risk prediction
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2022 ◽  
Vol 44 ◽  
pp. 24-29
Lili Yu ◽  
Yingqiang Li ◽  
Dongyun Zhang ◽  
Wanyun Huang ◽  
Runping Li ◽  

BMC Cancer ◽  
2022 ◽  
Vol 22 (1) ◽  
Michele Sassano ◽  
Marco Mariani ◽  
Gianluigi Quaranta ◽  
Roberta Pastorino ◽  
Stefania Boccia

Abstract Background Risk prediction models incorporating single nucleotide polymorphisms (SNPs) could lead to individualized prevention of colorectal cancer (CRC). However, the added value of incorporating SNPs into models with only traditional risk factors is still not clear. Hence, our primary aim was to summarize literature on risk prediction models including genetic variants for CRC, while our secondary aim was to evaluate the improvement of discriminatory accuracy when adding SNPs to a prediction model with only traditional risk factors. Methods We conducted a systematic review on prediction models incorporating multiple SNPs for CRC risk prediction. We tested whether a significant trend in the increase of Area Under Curve (AUC) according to the number of SNPs could be observed, and estimated the correlation between AUC improvement and number of SNPs. We estimated pooled AUC improvement for SNP-enhanced models compared with non-SNP-enhanced models using random effects meta-analysis, and conducted meta-regression to investigate the association of specific factors with AUC improvement. Results We included 33 studies, 78.79% using genetic risk scores to combine genetic data. We found no significant trend in AUC improvement according to the number of SNPs (p for trend = 0.774), and no correlation between the number of SNPs and AUC improvement (p = 0.695). Pooled AUC improvement was 0.040 (95% CI: 0.035, 0.045), and the number of cases in the study and the AUC of the starting model were inversely associated with AUC improvement obtained when adding SNPs to a prediction model. In addition, models constructed in Asian individuals achieved better AUC improvement with the incorporation of SNPs compared with those developed among individuals of European ancestry. Conclusions Though not conclusive, our results provide insights on factors influencing discriminatory accuracy of SNP-enhanced models. Genetic variants might be useful to inform stratified CRC screening in the future, but further research is needed.

Diabetologia ◽  
2022 ◽  
Katarzyna Dziopa ◽  
Folkert W. Asselbergs ◽  
Jasmine Gratton ◽  
Nishi Chaturvedi ◽  
Amand F. Schmidt

Abstract Aims/hypothesis We aimed to compare the performance of risk prediction scores for CVD (i.e., coronary heart disease and stroke), and a broader definition of CVD including atrial fibrillation and heart failure (CVD+), in individuals with type 2 diabetes. Methods Scores were identified through a literature review and were included irrespective of the type of predicted cardiovascular outcome or the inclusion of individuals with type 2 diabetes. Performance was assessed in a contemporary, representative sample of 168,871 UK-based individuals with type 2 diabetes (age ≥18 years without pre-existing CVD+). Missing observations were addressed using multiple imputation. Results We evaluated 22 scores: 13 derived in the general population and nine in individuals with type 2 diabetes. The Systemic Coronary Risk Evaluation (SCORE) CVD rule derived in the general population performed best for both CVD (C statistic 0.67 [95% CI 0.67, 0.67]) and CVD+ (C statistic 0.69 [95% CI 0.69, 0.70]). The C statistic of the remaining scores ranged from 0.62 to 0.67 for CVD, and from 0.64 to 0.69 for CVD+. Calibration slopes (1 indicates perfect calibration) ranged from 0.38 (95% CI 0.37, 0.39) to 0.74 (95% CI 0.72, 0.76) for CVD, and from 0.41 (95% CI 0.40, 0.42) to 0.88 (95% CI 0.86, 0.90) for CVD+. A simple recalibration process considerably improved the performance of the scores, with calibration slopes now ranging between 0.96 and 1.04 for CVD. Scores with more predictors did not outperform scores with fewer predictors: for CVD+, QRISK3 (19 variables) had a C statistic of 0.68 (95% CI 0.68, 0.69), compared with SCORE CVD (six variables) which had a C statistic of 0.69 (95% CI 0.69, 0.70). Scores specific to individuals with diabetes did not discriminate better than scores derived in the general population: the UK Prospective Diabetes Study (UKPDS) scores performed significantly worse than SCORE CVD (p value <0.001). Conclusions/interpretation CVD risk prediction scores could not accurately identify individuals with type 2 diabetes who experienced a CVD event in the 10 years of follow-up. All 22 evaluated models had a comparable and modest discriminative ability. Graphical abstract

2022 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Michelle Louise Gatt ◽  
Maria Cassar ◽  
Sandra C. Buttigieg

Purpose The purpose of this paper is to identify and analyse the readmission risk prediction tools reported in the literature and their benefits when it comes to healthcare organisations and management.Design/methodology/approach Readmission risk prediction is a growing topic of interest with the aim of identifying patients in particular those suffering from chronic diseases such as congestive heart failure, chronic obstructive pulmonary disease and diabetes, who are at risk of readmission. Several models have been developed with different levels of predictive ability. A structured and extensive literature search of several databases was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-analysis strategy, and this yielded a total of 48,984 records.Findings Forty-three articles were selected for full-text and extensive review after following the screening process and according to the eligibility criteria. About 34 unique readmission risk prediction models were identified, in which their predictive ability ranged from poor to good (c statistic 0.5–0.86). Readmission rates ranged between 3.1 and 74.1% depending on the risk category. This review shows that readmission risk prediction is a complex process and is still relatively new as a concept and poorly understood. It confirms that readmission prediction models hold significant accuracy at identifying patients at higher risk for such an event within specific context.Research limitations/implications Since most prediction models were developed for specific populations, conditions or hospital settings, the generalisability and transferability of the predictions across wider or other contexts may be difficult to achieve. Therefore, the value of prediction models remains limited to hospital management. Future research is indicated in this regard.Originality/value This review is the first to cover readmission risk prediction tools that have been published in the literature since 2011, thereby providing an assessment of the relevance of this crucial KPI to health organisations and managers.

Eileen O. Dareng ◽  
Jonathan P. Tyrer ◽  
Daniel R. Barnes ◽  
Michelle R. Jones ◽  
Xin Yang ◽  

AbstractPolygenic risk scores (PRS) for epithelial ovarian cancer (EOC) have the potential to improve risk stratification. Joint estimation of Single Nucleotide Polymorphism (SNP) effects in models could improve predictive performance over standard approaches of PRS construction. Here, we implemented computationally efficient, penalized, logistic regression models (lasso, elastic net, stepwise) to individual level genotype data and a Bayesian framework with continuous shrinkage, “select and shrink for summary statistics” (S4), to summary level data for epithelial non-mucinous ovarian cancer risk prediction. We developed the models in a dataset consisting of 23,564 non-mucinous EOC cases and 40,138 controls participating in the Ovarian Cancer Association Consortium (OCAC) and validated the best models in three populations of different ancestries: prospective data from 198,101 women of European ancestries; 7,669 women of East Asian ancestries; 1,072 women of African ancestries, and in 18,915 BRCA1 and 12,337 BRCA2 pathogenic variant carriers of European ancestries. In the external validation data, the model with the strongest association for non-mucinous EOC risk derived from the OCAC model development data was the S4 model (27,240 SNPs) with odds ratios (OR) of 1.38 (95% CI: 1.28–1.48, AUC: 0.588) per unit standard deviation, in women of European ancestries; 1.14 (95% CI: 1.08–1.19, AUC: 0.538) in women of East Asian ancestries; 1.38 (95% CI: 1.21–1.58, AUC: 0.593) in women of African ancestries; hazard ratios of 1.36 (95% CI: 1.29–1.43, AUC: 0.592) in BRCA1 pathogenic variant carriers and 1.49 (95% CI: 1.35–1.64, AUC: 0.624) in BRCA2 pathogenic variant carriers. Incorporation of the S4 PRS in risk prediction models for ovarian cancer may have clinical utility in ovarian cancer prevention programs.

2022 ◽  
Raija Lithovius ◽  
Anni A. Antikainen ◽  
Stefan Mutter ◽  
Erkka Valo ◽  
Carol Forsblom ◽  

OBJECTIVE Individuals with type 1 diabetes are at a high lifetime risk of coronary artery disease (CAD) calling for early interventions. This study explores the use of a genetic risk score (GRS) for CAD risk prediction, compares it to established clinical markers and investigates its performance according to the age and pharmacological treatment. <p>RESEARCH DESIGN AND METHODS This study in 3,295 individuals with type 1 diabetes from the Finnish Diabetic Nephropathy Study (467 incident CAD, 14.8 years follow-up) employed three risk scores: a GRS, a validated clinical score and their combined score. Hazard ratios (HR) were calculated with Cox regression and model performances compared with Harrel’s C-index. </p> <p>RESULTS A HR of 6.7 for CAD was observed between the highest and the lowest 5<sup>th</sup> percentile of the GRS (<i>P</i>=1.8×10<sup>-6</sup>). The performance of GRS (C-index [C] 0.562) was similar to HbA<sub>1c</sub> (C=0.563, <i>p</i>-value for difference 0.96), HDL (C=0.571, <i>P</i>=0.6) and total cholesterol (C=0.594, <i>P</i>=0.1). The GRS was not correlated with the clinical score (<i>r</i>=-0.013, <i>P</i>=0.5). The combined score outperformed the clinical score (C=0.813 vs C=0.820, <i>P</i>=0.003). The GRS performed better in individuals below the median age (38.6 years) compared to those above (C=0.637 vs C=0.546). </p> <p>CONCLUSIONS A GRS identified individuals at high risk of CAD and worked better in younger individuals. GRS was also an independent risk factor for CAD with a predictive power comparable to that of HbA<sub>1c</sub>, HDL and total cholesterol and, when incorporated into a clinical model, modestly improved the predictions. The GRS promises early risk stratification in clinical practice by enhancing the prediction of CAD. </p>

2022 ◽  
Tianyuan Lu ◽  
Vincenzo Forgetta ◽  
J. Brent Richards ◽  
Celia Greenwood

Abstract Genomic risk prediction is on the emerging path towards personalized medicine. However, the accuracy of polygenic prediction varies strongly in different individuals. In this study, based on up to 352,277 White British participants in the UK Biobank, we constructed polygenic risk scores for 15 physiological and biochemical quantitative traits after performing genome-wide association studies (GWASs). We identified 185 polygenic prediction variability quantitative trait loci (pvQTLs) for 11 traits by Levene’s test among 254,376 unrelated individuals. We validated the effects of pvQTLs using an independent test set of 58,927 individuals. A score aggregating 51 pvQTL SNPs for triglycerides had the strongest Spearman correlation of 0.185 (p-value < 1.0x10−300) with the squared prediction errors. We found a strong enrichment of complex genetic effects conferred by pvQTLs compared to risk loci identified in GWASs, including 89 pvQTLs exhibiting dominance effects. Incorporation of dominance effects into polygenic risk scores significantly improved polygenic prediction for triglycerides, low-density lipoprotein cholesterol, vitamin D, and platelet. After including 87 dominance effects for triglycerides, the adjusted R2 for the polygenic risk score had an 8.1% increase on the test set. In addition, 108 pvQTLs had significant interaction effects with measured environmental or lifestyle exposures. In conclusion, we have discovered and validated genetic determinants of polygenic prediction variability for 11 quantitative biomarkers, and partially profiled the underlying complex genetic effects. These findings may assist interpretation of genomic risk prediction in various contexts, and encourage novel approaches for constructing polygenic risk scores with complex genetic effects.

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