scholarly journals Calibrated rare variant genetic risk scores for complex disease prediction using large exome sequence repositories

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ricky Lali ◽  
Michael Chong ◽  
Arghavan Omidi ◽  
Pedrum Mohammadi-Shemirani ◽  
Ann Le ◽  
...  
Keyword(s):  
Rare Variant ◽  
Risk Score ◽  
Genetic Risk ◽  
Complex Disease ◽  
Rare Variants ◽  
Disease Risk ◽  
Genetic Risk Score ◽  
Risk Scores ◽  
Considerable Proportion ◽  
Asian Populations

AbstractRare variants are collectively numerous and may underlie a considerable proportion of complex disease risk. However, identifying genuine rare variant associations is challenging due to small effect sizes, presence of technical artefacts, and heterogeneity in population structure. We hypothesize that rare variant burden over a large number of genes can be combined into a predictive rare variant genetic risk score (RVGRS). We propose a method (RV-EXCALIBER) that leverages summary-level data from a large public exome sequencing database (gnomAD) as controls and robustly calibrates rare variant burden to account for the aforementioned biases. A calibrated RVGRS strongly associates with coronary artery disease (CAD) in European and South Asian populations by capturing the aggregate effect of rare variants through a polygenic model of inheritance. The RVGRS identifies 1.5% of the population with substantial risk of early CAD and confers risk even when adjusting for known Mendelian CAD genes, clinical risk factors, and a common variant genetic risk score.

scholarly journals Calibrated rare variant genetic risk scores for complex disease prediction using large exome sequence repositories

2020 ◽  
Author(s):  
Ricky Lali ◽  
Michael Chong ◽  
Arghavan Omidi ◽  
Pedrum Mohammadi-Shemirani ◽  
Ann Le ◽  
...  
Keyword(s):  
Rare Variant ◽  
Genetic Risk ◽  
Complex Disease ◽  
Rare Variants ◽  
Disease Risk ◽  
Genetic Risk Score ◽  
Risk Scores ◽  
Considerable Proportion ◽  
Asian Populations ◽  
Artery Disease

ABSTRACTRare variants are collectively numerous and may underlie a considerable proportion of complex disease risk. However, identifying genuine rare variant associations is challenging due to small effect sizes, presence of technical artefacts, and heterogeneity in population structure. We hypothesized that rare variant burden over a large number of genes can be combined into predictive rare variant genetic risk score (RVGRS). We propose a novel method (RV-EXCALIBER) that leverages summary-level data from a large public exome sequencing database (gnomAD) as controls and robustly calibrates rare variant burden to account for the aforementioned biases. A RVGRS was found to strongly associate with coronary artery disease (CAD) in European and South Asian populations. Calibrated RVGRS capture the aggregate effect of rare variants through a polygenic model of inheritance, identifies 1.5% of the population with substantial risk of early CAD, and confers risk even when adjusting for known Mendelian CAD genes, clinical risk factors, and common variant gene scores.

scholarly journals Prediction of Inflammatory Bowel Diseases using Genetic Risk Score in Asian  populations

2021 ◽  
Author(s):  
Shifteh Abedian ◽  
Sunny H Wong ◽  
Suzanne Van Sommeren ◽  
Atsushi Takahashi ◽  
Jae Hee Cheon ◽  
...  
Keyword(s):  
Genetic Risk ◽  
Rare Variants ◽  
Genetic Risk Score ◽  
East Asian ◽  
Risk Scores ◽  
Total Load ◽  
Asian Populations ◽  
Central Asian ◽  
Disease Occurrence ◽  
Inflammatory Bowel

Abstract Background and Aims: The incidence of Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and Ulcerative colitis (UC), is rising in Asian populations. We undertook a cross-population study to explore whether genetic risk scores (GRS) of IBD, CD and UC could explain their occurrence, and whether they can be used to predict disease occurrence in general populations from East Asia (EA) and Central Asia (CA). Methods We studied 9,698 subjects – 4,733 IBD patients (2,003 CD; 2,730 UC) and 4,965 matched controls – who had been genotyped using Immunochip. The subjects were from three East Asian (Japan, South Korea and China) and two Central Asian populations (India and Iran). We generated GRS for each population by combining information from up to 201 genome-wide significant IBD-associated variants to summarize the total load of genetic risk for each phenotype. We then estimated the explained variance and predictability of IBD using the GRS. Results IBD GRS could explain up to 4.40% and 4.14% of IBD variance at a significant level in East Asian and Central Asian populations, respectively, but, given a prevalence of 0.01% and 0.04% for IBD, these yield limited predictive probability. GRS for CD and UC separately proved less significant than GRS for IBD. Conclusion GRS alone can explain only a limited percentage of disease occurrence (< 5% of disease susceptibility) and cannot be used to predict IBD in Asian populations at this time. Our results highlight the significant missing heritability, which may be due to genetic epistasis, gene-environment interactions, or rare variants.

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 Progression from islet autoimmunity to clinical type 1 diabetes is influenced by genetic factors: results from the prospective TEDDY study

2018 ◽  
Vol 56 (9) ◽  
pp. 602-605 ◽  
Author(s):  
Andreas Beyerlein ◽  
Ezio Bonifacio ◽  
Kendra Vehik ◽  
Markus Hippich ◽  
Christiane Winkler ◽  
...  
Keyword(s):  
Type 1 Diabetes ◽  
Risk Score ◽  
Genetic Risk ◽  
Genetic Factors ◽  
Genetic Risk Score ◽  
Risk Scores ◽  
Islet Autoimmunity ◽  
Islet Autoantibody ◽  
Clinical Type

BackgroundProgression time from islet autoimmunity to clinical type 1 diabetes is highly variable and the extent that genetic factors contribute is unknown.MethodsIn 341 islet autoantibody-positive children with the human leucocyte antigen (HLA) DR3/DR4-DQ8 or the HLA DR4-DQ8/DR4-DQ8 genotype from the prospective TEDDY (The Environmental Determinants of Diabetes in the Young) study, we investigated whether a genetic risk score that had previously been shown to predict islet autoimmunity is also associated with disease progression.ResultsIslet autoantibody-positive children with a genetic risk score in the lowest quartile had a slower progression from single to multiple autoantibodies (p=0.018), from single autoantibodies to diabetes (p=0.004), and by trend from multiple islet autoantibodies to diabetes (p=0.06). In a Cox proportional hazards analysis, faster progression was associated with an increased genetic risk score independently of HLA genotype (HR for progression from multiple autoantibodies to type 1 diabetes, 1.27, 95% CI 1.02 to 1.58 per unit increase), an earlier age of islet autoantibody development (HR, 0.68, 95% CI 0.58 to 0.81 per year increase in age) and female sex (HR, 1.94, 95% CI 1.28 to 2.93).ConclusionsGenetic risk scores may be used to identify islet autoantibody-positive children with high-risk HLA genotypes who have a slow rate of progression to subsequent stages of autoimmunity and type 1 diabetes.

P3399Influence of TCF21 rs12190287 in the coronary artery disease risk prediction. An association study in a Portuguese population

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
J Sousa ◽  
M Mendonca ◽  
A Pereira ◽  
F Mendonca ◽  
J Monteiro ◽  
...  
Keyword(s):  
Risk Score ◽  
Genetic Variants ◽  
Genetic Risk ◽  
Disease Risk ◽  
Smoking Status ◽  
Genetic Risk Score ◽  
Strong Association ◽  
Portuguese Population ◽  
The Impact ◽  
Cad Risk

Abstract TCF21 is a member of the basic-helix-loop-helix (bHLH) transcriptor factor family, being critical for embryogenesis of the heart, kidney and spleen. TCF21 also regulates epicardium-derived cells differentiation into smooth muscle and fibroblast lineages. Aim Investigate the impact of TCF21 rs12190287 in the prediction and discrimination of CAD risk, individually or into a genetic risk score (GRS) formed by a set of 13 genetic variants. Methods We performed a case-control study with 3050 subjects (1619 coronary patients with 53.3±8 years; 78.9% male and 1431 controls with 52.8±8 years; 76.6% male) from GENEMACOR study. We investigated all traditional risk factors (TRF), as well as 13 genetic variants from GWAS with unknown pathophysiological pathway so far, including TCF21 (rs12190287), ZC3HC1 (rs11556924), PSRC1/SORTI (rs599839), PHACTR1 (rs1332844), MIA3 (rs17465637), SMAD3 (rs17228212), ZNF259 (rs964184), ADAMTS7 (rs3825807), CDKN2B (rs4977574), 9p21.3 (rs1333049), KIF6 (rs20455), PCSK9 (rs2114580) and GJA4 (rs618675). A multiplicative genetic risk score with these 13 genetic variants (m13GRS), was calculated. Subsequently, two logistic regressions were performed; primarily with all the TRF and all the genes individually and the second with TRF and m13GRS. Results The first multivariate analysis shows that, besides the strong association of the TRF with CAD risk (with smoking status on the top of the list, with an OR of 3.2; p<0.0001), TCF21 rs12190287 was the most significant variant from all the studied genetic set with a CAD risk of 1.5 (95% CI: 1.1–1.9; p=0.004), followed by the well-known genetic determinant CDKN2B rs4977574 (OR=1.4; 95% CI: 1.1–1.7; p<0.002) and ZC3HC1 rs11556924 (OR=1.3; 95% CI: 1.0–1.7; p=0.034). When GRS is included to the model, all the TRF remain in the equation by the same order, and the m13GRS persisted as an independent predictor for CAD risk (OR=1.7; 95% CI: 1.4–2.0; p<0.0001). Conclusion TCF21 rs12190287 is a risk factor for CAD in the Portuguese population, either individually or incorporated in a m13GRS. TCF21 risk is independent from TRF. In the future, TCF21 can provide a new clues to identify patients at high cardiovascular risk and become a potential target for gene therapy.

scholarly journals 959Coronary artery disease risk according to genetic risk score deciles, Age and cardiovascular risk factors

2017 ◽  
Vol 38 (suppl_1) ◽  
Author(s):  
A. Pereira ◽  
M. Neto ◽  
R. Rodrigues ◽  
J. Monteiro ◽  
A.C. Sousa ◽  
...  
Keyword(s):  
Risk Factors ◽  
Cardiovascular Risk ◽  
Cardiovascular Risk Factors ◽  
Risk Score ◽  
Genetic Risk ◽  
Disease Risk ◽  
Genetic Risk Score ◽  
Artery Disease

scholarly journals Incorporating a Genetic Risk Score Into Coronary Heart Disease Risk Estimates

Circulation ◽  
2016 ◽  
Vol 133 (12) ◽  
pp. 1181-1188 ◽  
Author(s):  
Iftikhar J. Kullo ◽  
Hayan Jouni ◽  
Erin E. Austin ◽  
Sherry-Ann Brown ◽  
Teresa M. Kruisselbrink ◽  
...  
Keyword(s):  
Coronary Heart Disease ◽  
Heart Disease ◽  
Risk Score ◽  
Coronary Heart Disease Risk ◽  
Genetic Risk ◽  
Disease Risk ◽  
Genetic Risk Score ◽  
Risk Estimates ◽  
Heart Disease Risk

scholarly journals Mitonuclear interactions influence Alzheimer’s disease risk

2019 ◽  
Author(s):  
Shea J Andrews ◽  
Brian Fulton-Howard ◽  
Christopher Patterson ◽  
G Peggy McFall ◽  
Alden Gross ◽  
...  
Keyword(s):  
Risk Score ◽  
Genetic Risk ◽  
Disease Risk ◽  
Age Of Onset ◽  
Genetic Risk Score ◽  
Polygenic Risk Score ◽  
List Type ◽  
Dementia Risk ◽  
Incident Cases ◽  
Antagonistic Interactions

AbstractWe examined the associations between mitochondrial DNA haplogroups (MT-hg) and their interactions with a polygenic risk score based on nuclear-encoded mitochondrial genes (nMT-PRS) with risk of dementia and age of onset of dementia (AOO). Logistic regression was used to determine the effect of MT-hgs and nMT-PRS on dementia at baseline (332 controls / 204 cases). Cox proportional hazards models were used to model dementia AOO (n=1047; 433 incident cases). Additionally, we tested for interactions between MT-hg and nMT-PRS in the logistic and Cox models. MT-hg K and a one SD larger nMT-PRS were associated with elevated odds of dementia. Significant antagonistic interactions between the nMT-PRS and MT-hg K and T were observed. Individual MT-hg were not associated with AOO; however, a significant antagonistic interactions was observed between the nMT-PRS and MT-hg T and a synergistic interaction between the nMT-PRS and MT-hg V. These results suggest that MT-hgs influence dementia risk, and that variants in the nuclear and mitochondrial genome interact to influence the age of onset of dementia.HighlightsMitochondrial dysfunction has been proposed to influence dementia riskMT-hg K and T interacted with a genetic risk score to reduce dementia riskMT-hg T and V interacted with a genetic risk score to influence dementia age of onset

Sign in / Sign up

Export Citation Format

Share Document