Has the time come to integrate genetic risk scores into clinical practice?

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
F.V Moniz Mendonca ◽  
M.I Mendonca ◽  
A Pereira ◽  
J Monteiro ◽  
J Sousa ◽  
...  
Keyword(s):  
Risk Factors ◽  
Clinical Practice ◽  
Genetic Variants ◽  
Genetic Risk ◽  
Odds Ratio ◽  
Risk Scores ◽  
Cumulative Number ◽  
Genetic Risk Scores ◽  
Risk Alleles ◽  
Cad Risk

Abstract Background The risk for Coronary Artery Disease (CAD) is determined by both genetic and environmental factors, as well as by the interaction between them. It is estimated that genetic factors could account for 40% to 55% of the existing variability among the population (inheritability). Therefore, some authors have advised that it is time we integrated genetic risk scores into clinical practice. Aim The aim of this study was to evaluate the magnitude of the association between an additive genetic risk score (aGRS) and CAD based on the cumulative number of risk alleles in these variants, and to estimate whether their use is valuable in clinical practice. Methods A case-control study was performed in a Portuguese population. We enrolled 3120 participants, of whom 1687 were CAD patients and 1433 were normal controls. Controls were paired to cases with respect to gender and age. 33 genetic variants known to be associated with CAD were selected, and an aGRS was calculated for each individual. The aGRS was further subdivided into deciles groups, in order to estimate the CAD risk in each decile, defined by the number of risk alleles. The magnitude of the risk (odds ratio) was calculated for each group by multiple logistic regression using the 5th decile as the reference group (median). In order to evaluate the ability of the aGRS to discriminate susceptibility to CAD, two genetic models were performed, the first with traditional risk factors (TRF) and second with TRF plus aGRS. The AUC of the two ROC curves was calculated. Results A higher prevalence of cases over controls became apparent from the 6th decile of the aGRS, reflecting the higher number of risk alleles present (see figure). The difference in CAD risk was only significant from the 6th decile, increasing gradually until the 10th decile. The odds ratio (OR) for the last decile related to 5th decile (median) was 1.87 (95% CI:1.36–2.56; p<0.0001). The first model yielded an AUC=0.738 (95% CI:0.720–0.755) and the second model was slightly more discriminative for CAD risk (AUC=0.748; 95% CI:0.730–0.765). The DeLong test was significant (p=0.0002). Conclusion Adding an aGRS to the non-genetic risk factors resulted in a modest improvement in the ability to discriminate the risk of CAD. Such improvement, even if statistically significant, does not appear to be of real value in clinical practice yet. We anticipate that with the development of further knowledge about different SNPs and their complex interactions, and with the inclusion of rare genetic variants, genetic risk scores will be better suited for use in a clinical setting. Funding Acknowledgement Type of funding source: None

scholarly journals MP044CAN GENETIC RISK SCORES IMPROVE THE PREDICTON POWER FOR MORTALITY OF STANDARD RISK FACTORS IN THE END STAGE KIDNEY DISEASE POPULATION? AN EXPLORATORY STUDY

2016 ◽  
Vol 31 (suppl_1) ◽  
pp. i357-i357
Author(s):  
Belinda Spoto ◽  
Alessandra Testa ◽  
Graziella D'Arrigo ◽  
Rosa M Parlongo ◽  
Maria C. Sanguedolce ◽  
...  
Keyword(s):  
Risk Factors ◽  
Kidney Disease ◽  
Genetic Risk ◽  
Exploratory Study ◽  
Risk Scores ◽  
End Stage Kidney Disease ◽  
Genetic Risk Scores ◽  
End Stage ◽  
Standard Risk

scholarly journals Subcutaneous fat mass is associated with genetic risk scores related to proinflammatory cytokine signaling and interact with physical activity in middle-aged obese adults

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
James W. Daily ◽  
Hye Jeong Yang ◽  
Meiling Liu ◽  
Min Jung Kim ◽  
Sunmin Park
Keyword(s):  
Physical Activity ◽  
Fat Mass ◽  
Visceral Fat ◽  
Genetic Variants ◽  
Genetic Risk ◽  
Odds Ratio ◽  
Subcutaneous Fat ◽  
Risk Scores ◽  
Obese Adults ◽  
High Physical Activity

Abstract Background and aims Subcutaneous fat mass is negatively correlated with atherogenic risk factors, but its putative benefits remain controversial. We hypothesized that genetic variants that influence subcutaneous fat mass would modulate lipid and glucose metabolism and have interactions with lifestyles in Korean middle-aged adults with high visceral fat. Materials and methods Subcutaneous fat mass was categorized by dividing the average of subscapular skin-fold thickness by BMI and its cutoff point was 1.2. Waist circumferences were used for representing visceral fat mass with Asian cutoff points. GWAS of subjects aged 40–65 years with high visceral fat (n = 3303) were conducted and the best gene-gene interactions from the genetic variants related to subcutaneous fat were selected and explored using the generalized multifactor dimensionality reduction. Genetic risk scores (GRS) were calculated by weighted GRS that was divided into low, medium and high groups. Results Subjects with high subcutaneous fat did not have dyslipidemia compared with those with low subcutaneous fat, although both subject groups had similar amounts of total fat. The best model to influence subcutaneous fat included IL17A_rs4711998, ADCY2_rs326149, ESRRG_rs4846514, CYFIP2_rs733730, TCF7L2_rs7917983, ZNF766_rs41497444 and TGFBR3_rs7526590. The odds ratio (OR) for increasing subcutaneous fat was higher by 2.232 folds in the high-GRS group, after adjusting for covariates. However, total and LDL cholesterol, triglyceride and C-reactive protein concentrations in the circulation were not associated with GRS. Subjects with high-GRS had higher serum HDL cholesterol levels than those with low-GRS. Physical activity and GRS had an interaction with subcutaneous fat. In subjects with low physical activity, the odds ratio for high subcutaneous fat increased by 2.232, but subcutaneous fat deposition was not affected in the high-GRS group with high physical activity. Conclusion Obese adults with high-GRS had more subcutaneous fat, but they did not show more dyslipidemia and inflammation compared to low-GRS. High physical activity prevented subcutaneous fat deposition in subjects with high GRS for subcutaneous fat.

scholarly journals Polygenic prediction of breast cancer: comparison of genetic predictors and implications for screening

2018 ◽  
Author(s):  
Kristi Läll ◽  
Maarja Lepamets ◽  
Marili Palover ◽  
Tõnu Esko ◽  
Andres Metspalu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Genetic Risk ◽  
Odds Ratio ◽  
Population Based ◽  
Risk Scores ◽  
Full Potential ◽  
Genome Wide Association Studies ◽  
Uk Biobank ◽  
Genetic Risk Scores ◽  
The Uk

AbstractBackgroundPublished genetic risk scores for breast cancer (BC) so far have been based on a relatively small number of markers and are not necessarily using the full potential of large-scale Genome-Wide Association Studies. This study aims to identify an efficient polygenic predictor for BC based on best available evidence and to assess its potential for personalized risk prediction and screening strategies.MethodsFour different genetic risk scores (two already published and two newly developed) and their combinations (metaGRS) are compared in the subsets of two population-based biobank cohorts: the UK Biobank (UKBB, 3157 BC cases, 43,827 controls) and Estonian Biobank (EstBB, 317 prevalent and 308 incident BC cases in 32,557 women). In addition, correlations between different genetic risk scores and their associations with BC risk factors are studied in both cohorts.ResultsThe metaGRS that combines two genetic risk scores (metaGRS2 - based on 75 and 898 Single Nucleotide Polymorphisms, respectively) has the strongest association with prevalent BC status in both cohorts. One standard deviation difference in the metaGRS2 corresponds to an Odds Ratio = 1.6 (95% CI 1.54 to 1.66, p = 9.7*10-135) in the UK Biobank and accounting for family history marginally attenuates the effect (Odds Ratio = 1.58, 95% CI 1.53 to 1.64, p = 9.1*10-129). In the EstBB cohort, the hazard ratio of incident BC for the women in the top 5% of the metaGRS2 compared to women in the lowest 50% is 4.2 (95% CI 2.8 to 6.2, p = 8.1*10-13). The different GRSs are only moderately correlated with each other and are associated with different known predictors of BC. The classification of genetic risk for the same individual may vary considerably depending on the chosen GRS.ConclusionsWe have shown that metaGRS2 that combines on the effects of more than 900 SNPs provides best predictive ability for breast cancer in two different population-based cohorts. The strength of the effect of metaGRS2 indicates that the GRS could potentially be used to develop more efficient strategies for breast cancer screening for genotyped women.

scholarly journals HUMAN LONGEVITY IS INFLUENCED BY MANY GENETIC VARIANTS: EVIDENCE FROM 75,000 UK BIOBANK PARTICIPANTS

2016 ◽  
Author(s):  
Luke C Pilling ◽  
Janice L Atkins ◽  
Kirsty Bowman ◽  
Samuel E Jones ◽  
Jessica Tyrrell ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Genetic Variants ◽  
Genetic Risk ◽  
Paternal Age ◽  
Risk Scores ◽  
Human Longevity ◽  
Uk Biobank ◽  
Age At Death ◽  
Genetic Risk Scores ◽  
A Genome

Variation in human lifespan is 20 to 30% heritable but few genetic variants have been identified. We undertook a Genome Wide Association Study (GWAS) using age at death of parents of middle-aged UK Biobank participants of European decent (n=75,244 with father's and/or mother's data). Genetic risk scores for 19 phenotypes (n=777 proven variants) were also tested. Genotyped variants (n=845,997) explained 10.2% (SD=1.3%) of combined parental longevity. In GWAS, a locus in the nicotine receptor CHRNA3 - previously associated with increased smoking and lung cancer - was associated with paternal age at death, with each protective allele (rs1051730[G]) being associated with 0.03 years later age at father's death (p=3x10-8). Offspring of longer lived parents had more protective alleles (lower genetic risk scores) for coronary artery disease, systolic blood pressure, body mass index, cholesterol and triglyceride levels, type-1 diabetes, inflammatory bowel disease and Alzheimer's disease. In candidate gene analyses, variants in the TOMM40/APOE locus were associated with longevity (including rs429358, p=3x10-5), but FOXO variants were not associated. These results support a multiple protective factors model for achieving longer lifespans in humans, with a prominent role for cardiovascular-related pathways. Several of these genetically influenced risks, including blood pressure and tobacco exposure, are potentially modifiable.

scholarly journals Multiple SNP testing improves risk prediction of first venous thrombosis

Blood ◽  
2012 ◽  
Vol 120 (3) ◽  
pp. 656-663 ◽  
Author(s):  
Hugoline G. de Haan ◽  
Irene D. Bezemer ◽  
Carine J. M. Doggen ◽  
Saskia Le Cessie ◽  
Pieter H. Reitsma ◽  
...  
Keyword(s):  
Venous Thrombosis ◽  
Risk Prediction ◽  
Genetic Risk ◽  
Risk Model ◽  
Cost Effective ◽  
Risk Scores ◽  
Nucleotide Polymorphisms ◽  
Risk Models ◽  
Genetic Risk Scores ◽  
Risk Alleles

Abstract There are no risk models available yet that accurately predict a person's risk for developing venous thrombosis. Our aim was therefore to explore whether inclusion of established thrombosis-associated single nucleotide polymorphisms (SNPs) in a venous thrombosis risk model improves the risk prediction. We calculated genetic risk scores by counting risk-increasing alleles from 31 venous thrombosis-associated SNPs for subjects of a large case-control study, including 2712 patients and 4634 controls (Multiple Environmental and Genetic Assessment). Genetic risk scores based on all 31 SNPs or on the 5 most strongly associated SNPs performed similarly (areas under receiver-operating characteristic curves [AUCs] of 0.70 and 0.69, respectively). For the 5-SNP risk score, the odds ratios for venous thrombosis ranged from 0.37 (95% confidence interval [CI], 0.25-0.53) for persons with 0 risk alleles to 7.48 (95% CI, 4.49-12.46) for persons with more than or equal to 6 risk alleles. The AUC of a risk model based on known nongenetic risk factors was 0.77 (95% CI, 0.76-0.78). Combining the nongenetic and genetic risk models improved the AUC to 0.82 (95% CI, 0.81-0.83), indicating good diagnostic accuracy. To become clinically useful, subgroups of high-risk persons must be identified in whom genetic profiling will also be cost-effective.

scholarly journals Relationship between Genetic Risk and Age of Diagnosis of Systemic Lupus Erythematosus

2020 ◽  
pp. jrheum.200002
Author(s):  
Daniela Dominguez ◽  
Sylvia Kamphuis ◽  
Joseph Beyene ◽  
Joan Wither ◽  
John B. Harley ◽  
...  
Keyword(s):  
Risk Score ◽  
Lupus Erythematosus ◽  
Genetic Risk ◽  
Genetic Risk Score ◽  
Risk Scores ◽  
Ancestral Population ◽  
Childhood Onset ◽  
Genetic Risk Scores ◽  
Risk Alleles ◽  
Age Of Diagnosis

Objective Specific risk alleles for childhood-onset SLE (cSLE) versus adult-onset SLE (aSLE) patients have not been identified. The aims of this study were to determine if: 1) There is an association between non-HLA-related genetic risk score (GRS) and age of SLE diagnosis; and if 2) There is an association between HLA-related genetic risk score and age of SLE diagnosis. Methods Genomic DNA was obtained from 2,001 multi-ethnic patients and genotyped using the Immunochip. Following quality control, genetic risk counting (GRCS), weighted (GRWS) and standardized counting (GRSCS) and standardized weighted (GRSWS) scores were calculated based on independent SNPs from validated SLE-loci. Scores were analyzed in a regression model and adjusted by sex and ancestral population. Results The analysed cohort consisted of 1,540 patients: 1,351 females and 189 males (675 cSLE and 865 aSLE). There were significant negative associations with age of SLE diagnosis p=0.011 and r2=0.175 for GRWS, p=0.008 and r2=0.178 for GRSCS, p=0.002 and r2=0.176 for GRSWS for all non-HLA genetic risk scores (higher GRS the lower the age of diagnosis.) All HLA genetic risk scores showed significant positive associations with age of diagnosis p=0.049 and r2=0.176 for GRCS, p=0.022 and r2=0.176 for GRWS, p=0.022 and r2=0.176 for GRSCS, p=0.011 and r2=0.177 for GRSWS: higher genetic scores correlated with higher age of diagnosis. Conclusion Our data suggested that there is a linear relationship between genetic risk and age of SLE diagnosis and that HLA and non-HLA genetic risk scores are associated with age of diagnosis in opposite directions.

scholarly journals Carbohydrate and sodium intake and physical activity interact with genetic risk scores of four genetic variants mainly related to lipid metabolism to modulate metabolic syndrome risk in Korean middle-aged adults

2019 ◽  
Vol 122 (8) ◽  
pp. 919-927 ◽  
Author(s):  
Jun-Yu Zhou ◽  
Mi Young Song ◽  
Sunmin Park
Keyword(s):  
Physical Activity ◽  
Metabolic Syndrome ◽  
Genetic Variants ◽  
Genetic Risk ◽  
Risk Scores ◽  
Moderate Activity ◽  
Middle Aged ◽  
Genetic Risk Scores ◽  
Daily Physical Activities ◽  
Middle Aged Adults

AbstractMetabolic syndrome (MetS) risk is influenced by genetic and environmental factors. The present study explored genetic risk scores (GRS) of genetic variants that influence the MetS and the effect of interactions between GRS and nutrient intake on MetS risk. The genetic variants that influence MetS risk were selected by genome-wide association study after adjusting for age, sex, area of residence and BMI in 8840 middle-aged adults. GRS were calculated by summing the risk alleles of the selected SNP and divided into low (0–1), medium (2–3) and high (4–7) risk groups, and the relationships between the MetS and GRS were determined by logistic regression after adjusting covariates involved in MetS risk. We also analysed the interaction between GRS and lifestyles. Four genetic variants (APOA5_rs651821, EFCAB4B_rs4766165, ZNF259_rs2160669 and APOBEC1_rs10845640) were selected because they increased MetS risk after adjusting for covariates. Individuals with medium-GRS and high-GRS alleles had a higher MetS risk by 1·48- and 2·23-fold, respectively, compared with those with low-GRS after adjusting for covariates. The increase in MetS risk was mainly related to serum TAG and HDL-cholesterol concentrations. The GRS had an interaction with carbohydrate (CHO) and Na intakes and daily physical activities for MetS risk. In conclusion, Asian middle-aged adults with high-GRS alleles were at increased MetS risk mainly due to dyslipidaemia. High daily physical activity (≥1 h moderate activity per d) reduced the MetS risk but a low-CHO diet (<65 % of total energy intake) increased the risk in carriers with high-GRS alleles. Low Na intake (<1·6 g Na intake/4 MJ) did not decrease its risk.

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