Polygenic Risk Scores Flashcards
____________ __________– underlying continuous trait
(genes plus environment) gives rise to phenotype
liability scale
Variants that are ______________ together are more likely to be
inherited together, resulting in correlation patterns
closer
_______ ______________: aggregate effect sizes without any reweighting
simple sum
_____________ + ____________: Select independent variants that meet a statistical threshold
Pruning + Thresholding
______________/Others: Reweight variants by how correlated
they are with each other and sum new weights together
LDPred
Sensitivity = ___/(_______ +_______)
TP/TP+FN
Specificity = ___/(_______ +_______)
TN/TN+FP
_________________ graphically depicts sensitivity and specificity as function of a
range of cut-offs
ROC - receiver operating characteristic
X (1-specificity) vs Y (sensitivity)
The ___________ in a ROC is a summary measure, probability
of random (+) ranking higher than random (-) * 0.5 means 50% of being right
AUC - area under the curve
PPV = ____ / (______ + _________)
TP/(TP+FP)
NPV = ____ / (______ + _________)
TN/(TN+FN)
PPV/NPV highly dependent on ____________ of disease
prevalence
PPV or NPV increases with low prevalence
NPV
The main uses of polygenic risk scores are in ____________ assessment, disease _________ or subtyping and disease _______________
risk assessment, diagnosis, prognosis
5 factors that determine PRS predictive ability
- Number of true SNP
- Affect size of true SNPs
- Significance level for SNP selection
- Power of underlying association test
- Value of estimated regression coefficients
