). However, none of the Bonferroni-corrected p values of the causal relationship between cortical structure and AD met the threshold. We show suggestive evidence of an association of the atrophy of the temporal pole and cuneus with higher AD risk. In the other direction, there was a suggestive causal relationship between vulnerability to AD and the decreased surface area of the precentral and isthmus cingulate. Our findings shed light on the associations of cortical structure with the occurrence of AD.

scholarly journals Vitamin D Receptor Gene Polymorphisms Have Negligible Effect on Human Height

2008 ◽  
Vol 11 (5) ◽  
pp. 488-494 ◽  
Author(s):  
Stuart Macgregor ◽  
Jouke-Jan Hottenga ◽  
Penelope A. Lind ◽  
H. Eka D. Suchiman ◽  
Gonneke Willemsen ◽  
...  
Keyword(s):  
Vitamin D ◽  
Vitamin D Receptor ◽  
Multiple Testing ◽  
Meta Analysis ◽  
Receptor Gene ◽  
Phenotypic Variance ◽  
Multiple Testing Correction ◽  
Vdr Gene ◽  
Vitamin D Levels ◽  
Human Height

AbstractHuman height is a highly heritable trait, with genetic factors explaining up to 90% of phenotypic variation. Vitamin D levels are known to influence several physiological processes, including skeletal growth. The vitamin D receptor (VDR) gene has been reported as contributing to variation in height. A meta-analysis of 13607 adult individuals found a small but significant association with the rs1544410 (BsmI) polymorphism. In contrast, the meta-analysis found no effect in a sample of 550 children. Two recent studies reported variants with large effect on height elsewhere in VDR (rs10735810 [FokI] and rs7139166 [-1521] polymorphisms). We genotyped large Caucasian samples from Australia (N= 3906) and the Netherlands (N= 1689) for polymorphisms in VDR. The Australian samples were twin families with height measures from 3 time points throughout adolescence. The Dutch samples were adult twins. We use the available family data to perform both within and between family tests of association. We found no significant associations for any of the genotyped variants after multiple testing correction. The (non-significant) effect of rs1544410 in the Australian adolescent cohort was in the same direction and of similar magnitude (additive effect 0.3cm) to the effect observed in the published adult meta-analysis. An effect of this size explains ~0.1% of the phenotypic variance in height — this implies that many, probably hundreds, of such variants are responsible for the observed genetic variation. Our results did not support any role for two other regions (rs10735810, rs7139166) of VDR in explaining variation in height.

scholarly journals Personality and local brain structure: their shared genetic basis and reproducibility

2019 ◽  
Author(s):  
Sofie L. Valk ◽  
Felix Hoffstaedter ◽  
Julia A. Camilleri ◽  
Peter Kochunov ◽  
B.T. Thomas Yeo ◽  
...  
Keyword(s):  
Personality Traits ◽  
Surface Area ◽  
Brain Structure ◽  
Large Scale ◽  
Local Variation ◽  
Total Surface Area ◽  
Frontal Surface ◽  
Cortical Structure ◽  
Human Connectome Project ◽  
Local Brain

AbstractLocal variation in cortical architecture is highly heritable and distinct genes are associated with specific cortical regions. Total surface area has been shown to be genetically correlated with complex cognitive capacities, suggesting cortical brain structure is a viable endophenotype linking genes to behavior. However, to what extend local brain structure has a genetic association with cognitive and emotional functioning is incompletely understood. Here, we study the genetic correlation between personality traits and local cortical structure in a large-scale twin sample (Human Connectome Project, n=1106, 22-37y). We found a genetic overlap between personality traits and local cortical structure in 10 of 17 observed phenotypic associations in predominantly frontal cortices. To evaluate the robustness of observed personality-brain associations we studied two independent age-matched samples (GSP: n=926, age=19-35y, eNKI: n=210, age: 19-39y). We observed anecdotal to moderate evidence for a successful replication of the negative association between surface area in medial prefrontal cortex and Neuroticism in both samples. Quantitative functional decoding indicated this region is implicated in emotional and socio-cognitive functional processes. In sum, our observations suggest that associations between local brain structure and personality are, in part, under genetic control. However, associations are weak and only the relation between frontal surface area and Neuroticism was consistently observed across three independent samples of young adults.

scholarly journals Validation of GWAS-Identified Variants for Anti-TNF Drug Response in Rheumatoid Arthritis: A Meta-Analysis of Two Large Cohorts

2021 ◽  
Vol 12 ◽  
Author(s):  
Jose Manuel Sánchez-Maldonado ◽  
Rafael Cáliz ◽  
Miguel Ángel López-Nevot ◽  
Antonio José Cabrera-Serrano ◽  
Ana Moñiz-Díez ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Multiple Testing ◽  
Drug Response ◽  
Disease Activity Score ◽  
Meta Analysis ◽  
Routine Care ◽  
Multiple Testing Correction ◽  
Discovery Cohort ◽  
E Coli ◽  
Inflammatory Effect

We aimed to validate the association of 28 GWAS-identified genetic variants for response to TNF inhibitors (TNFi) in a discovery cohort of 1361 rheumatoid arthritis (RA) patients monitored in routine care and ascertained through the REPAIR consortium and DANBIO registry. We genotyped selected markers and evaluated their association with response to TNFi after 6 months of treatment according to the change in disease activity score 28 (ΔDAS28). Next, we confirmed the most interesting results through meta-analysis of our data with those from the DREAM cohort that included 706 RA patients treated with TNFi. The meta-analysis of the discovery cohort and DREAM registry including 2067 RA patients revealed an overall association of the LINC02549rs7767069 SNP with a lower improvement in DAS28 that remained significant after correction for multiple testing (per-allele ORMeta=0.83, PMeta=0.000077; PHet=0.61). In addition, we found that each copy of the LRRC55rs717117G allele was significantly associated with lower improvement in DAS28 in rheumatoid factor (RF)-positive patients (per-allele ORMeta=0.67, P=0.00058; PHet=0.06) whereas an opposite but not significant effect was detected in RF-negative subjects (per-allele ORMeta=1.38, P=0.10; PHet=0.45; PInteraction=0.00028). Interestingly, although the identified associations did not survive multiple testing correction, the meta-analysis also showed overall and RF-specific associations for the MAFBrs6071980 and CNTN5rs1813443 SNPs with decreased changes in DAS28 (per-allele ORMeta_rs6071980 = 0.85, P=0.0059; PHet=0.63 and ORMeta_rs1813443_RF+=0.81, P=0.0059; PHet=0.69 and ORMeta_rs1813443_RF-=1.00, P=0.99; PHet=0.12; PInteraction=0.032). Mechanistically, we found that subjects carrying the LINC02549rs7767069T allele had significantly increased numbers of CD45RO+CD45RA+ T cells (P=0.000025) whereas carriers of the LINC02549rs7767069T/T genotype showed significantly increased levels of soluble scavengers CD5 and CD6 in serum (P=0.00037 and P=0.00041). In addition, carriers of the LRRC55rs717117G allele showed decreased production of IL6 after stimulation of PBMCs with B burgdorferi and E coli bacteria (P=0.00046 and P=0.00044), which suggested a reduced IL6-mediated anti-inflammatory effect of this marker to worsen the response to TNFi. In conclusion, this study confirmed the influence of the LINC02549 and LRRC55 loci to determine the response to TNFi in RA patients and suggested a weak effect of the MAFB and CNTN5 loci that need to be further investigated.

scholarly journals Epigenetic DNA methylation changes associated with headache chronification: A retrospective case-control study

Cephalalgia ◽  
2017 ◽  
Vol 38 (2) ◽  
pp. 312-322 ◽  
Author(s):  
Bendik S Winsvold ◽  
Priit Palta ◽  
Else Eising ◽  
Christian M Page ◽  
Arn MJM van den Maagdenberg ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Multiple Testing ◽  
Chronic Headache ◽  
Meta Analysis ◽  
Linear Regression Analysis ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Multiple Testing Correction ◽  
Retrospective Case ◽  
Cpg Sites

Background The biological mechanisms of headache chronification are poorly understood. We aimed to identify changes in DNA methylation associated with the transformation from episodic to chronic headache. Methods Participants were recruited from the population-based Norwegian HUNT Study. Thirty-six female headache patients who transformed from episodic to chronic headache between baseline and follow-up 11 years later were matched against 35 controls with episodic headache. DNA methylation was quantified at 485,000 CpG sites, and changes in methylation level at these sites were compared between cases and controls by linear regression analysis. Data were analyzed in two stages (Stages 1 and 2) and in a combined meta-analysis. Results None of the top 20 CpG sites identified in Stage 1 replicated in Stage 2 after multiple testing correction. In the combined meta-analysis the strongest associated CpG sites were related to SH2D5 and NPTX2, two brain-expressed genes involved in the regulation of synaptic plasticity. Functional enrichment analysis pointed to processes including calcium ion binding and estrogen receptor pathways. Conclusion In this first genome-wide study of DNA methylation in headache chronification several potentially implicated loci and processes were identified. The study exemplifies the use of prospectively collected population cohorts to search for epigenetic mechanisms of disease.

scholarly journals Significant non-existence of sequences in genomes and proteomes

2020 ◽  
Author(s):  
Grigorios Koulouras ◽  
Martin C. Frith
Keyword(s):  
Multiple Testing ◽  
Multiple Testing Correction ◽  
Web Based ◽  
A Genome ◽  
Restriction Sites ◽  
Human Proteins ◽  
Viral Mimicry ◽  
Human Viruses ◽  
Diversity Of Life

AbstractNullomers are minimal-length oligomers absent from a genome or proteome. Although research has shown that artificially synthesized nullomers have deleterious effects, there is still a lack of a strategy for the prioritisation and classification of non-occurring sequences as potentially malicious or benign. In this work, by using Markovian models with multiple-testing correction, we reveal significant absent oligomers which are statistically expected to exist. This strongly suggests that their absence is due to negative selection. We survey genomes and proteomes covering the diversity of life, and find thousands of significant absent sequences. Common significant nullomers are often mono- or dinucleotide tracts, or palindromic. Significant viral nullomers are often restriction sites, and may indicate unknown restriction motifs. Surprisingly, significant mammal genome nullomers are often present, but rare, in other mammals, suggesting that they are suppressed but not completely forbidden. Significant human nullomers are rarely present in human viruses, indicating viral mimicry of the host. More than 1/4 of human proteins are one substitution away from containing a significant nullomer. We provide a web-based, interactive database of significant nullomers across genomes and proteomes.

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