scholarly journals Cardiometabolic Polygenic Risk Scores and Osteoarthritis Outcomes: A Mendelian Randomization Study Using Data From the Malmö Diet and Cancer Study and the UK Biobank

2019 ◽  
Vol 71 (6) ◽  
pp. 925-934 ◽  
Author(s):  
George Hindy ◽  
Kristina E. Åkesson ◽  
Olle Melander ◽  
Krishna G. Aragam ◽  
Mary E. Haas ◽  
...  
PLoS Medicine ◽  
2021 ◽  
Vol 18 (10) ◽  
pp. e1003782
Author(s):  
Michael Wainberg ◽  
Samuel E. Jones ◽  
Lindsay Melhuish Beaupre ◽  
Sean L. Hill ◽  
Daniel Felsky ◽  
...  

Background Sleep problems are both symptoms of and modifiable risk factors for many psychiatric disorders. Wrist-worn accelerometers enable objective measurement of sleep at scale. Here, we aimed to examine the association of accelerometer-derived sleep measures with psychiatric diagnoses and polygenic risk scores in a large community-based cohort. Methods and findings In this post hoc cross-sectional analysis of the UK Biobank cohort, 10 interpretable sleep measures—bedtime, wake-up time, sleep duration, wake after sleep onset, sleep efficiency, number of awakenings, duration of longest sleep bout, number of naps, and variability in bedtime and sleep duration—were derived from 7-day accelerometry recordings across 89,205 participants (aged 43 to 79, 56% female, 97% self-reported white) taken between 2013 and 2015. These measures were examined for association with lifetime inpatient diagnoses of major depressive disorder, anxiety disorders, bipolar disorder/mania, and schizophrenia spectrum disorders from any time before the date of accelerometry, as well as polygenic risk scores for major depression, bipolar disorder, and schizophrenia. Covariates consisted of age and season at the time of the accelerometry recording, sex, Townsend deprivation index (an indicator of socioeconomic status), and the top 10 genotype principal components. We found that sleep pattern differences were ubiquitous across diagnoses: each diagnosis was associated with a median of 8.5 of the 10 accelerometer-derived sleep measures, with measures of sleep quality (for instance, sleep efficiency) generally more affected than mere sleep duration. Effect sizes were generally small: for instance, the largest magnitude effect size across the 4 diagnoses was β = −0.11 (95% confidence interval −0.13 to −0.10, p = 3 × 10−56, FDR = 6 × 10−55) for the association between lifetime inpatient major depressive disorder diagnosis and sleep efficiency. Associations largely replicated across ancestries and sexes, and accelerometry-derived measures were concordant with self-reported sleep properties. Limitations include the use of accelerometer-based sleep measurement and the time lag between psychiatric diagnoses and accelerometry. Conclusions In this study, we observed that sleep pattern differences are a transdiagnostic feature of individuals with lifetime mental illness, suggesting that they should be considered regardless of diagnosis. Accelerometry provides a scalable way to objectively measure sleep properties in psychiatric clinical research and practice, even across tens of thousands of individuals.


PLoS Genetics ◽  
2019 ◽  
Vol 15 (6) ◽  
pp. e1008202 ◽  
Author(s):  
Lars G. Fritsche ◽  
Lauren J. Beesley ◽  
Peter VandeHaar ◽  
Robert B. Peng ◽  
Maxwell Salvatore ◽  
...  

2017 ◽  
Author(s):  
Guillaume Paré ◽  
Shihong Mao ◽  
Wei Q. Deng

AbstractMachine-learning techniques have helped solve a broad range of prediction problems, yet are not widely used to build polygenic risk scores for the prediction of complex traits. We propose a novel heuristic based on machine-learning techniques (GraBLD) to boost the predictive performance of polygenic risk scores. Gradient boosted regression trees were first used to optimize the weights of SNPs included in the score, followed by a novel regional adjustment for linkage disequilibrium. A calibration set with sample size of ~200 individuals was sufficient for optimal performance. GraBLD yielded prediction R2 of 0.239 and 0.082 using GIANT summary association statistics for height and BMI in the UK Biobank study (N=130K; 1.98M SNPs), explaining 46.9% and 32.7% of the overall polygenic variance, respectively. For diabetes status, the area under the receiver operating characteristic curve was 0.602 in the UK Biobank study using summary-level association statistics from the DIAGRAM consortium. GraBLD outperformed other polygenic score heuristics for the prediction of height (p<2.2x10−16) and BMI (p<1.57x10−4), and was equivalent to LDpred for diabetes. Results were independently validated in the Health and Retirement Study (N=8,292; 688,398 SNPs). Our report demonstrates the use of machine-learning techniques, coupled with summary-level data from large genome-wide meta-analyses to improve the prediction of polygenic traits.


2020 ◽  
Author(s):  
Craig Smail ◽  
Nicole M. Ferraro ◽  
Matthew G. Durrant ◽  
Abhiram S. Rao ◽  
Matthew Aguirre ◽  
...  

SummaryPolygenic risk scores (PRS) aim to quantify the contribution of multiple genetic loci to an individual’s likelihood of a complex trait or disease. However, existing PRS estimate genetic liability using common genetic variants, excluding the impact of rare variants. We identified rare, large-effect variants in individuals with outlier gene expression from the GTEx project and then assessed their impact on PRS predictions in the UK Biobank (UKB). We observed large deviations from the PRS-predicted phenotypes for carriers of multiple outlier rare variants; for example, individuals classified as “low-risk” but in the top 1% of outlier rare variant burden had a 6-fold higher rate of severe obesity. We replicated these findings using data from the NHLBI Trans-Omics for Precision Medicine (TOPMed) biobank and the Million Veteran Program, and demonstrated that PRS across multiple traits will significantly benefit from the inclusion of rare genetic variants.


2021 ◽  
Author(s):  
Yosuke Tanigawa ◽  
Junyang Qian ◽  
Guhan Ram Venkataraman ◽  
Johanne M. Justesen ◽  
Ruilin Li ◽  
...  

We present a systematic assessment of polygenic risk score (PRS) prediction across more than 1,600 traits using genetic and phenotype data in the UK Biobank. We report 428 sparse PRS models with significant (p < 2.5e-5) incremental predictive performance when compared against the covariate-only model that considers age, sex, and the genotype principal components. We report a significant correlation between the number of genetic variants selected in the sparse PRS model and the incremental predictive performance in quantitative traits (Spearman's ρ = 0.54, p = 1.4e-15), but not in binary traits (ρ = 0.059, p = 0.35). The sparse PRS model trained on European individuals showed limited transferability when evaluated on individuals from non-European individuals in the UK Biobank. We provide the PRS model weights on the Global Biobank Engine (https://biobankengine.stanford.edu/prs).


2019 ◽  
Author(s):  
Ben Brumpton ◽  
Eleanor Sanderson ◽  
Fernando Pires Hartwig ◽  
Sean Harrison ◽  
Gunnhild Åberge Vie ◽  
...  

AbstractMendelian randomization (MR) is a widely-used method for causal inference using genetic data. Mendelian randomization studies of unrelated individuals may be susceptible to bias from family structure, for example, through dynastic effects which occur when parental genotypes directly affect offspring phenotypes. Here we describe methods for within-family Mendelian randomization and through simulations show that family-based methods can overcome bias due to dynastic effects. We illustrate these issues empirically using data from 61,008 siblings from the UK Biobank and Nord-Trøndelag Health Study. Both within-family and population-based Mendelian randomization analyses reproduced established effects of lower BMI reducing risk of diabetes and high blood pressure. However, while MR estimates from population-based samples of unrelated individuals suggested that taller height and lower BMI increase educational attainment, these effects largely disappeared in within-family MR analyses. We found differences between population-based and within-family based estimates, indicating the importance of controlling for family effects and population structure in Mendelian randomization studies.


Author(s):  
Wes Spiller ◽  
Fernando Pires Hartwig ◽  
Eleanor Sanderson ◽  
George Davey Smith ◽  
Jack Bowden

Studies leveraging gene-environment (GxE) interactions within Mendelian randomization (MR) analyses have prompted the emergence of two methodologies: MR-GxE and MR-GENIUS. Such methods are attractive in allowing for pleiotropic bias to be corrected when using individual instruments. Specifically, MR-GxE requires an interaction to be explicitly identified, while MR-GENIUS does not. We critically examine the assumptions of MR-GxE and MR-GENIUS, and propose sensitivity analyses to evaluate their performance. Finally, we explore the association between body mass index (BMI) and systolic blood pressure (SBP) using data from the UK Biobank. We find both approaches share similar assumptions, though differences between the approaches lend themselves to differing research settings. Where interactions are identified, MR-GxE relies on weaker assumptions and allows for further sensitivity analyses. MR-GENIUS circumvents the need to identify interactions, but relies on the MR-GxE assumptions holding globally. Through applied analyses we find evidence of a positive effect of BMI upon SBP.


Stroke ◽  
2021 ◽  
Vol 52 (Suppl_1) ◽  
Author(s):  
Julian N Acosta ◽  
Cameron Both ◽  
Natalia Szejko ◽  
Stacy Brown ◽  
Kevin N Sheth ◽  
...  

Introduction: Genome-wide association studies have identified numerous genetic risk variants for stroke and myocardial infarction (MI) in Europeans. However, the limited applicability of these results to non-Europeans due to racial/ethnic differences in the genetic architecture of cardiovascular disease (CVD), coupled with the limited availability of genomic data in non-Europeans, may create significant health disparities now that genomic-based precision medicine is a reality. We tested the hypothesis that the performance of polygenic risk scores (PRS) for CVD differ in Europeans versus non-Europeans. Methods: We conducted a nested study within the UK Biobank, a prospective, population-based study that enrolled ~500,000 participants across the UK. For this study, we identified self-reported black participants and randomly matched them 1:1 by age and sex with white participants. We created a PRS using previously discovered loci for stroke and MI. We then tested whether this PRS representing the aggregate polygenic susceptibility to CVD yielded similar precision in black versus white participants in logistic regression models. Results: Of the 502,536 participants enrolled in the UK Biobank, 8,061 were self-reported blacks, with 7,644 having available data for our analyses. We randomly matched these participants with white individuals, leading to a total sample size of 15,288 (mean age 51.9 [SD 8.1], female 8,722 [57%]). The total number of events was 741 overall, with 363 happening in blacks and 378 happening in whites. In logistic regression models including age, sex, and 5 principal components, the statistical precision (e.g. narrower confidence intervals) for the PRS was substantially higher for whites (OR 1.22, 95%CI 1.08 - 1.37; p<0.0001) compared to blacks (OR 1.24, 95%CI 1.05-1.47; p=0.01). Secondary analyses using genetically-determined ancestry yielded similar results. Conclusion: Because CVD-related PRSs are derived mainly using genetic risk factors identified in populations of European ancestry, their statistical performance is lower in non-European populations. This asymmetry can lead to significant health disparities now that these tools are being evaluated in multiple precision medicine approaches.


2020 ◽  
Vol 16 (S10) ◽  
Author(s):  
Rebecca E Graff ◽  
Sarah F Ackley ◽  
Monica Ospina Romero ◽  
Scott C Zimmerman ◽  
Fanny M Elahi ◽  
...  

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