Saturday, October 24, 2020

Composite Polygenic Risk Score predicts longevity

The paper below (senior author at Johns Hopkins University) builds a composite polygenic risk score for mortality (longevity). Outliers (top vs bottom 5%) differ by about 5 years in life expectancy. 

I expect longevity prediction to improve considerably with more and better data to analyze. See also Live Long and Prosper: Genetic Architecture of Complex Traits and Disease Risk Predictors:
We found that genetic risks are largely uncorrelated for different conditions. This suggests that there can exist individuals with, e.g., low risk simultaneously in each of multiple conditions, for essentially any combination of conditions. There is no trade-off required between different disease risks ... One could speculate that a lucky individual with exceptionally low risk across multiple conditions might have an unusually long life expectancy.

If I read the graph below correctly, in their late 70s a positive outlier (male) has ~90% chance of surviving (not sure of timescale, might be next few years? See comments), whereas for a negative outlier the odds are only ~75%.
Combined Utility of 25 Disease and Risk Factor Polygenic Risk Scores for Stratifying Risk of All-Cause Mortality 
Allison Meisner, Prosenjit Kundu, Yan Dora Zhang, Lauren V. Lan, Sungwon Kim, Disha Ghandwani, Parichoy Pal Choudhury, Sonja I. Berndt, Neal D. Freedman, Montserrat Garcia-Closas, Nilanjan Chatterjee 
doi: https://doi.org/10.1101/2020.03.13.20035527 
The American Journal of Human Genetics doi: 10.1016/j.ajhg.2020.07.002 
While genome-wide association studies have identified susceptibility variants for numerous traits, their combined utility for predicting broad measures of health, such as mortality, remains poorly understood. We used data from the UK Biobank to combine polygenic risk scores (PRS) for 13 diseases and 12 mortality risk factors into sex-specific composite PRS (cPRS). These cPRS were moderately associated with all-cause mortality in independent data: the estimated hazard ratios per standard deviation were 1.10 (95% confidence interval: 1.05, 1.16) and 1.15 (1.10, 1.19) for women and men, respectively. Differences in life expectancy between the top and bottom 5% of the cPRS were estimated to be 4.79 (1.76, 7.81) years and 6.75 (4.16, 9.35) years for women and men, respectively. These associations were substantially attenuated after adjusting for non-genetic mortality risk factors measured at study entry. The cPRS may be useful in counseling younger individuals at higher genetic risk of mortality on modification of non-genetic factors.

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