2015
DOI: 10.1016/j.ajhg.2015.09.001
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Abstract: Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD inform… Show more

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Cited by 1,149 publications
(1,265 citation statements)
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References 65 publications
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“…However, the San Council of Southern Africa prefers to keep these 18 terms separate (i.e., San and Khoe or Nama) to denote the different cultural groups. 19 Many of the "San" individuals prefer being called "Bushmen," while others consider the 20 word to be pejorative. Labels are only useful insofar as they are universally informative, 21…”
Section: Respect and Consent 17mentioning
confidence: 99%
See 1 more Smart Citation
“…However, the San Council of Southern Africa prefers to keep these 18 terms separate (i.e., San and Khoe or Nama) to denote the different cultural groups. 19 Many of the "San" individuals prefer being called "Bushmen," while others consider the 20 word to be pejorative. Labels are only useful insofar as they are universally informative, 21…”
Section: Respect and Consent 17mentioning
confidence: 99%
“…The impact on 6 research collaborations is evident, with some authors calling it 'neo-colonial science' 7 [18]. Such strained relations are more pronounced in collaborations involving genetic 8 studies, especially when shipping samples out of Africa and the Global South [19]. 9…”
mentioning
confidence: 99%
“…To generate the weights for the polygenic score, we performed meta-analyses of the pooled SWB phenotype excluding each of the holdout cohorts, applying a minimum-sample-size filter of 100,000 individuals. Using the summary statistics from this meta-analysis, we constructed two sets of polygenic scores: (1) LDpred polygenic scores, with weights constructed from conditional SNP effects estimated from summary statistics using information about LD structure from a reference sample 20 , and (2) linear polygenic scores using the unconditional GWAS effect sizes 46 . We examined the predictive power of the score for the following outcomes: SWB, LS, PA, depression, the NEO Big Five personality traits 47 , and height (the last being included as a negative control).…”
Section: Bayesian Credibility Analysesmentioning
confidence: 99%
“…The follow up study Okbay et al (2016) combines all genotyped SNPs into a polygenic score that attains a predictive power of up to 3.85% of the variation in educational attainment. 66 In our study, we use SNP weights β j that have been adjusted using a technique called LD Pred (Vilhjalmsson, 2015), and applied to the genetic data in the HRS. 67 We refer to the polygenic score created using these weights as the EA score, where "EA" stands for "educational attainment".…”
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confidence: 99%