Abstract A06: Association of environmental risk factors, family history, and polygenic risk scores with chronic lymphocytic leukemia

Author(s):  
Geffen Kleinstern ◽  
Dennis Robinson ◽  
Tim G. Call ◽  
Mark Liebow ◽  
Silvia de Sanjosé ◽  
...  
2020 ◽  
Vol 164 (4) ◽  
pp. 425-434
Author(s):  
Kamila Stranska ◽  
Karla Plevova ◽  
Hana Skuhrova Francova ◽  
Hana Skabrahova ◽  
Magdalena von Jagwitz-Biegnitz ◽  
...  

2017 ◽  
Author(s):  
Geffen Kleinstern ◽  
Silvia de Sanjosé ◽  
Nicola Camp ◽  
Claire M. Vajdic ◽  
Timothy G. Call ◽  
...  

2018 ◽  
Author(s):  
Alexandra C. Gillett ◽  
Evangelos Vassos ◽  
Cathryn M. Lewis

1.Abstract1.1.ObjectiveStratified medicine requires models of disease risk incorporating genetic and environmental factors. These may combine estimates from different studies and models must be easily updatable when new estimates become available. The logit scale is often used in genetic and environmental association studies however the liability scale is used for polygenic risk scores and measures of heritability, but combining parameters across studies requires a common scale for the estimates.1.2.MethodsWe present equations to approximate the relationship between univariate effect size estimates on the logit scale and the liability scale, allowing model parameters to be translated between scales.1.3.ResultsThese equations are used to build a risk score on the liability scale, using effect size estimates originally estimated on the logit scale. Such a score can then be used in a joint effects model to estimate the risk of disease, and this is demonstrated for schizophrenia using a polygenic risk score and environmental risk factors.1.4.ConclusionThis straightforward method allows conversion of model parameters between the logit and liability scales, and may be a key tool to integrate risk estimates into a comprehensive risk model, particularly for joint models with environmental and genetic risk factors.


2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Linda Kachuri ◽  
Rebecca E. Graff ◽  
Karl Smith-Byrne ◽  
Travis J. Meyers ◽  
Sara R. Rashkin ◽  
...  

AbstractCancer risk is determined by a complex interplay of environmental and heritable factors. Polygenic risk scores (PRS) provide a personalized genetic susceptibility profile that may be leveraged for disease prediction. Using data from the UK Biobank (413,753 individuals; 22,755 incident cancer cases), we quantify the added predictive value of integrating cancer-specific PRS with family history and modifiable risk factors for 16 cancers. We show that incorporating PRS measurably improves prediction accuracy for most cancers, but the magnitude of this improvement varies substantially. We also demonstrate that stratifying on levels of PRS identifies significantly divergent 5-year risk trajectories after accounting for family history and modifiable risk factors. At the population level, the top 20% of the PRS distribution accounts for 4.0% to 30.3% of incident cancer cases, exceeding the impact of many lifestyle-related factors. In summary, this study illustrates the potential for improving cancer risk assessment by integrating genetic risk scores.


2019 ◽  
Vol 28 (R2) ◽  
pp. R133-R142 ◽  
Author(s):  
Samuel A Lambert ◽  
Gad Abraham ◽  
Michael Inouye

Abstract Prediction of disease risk is an essential part of preventative medicine, often guiding clinical management. Risk prediction typically includes risk factors such as age, sex, family history of disease and lifestyle (e.g. smoking status); however, in recent years, there has been increasing interest to include genomic information into risk models. Polygenic risk scores (PRS) aggregate the effects of many genetic variants across the human genome into a single score and have recently been shown to have predictive value for multiple common diseases. In this review, we summarize the potential use cases for seven common diseases (breast cancer, prostate cancer, coronary artery disease, obesity, type 1 diabetes, type 2 diabetes and Alzheimer’s disease) where PRS has or could have clinical utility. PRS analysis for these diseases frequently revolved around (i) risk prediction performance of a PRS alone and in combination with other non-genetic risk factors, (ii) estimation of lifetime risk trajectories, (iii) the independent information of PRS and family history of disease or monogenic mutations and (iv) estimation of the value of adding a PRS to specific clinical risk prediction scenarios. We summarize open questions regarding PRS usability, ancestry bias and transferability, emphasizing the need for the next wave of studies to focus on the implementation and health-economic value of PRS testing. In conclusion, it is becoming clear that PRS have value in disease risk prediction and there are multiple areas where this may have clinical utility.


2021 ◽  
Vol 8 (4) ◽  
pp. e1007
Author(s):  
Benjamin Meir Jacobs ◽  
Alastair J. Noyce ◽  
Jonathan Bestwick ◽  
Daniel Belete ◽  
Gavin Giovannoni ◽  
...  

ObjectiveWe sought to determine whether genetic risk modifies the effect of environmental risk factors for multiple sclerosis (MS). To test this hypothesis, we tested for statistical interaction between polygenic risk scores (PRS) capturing genetic susceptibility to MS and environmental risk factors for MS in UK Biobank.MethodsPeople with MS were identified within UK Biobank using ICD-10–coded MS or self-report. Associations between environmental risk factors and MS risk were quantified with a case-control design using multivariable logistic regression. PRS were derived using the clumping-and-thresholding approach with external weights from the largest genome-wide association study of MS. Separate scores were created including major histocompatibility complex (MHC) (PRSMHC) and excluding (PRSnon-MHC) the MHC locus. The best-performing PRS were identified in 30% of the cohort and validated in the remaining 70%. Interaction between environmental and genetic risk factors was quantified using the attributable proportion due to interaction (AP) and multiplicative interaction.ResultsData were available for 2,250 people with MS and 486,000 controls. Childhood obesity, earlier age at menarche, and smoking were associated with MS. The optimal PRS were strongly associated with MS in the validation cohort (PRSMHC: Nagelkerke's pseudo-R2 0.033, p = 3.92 × 10−111; PRSnon-MHC: Nagelkerke's pseudo-R2 0.013, p = 3.73 × 10−43). There was strong evidence of interaction between polygenic risk for MS and childhood obesity (PRSMHC: AP = 0.17, 95% CI 0.06–0.25, p = 0.004; PRSnon-MHC: AP = 0.17, 95% CI 0.06–0.27, p = 0.006).ConclusionsThis study provides novel evidence for an interaction between childhood obesity and a high burden of autosomal genetic risk. These findings may have significant implications for our understanding of MS biology and inform targeted prevention strategies.


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