scholarly journals Thirteen Independent Genetic Loci Associated with Preserved Processing Speed in a Study of Cognitive Resilience in 330,097 Individuals in the UK Biobank

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 122
Author(s):  
Joan Fitzgerald ◽  
Laura Fahey ◽  
Laurena Holleran ◽  
Pilib Ó Broin ◽  
Gary Donohoe ◽  
...  
Keyword(s):  
Cognitive Performance ◽  
Processing Speed ◽  
Structural Equation ◽  
Genome Wide Association Study ◽  
Mendelian Randomisation ◽  
Specific Cell ◽  
Uk Biobank ◽  
Genetic Loci ◽  
A Genome ◽  
The Uk

Cognitive resilience is the ability to withstand the negative effects of stress on cognitive functioning and is important for maintaining quality of life while aging. The UK Biobank does not have measurements of the same cognitive phenotype at distal time points. Therefore, we used education years (EY) as a proxy phenotype for past cognitive performance and current cognitive performance was based on processing speed. This represented an average time span of 40 years between past and current cognitive performance in 330,097 individuals. A confounding factor was that EY is highly polygenic and masked the genetics of resilience. To overcome this, we employed Genomics Structural Equation Modelling (GenomicSEM) to perform a genome-wide association study (GWAS)-by-subtraction using two GWAS, one GWAS of EY and resilience and a second GWAS of EY but not resilience, to generate a GWAS of Resilience. Using independent discovery and replication samples, we found 13 independent genetic loci for Resilience. Functional analyses showed enrichment in several brain regions and specific cell types. Gene-set analyses implicated the biological process “neuron differentiation”, the cellular component “synaptic part” and the “WNT signalosome”. Mendelian randomisation analysis showed a causative effect of white matter volume on cognitive resilience. These results may contribute to the neurobiological understanding of resilience.

scholarly journals Identification of 13 independent genetic loci associated with cognitive resilience in healthy aging in 330,097 individuals in the UK Biobank

2021 ◽  
Author(s):  
Joan Fitzgerald ◽  
Laura Fahey ◽  
Laurena Holleran ◽  
Pilib Ó Broin ◽  
Gary Donohoe ◽  
...  
Keyword(s):  
Healthy Aging ◽  
Genome Wide Association Study ◽  
Cell Types ◽  
Brain Regions ◽  
Specific Cell ◽  
Uk Biobank ◽  
Negative Effects ◽  
Genome Wide ◽  
A Genome ◽  
The Uk

AbstractCognitive resilience is the ability to withstand the negative effects of stress on cognitive functioning and is important for maintaining quality of life while aging. Here we employed a proxy phenotype approach to create a longitudinal cognitive resilience phenotype using past education years and current processing speed, reflecting an average time span of 40 years, in 330,097 individuals from the UK Biobank. A genome-wide association study identified 13 independent genome-wide significant loci that implicate 33 genes. A portion of resilience’s genetic signal is distinct from the genetics of intelligence. Functional analyses showed enrichment in several brain regions and involvement of specific cell types, including GABAergic neurons (P=6.59×10−8) and glutamatergic neurons (P=6.98×10−6) in the cortex. Gene-set analyses implicated the biological process “neuron differentiation” (P=9.7×10−7) and the cellular component “synaptic part” (P=2.14×10−6). Mendelian randomization analysis showed a causative effect of white matter volume on cognitive resilience. These results enhance neurobiological understanding of resilience.

scholarly journals Brain age prediction using deep learning uncovers associated sequence variants

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
B. A. Jonsson ◽  
G. Bjornsdottir ◽  
T. E. Thorgeirsson ◽  
L. M. Ellingsen ◽  
G. Bragi Walters ◽  
...  
Keyword(s):  
Deep Learning ◽  
Genome Wide Association Study ◽  
Structural Mri ◽  
Machine Learning Algorithms ◽  
Age Difference ◽  
Sequence Variants ◽  
Uk Biobank ◽  
A Genome ◽  
The Uk ◽  
Brain Age

AbstractMachine learning algorithms can be trained to estimate age from brain structural MRI. The difference between an individual’s predicted and chronological age, predicted age difference (PAD), is a phenotype of relevance to aging and brain disease. Here, we present a new deep learning approach to predict brain age from a T1-weighted MRI. The method was trained on a dataset of healthy Icelanders and tested on two datasets, IXI and UK Biobank, utilizing transfer learning to improve accuracy on new sites. A genome-wide association study (GWAS) of PAD in the UK Biobank data (discovery set: $$N=12378$$N=12378, replication set: $$N=4456$$N=4456) yielded two sequence variants, rs1452628-T ($$\beta =-0.08$$β=−0.08, $$P=1.15\times{10}^{-9}$$P=1.15×10−9) and rs2435204-G ($$\beta =0.102$$β=0.102, $$P=9.73\times 1{0}^{-12}$$P=9.73×10−12). The former is near KCNK2 and correlates with reduced sulcal width, whereas the latter correlates with reduced white matter surface area and tags a well-known inversion at 17q21.31 (H2).

Abstract 14653: Genome-wide Association Study of Peripheral Artery Disease and Critical Limb Ischemia Identifies Novel Genetic Loci and Coagulation Pathways

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Chayakrit Krittanawong ◽  
Jagat Narula ◽  
Kipp W Johnson ◽  
Navneet Narula ◽  
Jeffrey S Berger ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Limb Ischemia ◽  
Case Control ◽  
Uk Biobank ◽  
Bonferroni Correction ◽  
Peripheral Artery ◽  
Genetic Loci ◽  
Genome Wide ◽  
Artery Disease ◽  
The Uk

Introduction: The pathogenesis of peripheral artery disease (PAD) and critical limb ischemia (CLI) are poorly understood. Hypothesis: We hypothesize that genetic factors related to abnormalities in coagulation or fibrinolysis, in addition to atherosclerosis, could play an important role in PAD patients and PAD with CLI patients. Methods: A genome-wide association study (GWAS) was performed testing for associations between single-nucleotide variants (SNVs) and PAD case-control (3,190 cases and 463,495 controls) and subgroup analysis of PAD with CLI case-control (142 cases and 3,048 controls) in the UK Biobank cohort. To further validate the results, we selected SNVs with the most significant Cochrane-Armitage trend p values without evidence of strong linkage disequilibrium (r2 > 0.8) for PAD with CLI case-control in the BioMe Biobank. We tested for association using BOLT-LMM with adjustment for age, sex, BMI, and the first ten principal components to control for population structure. The SNV association tests' significance level was set at P < 5x10–8 after Bonferroni correction. Results: 363 SNVs from 81 genetic loci reached the threshold for statistical significance based on a Bonferroni correction (p <5x10–8). (Figure) We then performed a subgroup analysis between PAD patients and PAD with CLI patients in the UK Biobank. We identified 63 SNVs with 52 genetic loci independent for PAD with CLI in the UK Biobank. We further validated those 63 SNVs with 52 genetic loci in the BioMe Biobank. In the validation cohort, 2 genetic loci ( PLG and CDKN2B ) were independent for PAD with CLI. On pathway analyses, we identify several new loci that implicate thrombotic, inflammation, glycosaminoglycan synthesis, coagulation, and fibrinolytic pathways involved in PAD along with known atherosclerosis pathways (p <0.05). Conclusions: We show that PLG gene related to coagulation pathways in PAD may play an important role in coagulation-related PAD pathogenesis.

scholarly journals A novel variant in GLIS3 is associated with osteoarthritis

2018 ◽  
Vol 77 (4) ◽  
pp. 620-623 ◽  
Author(s):  
Elisabetta Casalone ◽  
Ioanna Tachmazidou ◽  
Eleni Zengini ◽  
Konstantinos Hatzikotoulas ◽  
Sophie Hackinger ◽  
...  
Keyword(s):  
Complex Disease ◽  
Genome Wide Association Study ◽  
Total Joint Replacement ◽  
Population Based ◽  
Uk Biobank ◽  
Proteomics Data ◽  
Glucose Levels ◽  
Genome Wide ◽  
A Genome ◽  
The Uk

ObjectivesOsteoarthritis (OA) is a complex disease, but its genetic aetiology remains poorly characterised. To identify novel susceptibility loci for OA, we carried out a genome-wide association study (GWAS) in individuals from the largest UK-based OA collections to date.MethodsWe carried out a discovery GWAS in 5414 OA individuals with knee and/or hip total joint replacement (TJR) and 9939 population-based controls. We followed-up prioritised variants in OA subjects from the interim release of the UK Biobank resource (up to 12 658 cases and 50 898 controls) and our lead finding in operated OA subjects from the full release of UK Biobank (17 894 cases and 89 470 controls). We investigated its functional implications in methylation, gene expression and proteomics data in primary chondrocytes from 12 pairs of intact and degraded cartilage samples from patients undergoing TJR.ResultsWe detect a genome-wide significant association at rs10116772 with TJR (P=3.7×10−8; for allele A: OR (95% CI) 0.97 (0.96 to 0.98)), an intronic variant in GLIS3, which is expressed in cartilage. Variants in strong correlation with rs10116772 have been associated with elevated plasma glucose levels and diabetes.ConclusionsWe identify a novel susceptibility locus for OA that has been previously implicated in diabetes and glycaemic traits.

scholarly journals A genome-wide association study finds genetic variants associated with neck or shoulder pain in UK Biobank

2020 ◽  
Vol 29 (8) ◽  
pp. 1396-1404 ◽  
Author(s):  
Weihua Meng ◽  
Brian W Chan ◽  
Cameron Harris ◽  
Maxim B Freidin ◽  
Harry L Hebert ◽  
...  
Keyword(s):  
Association Study ◽  
Shoulder Pain ◽  
Genetic Variants ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Uk Biobank ◽  
Genome Wide ◽  
A Genome ◽  
Significant Locus ◽  
The Uk

Abstract Background Common types of musculoskeletal conditions include pain in the neck and shoulder areas. This study seeks to identify the genetic variants associated with neck or shoulder pain based on a genome-wide association approach using 203 309 subjects from the UK Biobank cohort and look for replication evidence from the Generation Scotland: Scottish Family Health Study (GS:SFHS) and TwinsUK. Methods A genome-wide association study was performed adjusting for age, sex, BMI and nine population principal components. Significant and independent genetic variants were then sent to GS:SFHS and TwinsUK for replication. Results We identified three genetic loci that were associated with neck or shoulder pain in the UK Biobank samples. The most significant locus was in an intergenic region in chromosome 17, rs12453010, having P = 1.66 × 10−11. The second most significant locus was located in the FOXP2 gene in chromosome 7 with P = 2.38 × 10−10 for rs34291892. The third locus was located in the LINC01572 gene in chromosome 16 with P = 4.50 × 10−8 for rs62053992. In the replication stage, among four significant and independent genetic variants, rs2049604 in the FOXP2 gene and rs62053992 in the LINC01572 gene were weakly replicated in GS:SFHS (P = 0.0240 and P = 0.0202, respectively). Conclusions We have identified three loci associated with neck or shoulder pain in the UK Biobank cohort, two of which were weakly supported in a replication cohort. Further evidence is needed to confirm their roles in neck or shoulder pain.

scholarly journals Genetic underpinnings of sociability in the UK Biobank

2019 ◽  
Author(s):  
J Bralten ◽  
CJHM Klemann ◽  
NR Mota ◽  
W De Witte ◽  
C Arango ◽  
...  
Keyword(s):  
Social Anxiety ◽  
Psychiatric Disorders ◽  
Genetic Correlation ◽  
Genome Wide Association Study ◽  
Autism Spectrum ◽  
Self Report ◽  
Uk Biobank ◽  
Genome Wide ◽  
A Genome ◽  
The Uk

ABSTRACTDifficulties with sociability include a tendency to avoid social contacts and activities, and to prefer being alone rather than being with others. While sociability is a continuously distributed trait in the population, decreased sociability represent a common early manifestation of multiple neuropsychiatric disorders such as Schizophrenia (SCZ), Bipolar Disorder (BP), Major Depressive Disorder (MDD), Autism Spectrum Disorders (ASDs), and Alzheimer’s disease (AD). We aimed to investigate the genetic underpinnings of sociability as a continuous trait in the general population. In this respect, we performed a genome-wide association study (GWAS) using a sociability score based on 4 social functioning-related self-report questions in the UK Biobank sample (n=342,461) to test the effect of individual genetic variants. This was followed by LD score analyses to investigate the genetic correlation with psychiatric disorders (SCZ, BP, MDD, ASDs) and a neurological disorder (AD) as well as related phenotypes (Loneliness and Social Anxiety). The phenotypic data indeed showed that the sociability score was decreased in individuals with ASD, (probable) MDD, BP and SCZ, but not in individuals with AD. Our GWAS showed 604 genome-wide significant SNPs, coming from 18 independent loci (SNP-based h2=0.06). Genetic correlation analyses showed significant correlations with SCZ (rg=0.15, p=9.8e-23), MDD (rg=0.68, p=6.6e-248) and ASDs (rg=0.27, p=4.5e-28), but no correlation with BP (rg=0.01, p=0.45) or AD (rg=0.04, p=0.55). Our sociability trait was also genetically correlated with Loneliness (rg=0.45, p=2.4e-8) and Social Anxiety (rg=0.48, p=0.002). Our study shows that there is a significant genetic component to variation in population levels of sociability, which is relevant to some psychiatric disorders (SCZ, MDD, ASDs), but not to BP and AD.

scholarly journals A genome-wide association study identifies that the GDF5 and COL27A1 genes are associated with knee pain in UK Biobank (N = 171, 516)

2019 ◽  
Author(s):  
Weihua Meng ◽  
Mark J Adams ◽  
Colin NA Palmer ◽  
Jingchunzi Shi ◽  
Adam Auton ◽  
...  
Keyword(s):  
Knee Pain ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Uk Biobank ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Genome Wide ◽  
A Genome ◽  
The Uk

SUMMARYObjectiveKnee pain is one of the most common musculoskeletal complaints that brings people to medical attention. We sought to identify the genetic variants associated with knee pain in 171,516 subjects from the UK Biobank cohort and replicate them using cohorts from 23andMe, the Osteoarthritis Initiative (OAI), and the Johnston County Osteoarthritis Study (JoCo).MethodsWe performed a genome-wide association study of knee pain in the UK Biobank, where knee pain was ascertained through self-report and defined as “knee pain in the last month interfering with usual activities”. A total of 22,204 cases and 149,312 controls were included in the discovery analysis. We tested our top and independent SNPs (P < 5 × 10−8) for replication in 23andMe, OAI, and JoCo, then performed a joint meta-analysis between discovery and replication cohorts using GWAMA. We calculated the narrow-sense heritability of knee pain using Genome-wide Complex Trait Analysis (GCTA).ResultsWe identified 2 loci that reached genome-wide significance, rs143384 located in the GDF5 (P = 1.32 × 10−12), a gene previously implicated in osteoarthritis, and rs2808772, located near COL27A1 (P = 1.49 × 10−8). These findings were subsequently replicated in independent cohorts and increased in significance in the joint meta-analysis (rs143384: P = 4.64 × 10−18; rs2808772: P −11 = 2.56 × 10−1’). The narrow sense heritability of knee pain was 0.08.ConclusionIn this first reported genome-wide association meta-analysis of knee pain, we identified and replicated two loci in or near GDF5 and COL27A1 that are associated with knee pain.

scholarly journals Genome-wide Association Study of Pulmonary Function in Europeans and Africans from the UK Biobank Identifies Distinct Variants

2022 ◽  
Author(s):  
Musalula Sinkala ◽  
Samar S. M. Elsheikh ◽  
Mamana Mbiyavanga ◽  
Joshua Cullinan ◽  
Nicola Mulder
Keyword(s):  
Pulmonary Function ◽  
Genome Wide Association Study ◽  
Well Being ◽  
Genome Wide Association ◽  
Significant Finding ◽  
Uk Biobank ◽  
Chromosome 11 ◽  
Genome Wide ◽  
A Genome ◽  
The Uk

Pulmonary function is an indicator of well-being, and pulmonary pathologies are the third major cause of death worldwide. FEV1, FVC, and PEF are quantitively used to assess pulmonary function. We conducted a genome-wide association analysis of pulmonary function in 383,471 individuals of European and 5,978 African descent represented in the UK Biobank. Here, we report 817 variants in Europeans and 3 in Africans associated (p-values < 5 x 10-8) with three pulmonary function parameters; FEV1, FVC and PEF. In addition to 377 variants in Europeans previously reported to be associated with phenotypes related to pulmonary function, we identified 330 novel loci, including an ISX intergenic variant rs369476290 on chromosome 22 in Africans and a KDM2A intron variant rs12790261 on chromosome 11 in Europeans. Remarkably, we find no shared variants among Africans and Europeans. Enrichment analyses of variants separately for each ancestry background revealed significant enrichment for terms related to pulmonary phenotypes in Europeans but not Africans. Further analysis of studies of pulmonary phenotypes revealed individuals of European background are disproportionally overrepresented in datasets compared to Africans, with the gap widening over the past five years. Our findings offer a better understanding of the different variants that modify pulmonary function in Africans and Europeans, a significant finding for future GWAS studies and medicine.

scholarly journals Association between birth weight and refractive error in adulthood: a Mendelian randomisation study

2019 ◽  
Vol 104 (2) ◽  
pp. 214-219 ◽  
Author(s):  
Denis Plotnikov ◽  
Cathy Williams ◽  
Jeremy A Guggenheim
Keyword(s):  
Birth Weight ◽  
Refractive Error ◽  
Genome Wide Association Study ◽  
Causal Effect ◽  
Ordinary Least Squares ◽  
Mendelian Randomisation ◽  
Uk Biobank ◽  
Normal Range ◽  
A Genome ◽  
The Impact

BackgroundPathological myopia is one of the leading causes of blindness globally. Lower birth weight (BW) within the normal range has been reported to increase the risk of myopia, although findings conflict. We sought to estimate the causal effect of BW on refractive error using Mendelian randomisation (MR), under the assumption of a linear relationship.MethodsGenetic variants associated with BW were identified from meta-analysis of a genome-wide association study (GWAS) for self-reported BW in 162 039 UK Biobank participants and a published Early Growth Genetics (EGG) consortium GWAS (n=26 836). We performed a one-sample MR analysis in 39 658 unrelated, adult UK Biobank participants (independent of the GWAS sample) using an allele score for BW as instrumental variable. A two-sample MR sensitivity analysis and conventional ordinary least squares (OLS) regression analyses were also undertaken.ResultsIn OLS analysis, BW showed a small, positive association with refractive error: +0.04 D per SD increase in BW (95% CI 0.02 to 0.07; p=0.002). The one-sample MR-estimated causal effect of BW on refractive error was higher, at +0.28 D per SD increase in BW (95% CI 0.05 to 0.52, p=0.02). A two-sample MR analysis provided similar causal effect estimates, with minimal evidence of directional pleiotropy.ConclusionsOur study suggests lower BW within the normal range is causally associated with a more myopic refractive error. However, the impact of the causal effect was modest (range 1.00 D covering approximately 95% of the population).

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