scholarly journals Construction of an exome-wide risk score for schizophrenia based on a weighted burden test

2017 ◽  
Author(s):  
David Curtis
Keyword(s):  
Risk Score ◽  
Rare Variants ◽  
Risk Scores ◽  
Individual Risk ◽  
Data Sets ◽  
Weighted Sum ◽  
Polygenic Risk ◽  
Whole Exome ◽  
Sequencing Studies ◽  
Burden Test

SummaryPolygenic risk scores obtained as a weighted sum of associated variants can be used to explore association in additional data sets and to assign risk scores to individuals. The methods used to derive polygenic risk scores from common SNPs are not suitable for variants detected in whole exome sequencing studies. Rare variants which may have major effects are seen too infrequently to judge whether they are associated and may not be shared between training and test subjects. A method is proposed whereby variants are weighted according to their frequency, their annotations and to the genes they affect. A weighted sum across all variants provides an individual risk score. Scores constructed in this way are used in a weighted burden test and are shown to be significantly different between schizophrenia cases and controls using a five-way cross validation procedure. This approach represents a first attempt to summarise exome sequence variation into a summary risk score, which could be combined with risk scores from common variants and from environmental factors. It is hoped that the method could be developed further.

scholarly journals Stress Mediating Genes in Aging, Health, and Longevity Traits: Effects of Multiple Interactions

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 286-286
Author(s):  
Anatoliy Yashin ◽  
Dequing Wu ◽  
Konstantin Arbeev ◽  
Arseniy Yashkin ◽  
Galina Gorbunova ◽  
...  
Keyword(s):  
Strong Interaction ◽  
Genetic Interaction ◽  
Interaction Effects ◽  
Genetic Interactions ◽  
Risk Scores ◽  
Data Sets ◽  
Interaction Patterns ◽  
Polygenic Risk ◽  
Drug Candidates ◽  
Aging Health

Abstract Persistent stress of external or internal origin accelerates aging, increases risk of aging related health disorders, and shortens lifespan. Stressors activate stress response genes, and their products collectively influence traits. The variability of stressors and responses to them contribute to trait heterogeneity, which may cause the failure of clinical trials for drug candidates. The objectives of this paper are: to address the heterogeneity issue; to evaluate collective interaction effects of genetic factors on Alzheimer’s disease (AD) and longevity using HRS data; to identify differences and similarities in patterns of genetic interactions within two genders; and to compare AD related genetic interaction patterns in HRS and LOADFS data. To reach these objectives we: selected candidate genes from stress related pathways affecting AD/longevity; implemented logistic regression model with interaction term to evaluate effects of SNP-pairs on these traits for males and females; constructed the novel interaction polygenic risk scores for SNPs, which showed strong interaction potential, and evaluated effects of these scores on AD/longevity; and compared patterns of genetic interactions within the two genders and within two datasets. We found there were many genes involved in highly significant interactions that were the same and that were different within the two genders. The effects of interaction polygenic risk scores on AD were strong and highly statistically significant. These conclusions were confirmed in analyses of interaction effects on longevity trait using HRS data. Comparison of HRS to LOADFS data showed that many genes had strong interaction effects on AD in both data sets.

scholarly journals Identifying individuals with high risk of Alzheimer’s disease using polygenic risk scores

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ganna Leonenko ◽  
Emily Baker ◽  
Joshua Stevenson-Hoare ◽  
Annerieke Sierksma ◽  
Mark Fiers ◽  
...  
Keyword(s):  
High Risk ◽  
Risk Score ◽  
Genetic Risk ◽  
Prediction Accuracy ◽  
Genetic Risk Score ◽  
Low Risk ◽  
Risk Scores ◽  
Sample Mean ◽  
Polygenic Risk ◽  
Reliable Identification

AbstractPolygenic Risk Scores (PRS) for AD offer unique possibilities for reliable identification of individuals at high and low risk of AD. However, there is little agreement in the field as to what approach should be used for genetic risk score calculations, how to model the effect of APOE, what the optimal p-value threshold (pT) for SNP selection is and how to compare scores between studies and methods. We show that the best prediction accuracy is achieved with a model with two predictors (APOE and PRS excluding APOE region) with pT<0.1 for SNP selection. Prediction accuracy in a sample across different PRS approaches is similar, but individuals’ scores and their associated ranking differ. We show that standardising PRS against the population mean, as opposed to the sample mean, makes the individuals’ scores comparable between studies. Our work highlights the best strategies for polygenic profiling when assessing individuals for AD risk.

scholarly journals Assessing the geographical distribution of comorbidity among commercially insured individuals in South Africa

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Cristina Mannie ◽  
Hadi Kharrazi
Keyword(s):  
Public Health ◽  
South Africa ◽  
Geographical Distribution ◽  
Healthcare Utilization ◽  
Risk Score ◽  
Disease Burden ◽  
Risk Scores ◽  
Individual Risk ◽  
Average Risk ◽  
Healthcare Needs

Abstract Background Comorbidities are strong predictors of current and future healthcare needs and costs; however, comorbidities are not evenly distributed geographically. A growing need has emerged for comorbidity surveillance that can inform decision-making. Comorbidity-derived risk scores are increasingly being used as valuable measures of individual health to describe and explain disease burden in populations. Methods This study assessed the geographical distribution of comorbidity and its associated financial implications among commercially insured individuals in South Africa (SA). A retrospective, cross-sectional analysis was performed comparing the geographical distribution of comorbidities for 2.6 million commercially insured individuals over 2016–2017, stratified by geographical districts in SA. We applied the Johns Hopkins ACG® System across the insurance claims data of a large health plan administrator in SA to measure comorbidity as a risk score for each individual. We aggregated individual risk scores to determine the average risk score per district, also known as the comorbidity index (CMI), to describe the overall disease burden of each district. Results We observed consistently high CMI scores in districts of the Free State and KwaZulu-Natal provinces for all population groups before and after age adjustment. Some areas exhibited almost 30% higher healthcare utilization after age adjustment. Districts in the Northern Cape and Limpopo provinces had the lowest CMI scores with 40% lower than expected healthcare utilization in some areas after age adjustment. Conclusions Our results show underlying disparities in CMI at national, provincial, and district levels. Use of geo-level CMI scores, along with other social data affecting health outcomes, can enable public health departments to improve the management of disease burdens locally and nationally. Our results could also improve the identification of underserved individuals, hence bridging the gap between public health and population health management efforts.

Performance of polygenic risk scores for cancer prediction in an academic biobank.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 1528-1528
Author(s):  
Heena Desai ◽  
Anh Le ◽  
Ryan Hausler ◽  
Shefali Verma ◽  
Anurag Verma ◽  
...  
Keyword(s):  
Risk Score ◽  
Genetic Variants ◽  
Association Studies ◽  
Risk Scores ◽  
Polygenic Risk Score ◽  
Genome Wide Association Studies ◽  
Polygenic Risk ◽  
European Americans ◽  
Genome Wide ◽  
Common Genetic Variants

1528 Background: The discovery of rare genetic variants associated with cancer have a tremendous impact on reducing cancer morbidity and mortality when identified; however, rare variants are found in less than 5% of cancer patients. Genome wide association studies (GWAS) have identified hundreds of common genetic variants significantly associated with a number of cancers, but the clinical utility of individual variants or a polygenic risk score (PRS) derived from multiple variants is still unclear. Methods: We tested the ability of polygenic risk score (PRS) models developed from genome-wide significant variants to differentiate cases versus controls in the Penn Medicine Biobank. Cases for 15 different cancers and cancer-free controls were identified using electronic health record billing codes for 11,524 European American and 5,994 African American individuals from the Penn Medicine Biobank. Results: The discriminatory ability of the 15 PRS models to distinguish their respective cancer cases versus controls ranged from 0.68-0.79 in European Americans and 0.74-0.93 in African Americans. Seven of the 15 cancer PRS trended towards an association with their cancer at a p<0.05 (Table), and PRS for prostate, thyroid and melanoma were significantly associated with their cancers at a bonferroni corrected p<0.003 with OR 1.3-1.6 in European Americans. Conclusions: Our data demonstrate that common variants with significant associations from GWAS studies can distinguish cancer cases versus controls for some cancers in an unselected biobank population. Given the small effects, future studies are needed to determine how best to incorporate PRS with other risk factors in the precision prediction of cancer risk. [Table: see text]

scholarly journals The Schizophrenia Variant V1282F in SCN2A Causes Functional Impairment of NaV1.2

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Kohlnhofer B ◽  
◽  
Liu Y ◽  
Woodruff G ◽  
Lovenberg T ◽  
...  
Keyword(s):  
Cortical Neurons ◽  
Rare Variants ◽  
Sodium Current ◽  
Biological Complexity ◽  
Large Effect Size ◽  
Mutant Channel ◽  
Recombinant Cells ◽  
Whole Exome ◽  
Sequencing Studies ◽  
Underlying Pathophysiology

Neuropsychiatric disorders such as schizophrenia are challenging to treat due to the biological complexity of the disease and the lack of knowledge of the underlying pathophysiology. Whole exome and genome sequencing studies have identified disease-linked rare variants in patients with large effect size. Here, we functionally characterize the schizophrenia linked variant V1282F in SCN2A, encoding the sodium channel Nav1.2. This variant was introduced into isogenic lines of hiPSCs using CRISPR/CAS9 genome editing tools. hiPSCs were then differentiated into cortical neurons to understand how the variant and gene may be contributing to disease. We observed a significant (~25%) decrease in sodium current in the V1282F neurons compared to control neurons, suggesting the mutation is causing a loss-of-channel function. These results were supported by recordings in recombinant cells overexpressing either the mutant or wildtype Nav1.2, with the mutant channel having significantly (~75%) lower current amplitude than wildtype. We hypothesize that this phenotype may contribute to disease either through the direct loss of neuronal activity or through subsequent abnormal neurodevelopment.

scholarly journals Comparisons of Polyexposure, Polygenic, and Clinical Risk Scores in Risk Prediction of Type 2 Diabetes

2021 ◽  
Author(s):  
Yixuan He ◽  
Chirag M Lakhani ◽  
Danielle Rasooly ◽  
Arjun K Manrai ◽  
Ioanna Tzoulaki ◽  
...  
Keyword(s):  
Risk Factors ◽  
Risk Prediction ◽  
Risk Score ◽  
Prediction Models ◽  
Disease Risk ◽  
Clinical Risk Factors ◽  
Risk Scores ◽  
Polygenic Risk Score ◽  
Polygenic Risk ◽  
Clinical Risk

OBJECTIVE: <p>Establish a polyexposure score for T2D incorporating 12 non-genetic exposure and examine whether a polyexposure and/or a polygenic risk score improves diabetes prediction beyond traditional clinical risk factors.</p> <h2><a></a>RESEARCH DESIGN AND METHODS:</h2> <p>We identified 356,621 unrelated individuals from the UK Biobank of white British ancestry with no prior diagnosis of T2D and normal HbA1c levels. Using self-reported and hospital admission information, we deployed a machine learning procedure to select the most predictive and robust factors out of 111 non-genetically ascertained exposure and lifestyle variables for the polyexposure risk score (PXS) in prospective T2D. We computed the clinical risk score (CRS) and polygenic risk score (PGS) by taking a weighted sum of eight established clinical risk factors and over six million SNPs, respectively.</p> <h2><a></a>RESULTS:</h2> <p>In the study population, 7,513 had incident T2D. The C-statistics for the PGS, PXS, and CRS models were 0.709, 0.762, and 0.839, respectively. Hazard ratios (HR) associated with risk score values in the top 10% percentile versus the remaining population is 2.00, 5.90, and 9.97 for PGS, PXS, and CRS respectively. Addition of PGS and PXS to CRS improves T2D classification accuracy with a continuous net reclassification index of 15.2% and 30.1% for cases, respectively, and 7.3% and 16.9% for controls, respectively. </p> <h2><a></a>CONCLUSIONS:</h2> <p>For T2D, the PXS provides modest incremental predictive value over established clinical risk factors. The concept of PXS merits further consideration in T2D risk stratification and is likely to be useful in other chronic disease risk prediction models.</p>

scholarly journals Integration of rare large-effect expression variants improves polygenic risk prediction

2020 ◽  
Author(s):  
Craig Smail ◽  
Nicole M. Ferraro ◽  
Matthew G. Durrant ◽  
Abhiram S. Rao ◽  
Matthew Aguirre ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Rare Variants ◽  
Complex Trait ◽  
Risk Scores ◽  
Multiple Traits ◽  
Polygenic Risk ◽  
Common Genetic Variants ◽  
Using Data ◽  
The Uk ◽  
The Impact

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.

scholarly journals MetS Risk Score: A Clear Scoring Model to Predict a 3-Year Risk for Metabolic Syndrome

2018 ◽  
Vol 50 (09) ◽  
pp. 683-689 ◽  
Author(s):  
Tian-Tian Zou ◽  
Yu-Jie Zhou ◽  
Xiao-Dong Zhou ◽  
Wen-Yue Liu ◽  
Sven Van Poucke ◽  
...  
Keyword(s):  
Risk Factors ◽  
Metabolic Syndrome ◽  
Risk Score ◽  
Validation Cohort ◽  
Medical Center ◽  
Characteristic Curve ◽  
Model Development ◽  
Predictive Performance ◽  
Risk Scores ◽  
Individual Risk

AbstractAlthough several risk factors for metabolic syndrome (MetS) have been reported, there are few clinical scores that predict its incidence. Therefore, we created and validated a risk score for prediction of 3-year risk for MetS. Three-year follow-up data of 4395 initially MetS-free subjects, enrolled for an annual physical examination from Wenzhou Medical Center were analyzed. Subjects at enrollment were randomly divided into the training and the validation cohort. Univariate and multivariate logistic regression models were employed for model development. The selected variables were assigned an integer or half-integer risk score proportional to the estimated coefficient from the logistic model. Risk scores were tested in a validation cohort. The predictive performance of the model was tested by computing the area under the receiver operating characteristic curve (AUROC). Four independent predictors were chosen to construct the MetS risk score, including BMI (HR=1.906, 95% CI: 1.040–1.155), FPG (HR=1.507, 95% CI: 1.305–1.741), DBP (HR=1.061, 95% CI: 1.002–1.031), HDL-C (HR=0.539, 95% CI: 0.303–0.959). The model was created as –1.5 to 4 points, which demonstrated a considerable discrimination both in the training cohort (AUROC=0.674) and validation cohort (AUROC=0.690). Comparison of the observed with the estimated incidence of MetS revealed satisfactory precision. We developed and validated the MetS risk score with 4 risk factors to predict 3-year risk of MetS, useful for assessing the individual risk for MetS in medical practice.

The Differential Influence of Immune, Endocytotic, and Lipid Metabolism Genes on Amyloid Deposition and Neurodegeneration in Subjects at Risk of Alzheimer’s Disease

2021 ◽  
Vol 79 (1) ◽  
pp. 127-139
Author(s):  
Grazia Daniela Femminella ◽  
Denise Harold ◽  
James Scott ◽  
Julie Williams ◽  
Paul Edison ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Lipid Metabolism ◽  
Risk Score ◽  
Amyloid Deposition ◽  
Risk Scores ◽  
Healthy Controls ◽  
Cognitive Measures ◽  
Polygenic Risk ◽  
Increased Risk

Background: Over 20 single-nucleotide polymorphisms (SNPs) are associated with increased risk of Alzheimer’s disease (AD). We categorized these loci into immunity, lipid metabolism, and endocytosis pathways, and associated the polygenic risk scores (PRS) calculated, with AD biomarkers in mild cognitive impairment (MCI) subjects. Objective: The aim of this study was to identify associations between pathway-specific PRS and AD biomarkers in patients with MCI and healthy controls. Methods: AD biomarkers ([18F]Florbetapir-PET SUVR, FDG-PET SUVR, hippocampal volume, CSF tau and amyloid-β levels) and neurocognitive tests scores were obtained in 258 healthy controls and 451 MCI subjects from the ADNI dataset at baseline and at 24-month follow up. Pathway-related (immunity, lipid metabolism, and endocytosis) and total polygenic risk scores were calculated from 20 SNPs. Multiple linear regression analysis was used to test predictive value of the polygenic risk scores over longitudinal biomarker and cognitive changes. Results: Higher immune risk score was associated with worse cognitive measures and reduced glucose metabolism. Higher lipid risk score was associated with increased amyloid deposition and cortical hypometabolism. Total, immune, and lipid scores were associated with significant changes in cognitive measures, amyloid deposition, and brain metabolism. Conclusion: Polygenic risk scores highlights the influence of specific genes on amyloid-dependent and independent pathways; and these pathways could be differentially influenced by lipid and immune scores respectively.

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